Relevant bibliographies by topics / Domains of topological association

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Domains of topological association'

Author: Grafiati
Published: 25 May 2024

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Journal articles on the topic "Domains of topological association"

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Warfield, Linda, Jie Luo, Jeffrey Ranish, and Steven Hahn. "Function of Conserved Topological Regions within the Saccharomyces cerevisiae Basal Transcription Factor TFIIH." Molecular and Cellular Biology 36, no. 19 (July 5, 2016): 2464–75. http://dx.doi.org/10.1128/mcb.00182-16.

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TFIIH is a 10-subunit RNA polymerase II basal transcription factor with a dual role in DNA repair. TFIIH contains three enzymatic functions and over 30 conserved subdomains and topological regions. We systematically tested the function of these regions in three TFIIH core module subunits, i.e., Ssl1, Tfb4, and Tfb2, in the DNA translocase subunit Ssl2, and in the kinase module subunit Tfb3. Our results are consistent with previously predicted roles for the Tfb2 Hub, Ssl2 Lock, and Tfb3 Latch regions, with mutations in these elements typically having severe defects in TFIIH subunit association. We also found unexpected roles for other domains whose function had not previously been defined. First, the Ssl1-Tfb4 Ring domains are important for TFIIH assembly. Second, the Tfb2 Hub and HEAT domains have an unexpected role in association with Tfb3. Third, the Tfb3 Ring domain is important for association with many other TFIIH subunits. Fourth, a partial deletion of the Ssl1 N-terminal extension (NTE) domain inhibits TFIIH function without affecting subunit association. Finally, we used site-specific cross-linking to localize the Tfb3-binding surface on the Rad3 Arch domain. Our cross-linking results suggest that Tfb3 and Rad3 have an unusual interface, with Tfb3 binding on two opposite faces of the Arch.
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Marinov, Georgi K., Alexandro E. Trevino, Tingting Xiang, Anshul Kundaje, Arthur R. Grossman, and William J. Greenleaf. "Transcription-dependent domain-scale three-dimensional genome organization in the dinoflagellate Breviolum minutum." Nature Genetics 53, no. 5 (April 29, 2021): 613–17. http://dx.doi.org/10.1038/s41588-021-00848-5.

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AbstractDinoflagellate chromosomes represent a unique evolutionary experiment, as they exist in a permanently condensed, liquid crystalline state; are not packaged by histones; and contain genes organized into tandem gene arrays, with minimal transcriptional regulation. We analyze the three-dimensional genome of Breviolum minutum, and find large topological domains (dinoflagellate topologically associating domains, which we term ‘dinoTADs’) without chromatin loops, which are demarcated by convergent gene array boundaries. Transcriptional inhibition disrupts dinoTADs, implicating transcription-induced supercoiling as the primary topological force in dinoflagellates.
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Liu, Qian, Nelly Pante, Tom Misteli, Mohamed Elsagga, Melissa Crisp, Didier Hodzic, Brian Burke, and Kyle J. Roux. "Functional association of Sun1 with nuclear pore complexes." Journal of Cell Biology 178, no. 5 (August 27, 2007): 785–98. http://dx.doi.org/10.1083/jcb.200704108.

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Sun1 and 2 are A-type lamin-binding proteins that, in association with nesprins, form a link between the inner nuclear membranes (INMs) and outer nuclear membranes of mammalian nuclear envelopes. Both immunofluorescence and immunoelectron microscopy reveal that Sun1 but not Sun2 is intimately associated with nuclear pore complexes (NPCs). Topological analyses indicate that Sun1 is a type II integral protein of the INM. Localization of Sun1 to the INM is defined by at least two discrete regions within its nucleoplasmic domain. However, association with NPCs is dependent on the synergy of both nucleoplasmic and lumenal domains. Cells that are either depleted of Sun1 by RNA interference or that overexpress dominant-negative Sun1 fragments exhibit clustering of NPCs. The implication is that Sun1 represents an important determinant of NPC distribution across the nuclear surface.
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Willemin, Andréa, Lucille Lopez-Delisle, Christopher Chase Bolt, Marie-Laure Gadolini, Denis Duboule, and Eddie Rodriguez-Carballo. "Induction of a chromatin boundary in vivo upon insertion of a TAD border." PLOS Genetics 17, no. 7 (July 22, 2021): e1009691. http://dx.doi.org/10.1371/journal.pgen.1009691.

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Mammalian genomes are partitioned into sub-megabase to megabase-sized units of preferential interactions called topologically associating domains or TADs, which are likely important for the proper implementation of gene regulatory processes. These domains provide structural scaffolds for distant cis regulatory elements to interact with their target genes within the three-dimensional nuclear space and architectural proteins such as CTCF as well as the cohesin complex participate in the formation of the boundaries between them. However, the importance of the genomic context in providing a given DNA sequence the capacity to act as a boundary element remains to be fully investigated. To address this question, we randomly relocated a topological boundary functionally associated with the mouse HoxD gene cluster and show that it can indeed act similarly outside its initial genomic context. In particular, the relocated DNA segment recruited the required architectural proteins and induced a significant depletion of contacts between genomic regions located across the integration site. The host chromatin landscape was re-organized, with the splitting of the TAD wherein the boundary had integrated. These results provide evidence that topological boundaries can function independently of their site of origin, under physiological conditions during mouse development.
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Zhan, Y., L. Giorgetti, and G. Tiana. "Modelling genome-wide topological associating domains in mouse embryonic stem cells." Chromosome Research 25, no. 1 (January 20, 2017): 5–14. http://dx.doi.org/10.1007/s10577-016-9544-6.

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Zhang, Guangzhi, and Hélène Sanfaçon. "Characterization of Membrane Association Domains within the Tomato Ringspot Nepovirus X2 Protein, an Endoplasmic Reticulum-Targeted Polytopic MembraneProtein." Journal of Virology 80, no. 21 (August 23, 2006): 10847–57. http://dx.doi.org/10.1128/jvi.00789-06.

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ABSTRACT Replication of nepoviruses (family Comoviridae) occurs in association with endoplasmic reticulum (ER)-derived membranes. We have previously shown that the putative nucleoside triphosphate-binding protein (NTB) of Tomato ringspot nepovirus is an integral membrane protein with two ER-targeting sequences and have suggested that it anchors the viral replication complex (VRC) to the membranes. A second highly hydrophobic protein domain (X2) is located immediately upstream of the NTB domain in the RNA1-encoded polyprotein. X2 shares conserved sequence motifs with the comovirus 32-kDa protein, an ER-targeted protein implicated in VRC assembly. In this study, we examined the ability of X2 to associate with intracellular membranes. The X2 protein was fused to the green fluorescent protein and expressed in Nicotiana benthamiana by agroinfiltration. Confocal microscopy and membrane flotation experiments suggested that X2 is targeted to ER membranes. Mutagenesis studies revealed that X2 contains multiple ER-targeting domains, including two C-terminal transmembrane helices and a less-well-defined domain further upstream. To investigate the topology of the protein in the membrane, in vitro glycosylation assays were conducted using X2 derivatives that contained N-glycosylation sites introduced at the N or C termini of the protein. The results led us to propose a topological model for X2 in which the protein traverses the membrane three times, with the N terminus oriented in the lumen and the C terminus exposed to the cytoplasmic face. Taken together, our results indicate that X2 is an ER-targeted polytopic membrane protein and raises the possibility that it acts as a second membrane anchor for the VRC.
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Davidson, Iain F., Benedikt Bauer, Daniela Goetz, Wen Tang, Gordana Wutz, and Jan-Michael Peters. "DNA loop extrusion by human cohesin." Science 366, no. 6471 (November 21, 2019): 1338–45. http://dx.doi.org/10.1126/science.aaz3418.

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Eukaryotic genomes are folded into loops and topologically associating domains, which contribute to chromatin structure, gene regulation, and gene recombination. These structures depend on cohesin, a ring-shaped DNA-entrapping adenosine triphosphatase (ATPase) complex that has been proposed to form loops by extrusion. Such an activity has been observed for condensin, which forms loops in mitosis, but not for cohesin. Using biochemical reconstitution, we found that single human cohesin complexes form DNA loops symmetrically at rates up to 2.1 kilo–base pairs per second. Loop formation and maintenance depend on cohesin’s ATPase activity and on NIPBL-MAU2, but not on topological entrapment of DNA by cohesin. During loop formation, cohesin and NIPBL-MAU2 reside at the base of loops, which indicates that they generate loops by extrusion. Our results show that cohesin and NIPBL-MAU2 form an active holoenzyme that interacts with DNA either pseudo-topologically or non-topologically to extrude genomic interphase DNA into loops.
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Li, Yufang, Aoshen Wu, Gang Liu, and Lei Liu. "A Review of Methods to Quantify the Genomic Similarity of Topological Associating Domains." Journal of Computational Biology 26, no. 11 (November 1, 2019): 1326–38. http://dx.doi.org/10.1089/cmb.2019.0129.

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Franzini, Stefano, Marco Di Stefano, and Cristian Micheletti. "essHi-C: essential component analysis of Hi-C matrices." Bioinformatics 37, no. 15 (February 1, 2021): 2088–94. http://dx.doi.org/10.1093/bioinformatics/btab062.

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Abstract Motivation Hi-C matrices are cornerstones for qualitative and quantitative studies of genome folding, from its territorial organization to compartments and topological domains. The high dynamic range of genomic distances probed in Hi-C assays reflects in an inherent stochastic background of the interactions matrices, which inevitably convolve the features of interest with largely non-specific ones. Results Here, we introduce and discuss essHi-C, a method to isolate the specific or essential component of Hi-C matrices from the non-specific portion of the spectrum compatible with random matrices. Systematic comparisons show that essHi-C improves the clarity of the interaction patterns, enhances the robustness against sequencing depth of topologically associating domains identification, allows the unsupervised clustering of experiments in different cell lines and recovers the cell-cycle phasing of single-cells based on Hi-C data. Thus, essHi-C provides means for isolating significant biological and physical features from Hi-C matrices. Availability and implementation The essHi-C software package is available at https://github.com/stefanofranzini/essHIC. Supplementary information Supplementary data are available at Bioinformatics online.
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Soler-Vila, Paula, Pol Cuscó, Irene Farabella, Marco Di Stefano, and Marc A. Marti-Renom. "Hierarchical chromatin organization detected by TADpole." Nucleic Acids Research 48, no. 7 (February 21, 2020): e39-e39. http://dx.doi.org/10.1093/nar/gkaa087.

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Abstract The rapid development of Chromosome Conformation Capture (3C-based techniques), as well as imaging together with bioinformatics analyses, has been fundamental for unveiling that chromosomes are organized into the so-called topologically associating domains or TADs. While TADs appear as nested patterns in the 3C-based interaction matrices, the vast majority of available TAD callers are based on the hypothesis that TADs are individual and unrelated chromatin structures. Here we introduce TADpole, a computational tool designed to identify and analyze the entire hierarchy of TADs in intra-chromosomal interaction matrices. TADpole combines principal component analysis and constrained hierarchical clustering to provide a set of significant hierarchical chromatin levels in a genomic region of interest. TADpole is robust to data resolution, normalization strategy and sequencing depth. Domain borders defined by TADpole are enriched in main architectural proteins (CTCF and cohesin complex subunits) and in the histone mark H3K4me3, while their domain bodies, depending on their activation-state, are enriched in either H3K36me3 or H3K27me3, highlighting that TADpole is able to distinguish functional TAD units. Additionally, we demonstrate that TADpole's hierarchical annotation, together with the new DiffT score, allows for detecting significant topological differences on Capture Hi-C maps between wild-type and genetically engineered mouse.
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Dissertations / Theses on the topic "Domains of topological association"

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Kerlin, Maciej. "Gene coregulation in cis within the 3D genome – A single-molecule imaging study." Electronic Thesis or Diss., Sorbonne université, 2021. http://www.theses.fr/2021SORUS124.

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Le génome eucaryote est organisé dans l’espace et le long de sa séquence. Du chromosome aux gènes, son organisation 3D est étroitement liée à son activité transcriptionnelle. A une échelle inférieure à la mégabase, le génome est organisé physiquement en domaines d’auto-interaction (TAD, pour topologically associating domains), que l’on pense influencer l’action de séquences régulatrices des gènes, appelées ‘amplificateurs’. Les TAD sont parfois vus comme des ‘unités de régulation’ permettant de coréguler plusieurs gènes en les exposant aux mêmes amplificateurs. L’expression de gènes d’un même TAD est en effet souvent corrélée entre tissus et types cellulaires. On sait d’autre part que l’expression de gènes fonctionnellement liés est aussi souvent corrélée. Cependant, le rôle que joue l’organisation 3D d’un locus génomique dans la corégulation de gènes fonctionnellement liés reste mal compris. Par des techniques d’imagerie de molécules uniques, j’ai observé, dans des cellules individuelles, la position et la transcription de trois gènes adjacents et fonctionnellement liés, partageant –ou non– les mêmes amplificateurs. J’ai utilisé comme système modèle la réponse à l’œstrogène dans des cellules MCF7. En combinant les techniques de FISH ARN et ADN, j’ai mesuré le couplage transcriptionnel de paires de gènes en cis, mettant en évidence une augmentation de la corrélation entre gènes d’un même TAD en réponse à l’œstrogène. Une perturbation de la frontière entre TAD indique également le rôle des contacts génomiques dans la corégulation de gènes. Ces travaux posent les bases pour comprendre comment les amplificateurs et les gènes communiquent et coordonnent leur activité en 3D
The eukaryotic genome is highly organized in both space and sequence. From entire chromosomes to individual genes the 3D organization of the genome is linked to transcription and many regulatory mechanisms likely coexist at different scales. At the sub-megabase scale, the genome is physically organized into self-interacting topologically associating domains (TADs) that are thought to constrain the range of action of gene regulatory elements called ‘enhancers’. Current data suggest that TADs serve as ‘regulatory units’ to coregulate multiple genes by exposing them to the same enhancers. Genes from the same TAD indeed often display correlated expression across different tissues and cell types. Interestingly, correlated expression is seen between functionally related genes. However, how 3D organization at an individual locus plays a mechanistic role in coregulating functionally related genes is unknown. Using single-molecule imaging, I observed in single cells the spatial positions and transcription of three adjacent functionally related genes regulated by the same/different enhancers. I used estrogen stimulation in MCF7 cells as a model system to study hormone-responsive genes and enhancers. Using combined RNA-DNA FISH, I measured the coupling between genes as the correlation in cis of their transcription. I found, that stimulation with estrogen increases the correlation in cis between genes belonging to the same TAD. Perturbation of the TAD boundary revealed the contribution of contact insulation to gene coregulation. Together, this work lays the ground towards an understanding of how enhancers and genes communicate and coordinate their activity within the 3D genome
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Wiedermann, Marc. "Classification of complex networks in spatial, topological and information theoretic domains." Doctoral thesis, Humboldt-Universität zu Berlin, 2018. http://dx.doi.org/10.18452/18818.

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Die Netzwerktheorie ist eine wirksame Methode, um die Struktur realer Systeme, z.B. des Klimasystems, zu beschreiben und zu klassifizieren. Der erste Teil dieser Arbeit nutzt diese Diskriminanzfähigkeit um die Ost- und Zentralpazifischen Phasen von El Niño und La Niña mittels eines Index basierend auf der Evaluation zeitlich entwickelnder Klimanetzwerke zu unterscheiden. Nach dem Studium der klimatischen Einflüsse dieser unterschiedenen Phasen verlegt die Arbeit ihren Schwerpunkt von der Klassifikation einzelner klimatischer Schichten auf den generelleren Fall interagierender Netzwerke. Hier repräsentieren die Teilnetzwerke entsprechende Variabilitäten in Ozean und Atmosphäre. Es zeigt sich, dass die Ozean-Atmosphären-Wechselwirkung einer hierarchischen Struktur folgt wobei makroskopische Netzwerkmaße einzelne Atmosphärenschichten bezüglich ihrer Wechselwirkung mit dem Ozean unterscheiden. Der zweite Teil dieser Arbeit untersucht den Einfluss der räumlichen Einbettung von Knoten auf topologische Netzwerkeigenschaften. Hierzu werden Nullmodelle eingeführt, welche zufällige Surrogate eines gegebenen Netzwerks erzeugen, sodass globale und lokale räumliche Eigenschaften erhalten bleiben. Diese Modelle erfassen die makroskopischen Eigenschaften der studierten Netzwerke besser als bisherige Standardmodelle zur Erzeugung von Zufallsnetzwerken. Abhängig von der Performanz der vorgeschlagenen Modelle können gegebene Netzwerke schlussendlich in verschiedene Klassen eingeteilt werden. Die Arbeit schließt mit einer Erweiterung der bisherigen Netzwerkklassifikatoren um eine zweidimensionale Metrik, welche Netzwerke auf Basis ihrer Komplexität unterscheidet. Es wird gezeigt, dass Netzwerke des gleichen Typs dazu neigen in individuellen Bereichen der resultierenden Komplexitäts-Entropie-Ebene zu liegen. Die eingeführte Methode ermöglicht auch die objektive Konstruktion von Klimanetzwerken indem Schwellwerte gewählt werden, die die statistische Komplexität maximieren.
Complex network theory provides a powerful tool to quantify and classify the structure of many real-world complex systems, including the climate system. In its first part, this work demonstrates the discriminative power of complex network theory to objectively classify Eastern and Central Pacific phases of El Niño and La Niña by proposing an index based on evolving climate networks. After an investigation of the climatic impacts of these discriminated flavors, this work moves from the classification of sets of single-layer networks to the more general study of interacting networks. Here, subnetworks represent oceanic and atmospheric variability. It is revealed that the ocean-to-atmosphere interaction in the Northern hemisphere follows a hierarchical structure and macroscopic network characteristics discriminate well different parts of the atmosphere with respect to their interaction with the ocean. The second part of this work assesses the effect of the nodes’ spatial embedding on the networks’ topological characteristics. A hierarchy of null models is proposed which generate random surrogates from a given network such that global and local statistics associated with the spatial embedding are preserved. The proposed models capture macroscopic properties of the studied spatial networks much better than standard random network models. Depending on the models’ actual performance networks can ultimately be categorized into different classes. This thesis closes with extending the zoo of network classifiers by a two-fold metric to discriminate different classes of networks based on assessing their complexity. Within this framework networks of the same category tend to cluster in distinct areas of the complexity-entropy plane. The proposed framework further allows to objectively construct climate networks such that the statistical network complexity is maximized.
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Shank, Jessica. "Topological Domain Variations Among Patients Undergoing Microarray Testing." University of Cincinnati / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1491308068052218.

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Hale, Christopher R. "Effects of background knowledge on associative learning in causal domains." Diss., Georgia Institute of Technology, 1992. http://hdl.handle.net/1853/30252.

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Despang, Alexandra Friederike [Verfasser]. "The Role of Topologically Associating Domains for Developmental Gene Regulation - ⁠ A Systematic Functional Analysis at the Sox9 and Shh Loci / Alexandra Friederike Despang." Berlin : Freie Universität Berlin, 2021. http://d-nb.info/123498332X/34.

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Wiedermann, Marc [Verfasser], Jürgen [Gutachter] Kurths, Holger [Gutachter] Lange, and Jörn [Gutachter] Davidsen. "Classification of complex networks in spatial, topological and information theoretic domains / Marc Wiedermann ; Gutachter: Jürgen Kurths, Holger Lange, Jörn Davidsen." Berlin : Humboldt-Universitaet zu Berlin, 2018. http://d-nb.info/1175995053/34.

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Herold, Eva-Maria [Verfasser], Johannes [Akademischer Betreuer] Buchner, and Bernd [Akademischer Betreuer] Reif. "Folding and association of antibody domains / Eva-Maria Herold. Gutachter: Bernd Reif ; Johannes Buchner. Betreuer: Johannes Buchner." München : Universitätsbibliothek der TU München, 2013. http://d-nb.info/1076639526/34.

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Chan, J. J. "Comparative analysis of interactions of the RASSF family mediated by the Ras-association (RA) and SARAH domains." Thesis, University College London (University of London), 2013. http://discovery.ucl.ac.uk/1415675/.

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Members of the RASSF family (RASSF1-10) have been identified as candidate tumour suppressors that are frequently downregulated by promoter hypermethylation in cancers. These adaptor proteins carry a common Ras-association (RA) and SARAH domain (RASSF1-6) that can potentially bind Ras oncoproteins and mediate protein-protein interactions with other SARAH domain proteins (e.g. MST kinase). However, there is a notable lack of comparative characterisation of the RASSF family, as well as of molecular and structural information that facilitate their tumour suppressive functions. As part of our comparative analysis, we modelled the RA and SARAH domains of the RASSF members based on existing structures and predicted their potential interactions and the key residues involved. These in silico predictions were compared to in vitro studies and intracellular binding assays using Förster Resonance Energy Transfer (FRET). Several SARAH domain mutants were also investigated for their effects on RASSF interactions. Furthermore, we compared the interactions of the RASSF family with several key proteins involved in death and NFκB signalling. Our biochemical data show a diversity of interactions within the RASSF family RA domain, whereas interactions between RASSF and MST correlate with the presence of the SARAH domain, which is supported by the FRET experiments. Mutations of specific non-polar residues in the dimerisation interface of the SARAH domain also prove detrimental to the interaction between selected RASSF members and MST. Moreover, we observed stimulation-dependent interactions between specific RASSF members and MOAP1, TNF-R1, DAPK and TBK1. These results suggest that different members, despite shared general architecture, may have distinct binding properties, but ultimately could share overlapping functions. Current data also support an interaction model where RASSF serves as an adaptor for the assembly of multiple protein complexes and further functional interactions, involving MST kinases and other interacting partners, which could be regulated by Ras.
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Yoshihara, Minako. "Genome-wide profiling of 8-oxoguanine reveals its association with spatial positioning in nucleus." Kyoto University, 2014. http://hdl.handle.net/2433/192146.

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Burks, Jared K. "Identification of the membrane association of BV/ODV E26 and the domains in BV/ODV E26 responsible for nuclear trafficking to intranuclear microvesicles." Texas A&M University, 2005. http://hdl.handle.net/1969.1/4924.

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The baculovirus Autographa californica nucleopolyhedrovirus (AcNPV) has two viral forms, budded virus (BV) and occlusion derived virus (ODV). The envelopment of these two viral forms occurs at different locations: BV acquires envelopes at the plasma membrane while ODV acquires envelopes in the nucleus. The two viral forms carry out different functions in the viral life cycle. The purpose of this study is to investigate how viral envelope proteins sort/traffic to the nucleus. Of particular interest is BV/ODV E26 (E26). E26 is an envelope protein of both BV and ODV (Braunagel and Summers, 1994); therefore it must traffic to the plasma membrane and the nucleus during infection. Thus, E26 is a bi-directional trafficking protein, which interacts with membranes in both locations of the cell. As such it has been shown that there are several immunoreactive forms of E26 (Beniya, Braunagel, and Summers, 1998). The da26 gene produces at least 2 protein products of 26 and 28 kDa with different functions respectively, which correlate with localization, solubility, membrane association, and temporal requirements. The 28 kDa form is likely a soluble protein that interacts with transcriptional activators and DNA in the nucleus in the early stages of infection. A part of the 26 kDa population is a membrane bound form interacting with an integral membrane protein in the ER and likely functions as an INM sorting factor. The 26 kDa membrane bond form is also found in the inner nuclear membrane, intra-nuclear microvesicles, ODV envelopes, and ODV in the nucleus.
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Books on the topic "Domains of topological association"

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Alestalo, Pekka. Uniform domains of higher order. Helsinki: Suomalainen Tiedeakatemia, 1994.

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Chan, Jonathan Ka Lok. Association of DNAse hypersensitive chromatin domains with the nuclear envelope and with nuclear pore complexes in 3T3 fibroblasts. Ottawa: National Library of Canada, 1999.

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Milnor, John W. Dynamical systems (1984-2012). Edited by Bonifant Araceli 1963-. Providence, Rhode Island: American Mathematical Society, 2014.

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Christensen, Jens Gerlach. Trends in harmonic analysis and its applications: AMS special session on harmonic analysis and its applications : March 29-30, 2014, University of Maryland, Baltimore County, Baltimore, MD. Providence, Rhode Island: American Mathematical Society, 2015.

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Theory of Complex Homogeneous Bounded Domains. Current Medicine Group Limited, 2005.

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Xu, Yichao. Theory of Complex Homogeneous Bounded Domains. Springer, 2010.

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Theory of Complex Homogeneous Bounded Domains. Springer, 2006.

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Xu, Yichao. Theory Of Complex Homogeneous Bounded Domains. Science Press, 2005.

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Holmes, R. B. Geometric Functional Analysis and Its Applications. Springer London, Limited, 2012.

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Holmes, R. B. Geometric Functional Analysis and its Applications. Springer, 2012.

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Book chapters on the topic "Domains of topological association"

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Nanni, Luca. "Computational Inference of DNA Folding Principles: From Data Management to Machine Learning." In Special Topics in Information Technology, 79–88. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-030-85918-3_7.

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AbstractDNA is the molecular basis of life and would total about three meters if linearly untangled. To fit in the cell nucleus at the micrometer scale, DNA has, therefore, to fold itself into several layers of hierarchical structures, which are thought to be associated with functional compartmentalization of genomic features like genes and their regulatory elements. For this reason, understanding the mechanisms of genome folding is a major biological research problem. Studying chromatin conformation requires high computational resources and complex data analyses pipelines. In this chapter, we first present the PyGMQL software for interactive and scalable data exploration for genomic data. PyGMQL allows the user to inspect genomic datasets and design complex analysis pipelines. The software presents itself as a easy-to-use Python library and interacts seamlessly with other data analysis packages. We then use the software for the study of chromatin conformation data. We focus on the epigenetic determinants of Topologically Associating Domains (TADs), which are region of high self chromatin interaction. The results of this study highlight the existence of a “grammar of genome folding” which dictates the formation of TADs and boundaries, which is based on the CTCF insulator protein. Finally we focus on the relationship between chromatin conformation and gene expression, designing a graph representation learning model for the prediction of gene co-expression from gene topological features obtained from chromatin conformation data. We demonstrate a correlation between chromatin topology and co-expression, shedding a new light on this debated topic and providing a novel computational framework for the study of co-expression networks.
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Dey, Tamal K., Arunabha Roy, and Nimish R. Shah. "Approximating geometric domains through topological triangulations." In Lecture Notes in Computer Science, 6–21. Berlin, Heidelberg: Springer Berlin Heidelberg, 1997. http://dx.doi.org/10.1007/bfb0058019.

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Zufferey, Marie, Daniele Tavernari, and Giovanni Ciriello. "Methods for the Analysis of Topologically Associating Domains (TADs)." In Methods in Molecular Biology, 39–59. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1390-0_3.

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Hua, Dunming, Ming Gu, Yanyi Du, Li Qi, Xiangjun Du, Zhidong Bai, Xiaopeng Zhu, and Dechao Tian. "DiffDomain Enables Identification of Structurally Reorganized Topologically Associating Domains." In Lecture Notes in Computer Science, 302–3. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-031-04749-7_20.

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Kou, Hui, and Maokang Luo. "The Largest Topologically Cartesian Closed Categories of Domains as Topological Spaces." In Domains and Processes, 51–66. Dordrecht: Springer Netherlands, 2001. http://dx.doi.org/10.1007/978-94-010-0654-5_4.

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Novotny, Antonio André, Jan Sokołowski, and Antoni Żochowski. "Theory in Singularly Perturbed Geometrical Domains." In Applications of the Topological Derivative Method, 13–39. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-030-05432-8_2.

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Filippova, Darya, Rob Patro, Geet Duggal, and Carl Kingsford. "Multiscale Identification of Topological Domains in Chromatin." In Lecture Notes in Computer Science, 300–312. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-40453-5_23.

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Ballard, David. "Chapter 7. Topological Determinacy of Internal Domains." In Foundational Aspects of “Non”standard Mathematics, 51–62. Providence, Rhode Island: American Mathematical Society, 1994. http://dx.doi.org/10.1090/conm/176/07.

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Adams, Brooks, Henry Adams, and Colin Roberts. "Sweeping Costs of Planar Domains." In Association for Women in Mathematics Series, 71–92. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-89593-2_5.

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Zhang, Shilei. "Measurement of the Skyrmion Lattice Domains." In Chiral and Topological Nature of Magnetic Skyrmions, 59–70. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-98252-6_3.

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Conference papers on the topic "Domains of topological association"

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Li, Weishi, and Ralph R. Martin. "Global Topological Changes of Offset Domains." In 2011 Eighth International Symposium on Voronoi Diagrams in Science and Engineering (ISVD). IEEE, 2011. http://dx.doi.org/10.1109/isvd.2011.19.

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Fernández-Breis, J. T., D. Castellanos-Nieves, R. Valencia-Garcia, P. J. Vivancos-Vicente, R. Martínez Béjar, and M. De las Heras-Gónzalez. "Towards scott domains-based topological ontology models." In the international conference. New York, New York, USA: ACM Press, 2001. http://dx.doi.org/10.1145/505168.505181.

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Szeptycki, Paweł. "Locally convex domains of integral operators." In Topological Algebras, their Applications, and Related Topics. Warsaw: Institute of Mathematics Polish Academy of Sciences, 2005. http://dx.doi.org/10.4064/bc67-0-28.

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Liu, Tong, and Zheng Wang. "Measuring the three-dimensional structural properties of topologically associating domains." In 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2018. http://dx.doi.org/10.1109/bibm.2018.8621459.

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ZHU, Yin Lian. "Atomic mapping of topological domains in strained ferroelectric films." In European Microscopy Congress 2020. Royal Microscopical Society, 2021. http://dx.doi.org/10.22443/rms.emc2020.21.

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Chen, Zhifeng, Lvda Wang, Ying Li, and Shihui Ying. "Unsupervised Multi-Source Domains Adaptation with Locally Topological Persevering." In 2023 China Automation Congress (CAC). IEEE, 2023. http://dx.doi.org/10.1109/cac59555.2023.10451721.

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Leugering, Gunter, Jan Sokolowski, and Antoni Zochowski. "Shape-topological differentiability of energy functionals in domains with cracks." In 2013 18th International Conference on Methods & Models in Automation & Robotics (MMAR). IEEE, 2013. http://dx.doi.org/10.1109/mmar.2013.6669965.

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"A binary segmentation method for detecting topological domains in Hi-C data." In 25th International Congress on Modelling and Simulation. Modelling and Simulation Society of Australia and New Zealand, 2023. http://dx.doi.org/10.36334/modsim.2023.raveendran.

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Hoblyn, J., Tayler Sulse, Emma Mae Huston, Melanie Ryberg, P. Byrne, and Kieran O’Driscoll. "41 Korsakoff’s syndrome: neurocognitive domains impairments and potential therapeutic interventions." In The British Neuropsychiatry Association – Annual Meeting. BMJ Publishing Group Ltd, 2019. http://dx.doi.org/10.1136/jnnp-2019-bnpa.41.

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Prabhumoye, Shrimai, Ruslan Salakhutdinov, and Alan W. Black. "Topological Sort for Sentence Ordering." In Proceedings of the 58th Annual Meeting of the Association for Computational Linguistics. Stroudsburg, PA, USA: Association for Computational Linguistics, 2020. http://dx.doi.org/10.18653/v1/2020.acl-main.248.

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Reports on the topic "Domains of topological association"

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Buczyłowska, Dorota, Tianyu Zhao, Nitika Singh, Agnieszka Siry, Anna Jurczak, and Iana Markevych. Exposure to greenspace and bluespace and cognitive functioning in children - a systematic review protocol. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, February 2022. http://dx.doi.org/10.37766/inplasy2022.2.0018.

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Review question / Objective: Following review questions should be addressed: Is there any association between exposure to greenspace or bluespace and cognitive functioning in children as assessed by observational and interventional research? Does exposure to greenspace or bluespace is more strongly associated with a particular domain of cognitive functioning in children compared to other domains of cognitive functioning? Does the association between exposure to greenspace or bluespace and cognitive functioning in children differ according to age? Does the association between greenspace and bluespace differ depending on type and methods of the exposure assessment? Information sources: PubMed and PsycINFO via EBSCO will be searched. We will also conduct a ‘snowball’ search to detect additional studies by searching the reference lists of publications eligible for full-text review. Further, we will manually search reference lists of previously published reviews.
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Dorsey, Achsah, Elissa M. Scherer, Randy Eckhoff, and Robert Furberg. Measurement of Human Stress: A Multidimensional Approach. RTI Press, June 2022. http://dx.doi.org/10.3768/rtipress.2022.op.0073.2206.

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Stress is a multidimensional construct that comprises exposure to events, perceptions of stress, and physiological responses to stress. Research consistently demonstrates a strong association between stress and a myriad of physical and mental health concerns, resulting in a pervasive and interdisciplinary agreement on the importance of investigating the relationship between stress and health. Developing a holistic understanding of stress requires assessment of the three domains vital to the study of stress: (1) the presence of environmental stressors, (2) psychological and biological reactions to stressors, and (3) the length of time over which the stressor or stress response occurs. Research into all three domains requires multiple methods. Self-reports allow for subjective evaluations of stress that illuminate the duration and severity of the psychological response to stressors. Biomarkers, in turn, capture a more-objective measure of stress and create a deeper understanding of the biological response to chronic and acute stress. Finally, the use of digital biomarkers allows for further exploration of the physiological fluctuations caused by stress by measuring the changes occurring at the same time as the stressor. Future research on stress and health should favor a multidimensional approach that creates a triangulated picture of stress, drawing from each of the three aforementioned method groups.
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Verdisco, Aimee, Jennelle Thompson, and Santiago Cueto. Early Childhood Development: Wealth, the Nurturing Environment and Inequality First Results from the PRIDI Database. Inter-American Development Bank, July 2016. http://dx.doi.org/10.18235/0011753.

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This paper presents findings from the Regional Project on Child Development Indicators, PRIDI for its acronym in Spanish. PRIDI created a new tool, the Engle Scale, for evaluating development in children aged 24 to 59 months in four domains: cognition, language and communication, socio-emotional and motor skills. It also captures and identifies factors associated with child development. The Engle Scale was applied in nationally representative samples in four Latin American countries: Costa Rica, Nicaragua, Paraguay and Peru. The results presented here are descriptive, but they offer new insight regarding the complexity of child development in Latin America. The basic message emerging from this study is that child development in Latin America is unequal. Inequality in results appears as early as 24 months and increases with age. There is variation in inequality. For example, correlations with the socio-economic characteristics of the home and maternal education are stronger for cognition, and language and communication than for motor development. The environment within which children develop and the adult-child interactions predominant within this environment ¿ referred to in this study as the nurturing environment - is important for all domains of child development utilized in this study, although stronger associations appear for cognition, language and communication, and socio-emotional development. For all domains measured by the Engle Scale, the nurturing environment bears a statistically stronger correlation than the socio-economic endowment of the home or maternal education. Gaps between the development of children in the top and low extremes in these factors matter. By 59 months, the development of a poor and under-nurtured child will lag by as much as 18 months behind her richer and more nurtured peers. For this child it will be more difficult to recognize basic shapes like triangles or squares, count to 20, or understand temporal sequences. She will also have gaps in her basic executive functioning and socio-emotional skills, including empathy and autonomy. She will not likely be ready for school and may not have success once there. Notably, however, if this same child, in the same poor household, were to benefit from a nurturing environment, her level of development would rise and would start to approach levels found in children in richer but less nurtured households. The nurturing environment thus appears to mitigate the negative association lower levels of wealth have with the domains of development included in this study.
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Jacinto, Miguel, Anabela Pereira dos Santos de Vitorino, Rui Matos, Diogo Mendes, and Teresa Bento. Effects of a physical exercise program on the quality of life in individuals with intellectual disability: systematic review. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, November 2021. http://dx.doi.org/10.37766/inplasy2021.11.0025.

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Review question / Objective: The objective of the present study is, through the methodology of systematic review, to identify the benefits in QoL, starting from a PE program in individuals with ID and relate them to the model of Schalock et al. (2002). Condition being studied: In individuals with ID, characterized by a deficit of intellectual and adaptive functioning in the conceptual, social and practical domains, identified with mild, moderate, severe and profound degrees and develops before 18 or 22 years old (American Psychiatric Association, 2013; Schalock et al., 2010; 2021), measuring QoL allows: i) to understand their degree of satisfaction; ii) understand personal perceptions; iii) support decision-making; iv) evaluate the intervention; v) evaluate theoretical models. This measurement allows us to direct the individual to the life he likes and values (Schalock & Verdugo, 2002). Thus, the objective of the present study is, through the methodology of systematic review, to identify the benefits in QoL, starting from a PE program in individuals with ID and relate them to the model of Schalock et al. (2002).
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Bassi, Andrea. From “Social Impact” to “Social Value”. Liège: CIRIEC, 2022. http://dx.doi.org/10.25518/ciriec.wp202206.

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After the financial-economic crisis of 2008 there has been an increasing diffusion of discourses by international institutions stressing the necessity towards the adoption of impact evaluation methods both by for profit and SSE organizations. This craze for impact measurement is generally led by the need of the stock exchange to find new financial markets (demand) for an increasing offer of socially or environmentally oriented financial products (such as the Social Impact Bond). This pressure had the effect to spread terms and concept typically of the financial world to other domains, such as the welfare policy (Social Investment State) and the traditional philanthropic sector (Social Return on Investment). Even the SSE has not been immune from this “epidemic” of measurement, standardization, quantification of its activities’ effects (Salathé-Beaulieu, G. in collaboration with M. J. Bouchard and M. Mendell, 2019). The paper’s main aim is to argue in favour of the adoption of a broader conceptualization of the SSE contribution to the local community (and to the society as a whole) that the one implied by the term “impact”. It proposes a conceptual framework based on the “social value” notion, which requires to consider the worth (Bouchard, M. J. ed., 2009) linked to the presence of the organization itself and not only of its activities/ programs/services. The paper will illustrate and comment the main results from an empirical research on the Social Added Value Evaluation of an umbrella recreation association in the Emilia-Romagna Region. The inquire adopts an experimental design based on qualitative methods such as: focus groups, face to face interviews and on site observations, in order to build a consensual system of social value/impact evaluation to be adopted by the local branches of the regional association.
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Wisniewski, Michael, Samir Droby, John Norelli, Dov Prusky, and Vera Hershkovitz. Genetic and transcriptomic analysis of postharvest decay resistance in Malus sieversii and the identification of pathogenicity effectors in Penicillium expansum. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597928.bard.

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Use of Lqh2 mutants (produced at TAU) and rNav1.2a mutants (produced at the US side) for identifying receptor site-3: Based on the fact that binding of scorpion alpha-toxins is voltage-dependent, which suggests toxin binding at the mobile voltage-sensing region, we analyzed which of the toxin bioactive domains (Core-domain or NC-domain) interacts with the DIV Gating-module of rNav1.2a. This analysis was based on the assumption that the dissociation of toxin mutants upon depolarization would vary from that of the unmodified toxin should the substitutions affect a site of interaction with the channel Gating-module. Using a series of toxin mutants (mutations at both domains) and two channel mutants that were shown to reduce the sensitivity to scorpion alpha-toxins, and by comparison of depolarization-driven dissociation of Lqh2 derivatives off their binding site at rNav1.2a mutant channels we found that the toxin Core-domain interacts with the Gating-module of DIV. Details of the experiments and results appear in Guret al (2011). Mapping receptor site 3 at Nav1.2a by extensive channel mutagenesis (Seattle): Since previous studies with photoaffinity labeling and antibody mapping implicated domains I and IV in scorpion alpha-toxin binding, Nav1.2 channel mutants containing substitutions at these extracellular regions were expressed and tested for receptor function by whole-cell voltage clamp. Of a large number of channel mutants, T1560A, F1610A, and E1613A in domain IV had ~5.9-, ~10.7-, and ~3.9-fold lower affinities for the scorpion toxin Lqh2, respectively, and mutant E1613R had 73-fold lower affinity. Toxin dissociation was accelerated by depolarization for both wild-type and mutants, and the rates of dissociation were also increased by mutations T1560A, F1610A and E1613A. In contrast, association rates for these three mutant channels at negative membrane potentials were not significantly changed and were not voltage-dependent. These results indicated that Thr1560 in the S1-S2 loop, Phe1610 in the S3 segment, and Glu1613 in the S3-S4 loop in domain IV participate in toxin binding. T393A in the SS2-S6 loop in domain I also showed a ~3.4-fold lower affinity for Lqh2, indicating that this extracellular loop may form a secondary component of the toxin binding site. Analysis with the Rosetta-Membrane algorithm revealed a three-dimensional model of Lqh2 binding to the voltage sensor in a resting state. In this model, amino acid residues in an extracellular cleft formed by the S1-S2 and S3-S4 loops in domain IV that are important for toxin binding interact with amino acid residues on two faces of the wedge-shaped Lqh2 molecule that are important for toxin action. The conserved gating charges in the S4 transmembrane segment are in an inward position and likely form ion pairs with negatively charged amino acid residues in the S2 and S3 segments (Wang et al 2011; Gurevitz 2012; Gurevitzet al 2013).
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De la O, Ana, Cecilia Rossel, and Pilar Manzi. Opting Out from Public Services and the Social Contract in Latin America. Inter-American Development Bank, December 2023. http://dx.doi.org/10.18235/0005329.

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The seemingly upward trend in opting out from public services and the segregation of income groups in public and private education and health systems has raised concerns about the future of an already fragmented social contract in Latin America. In this chapter, we examine the evolution of the use of private education and private health insurance in selected countries during the first two decades of the 2000s. We also examine the socio-demographic correlates of the decision to opt out, and the association it has with attitudes that are relevant to understand the foundations of the social contract in the region. Overall, the evidence suggests that scholars concerns about the fragility of the social contract are justified, but with some nuances. Wealthy households are mostly opting out of the public education system, and the middle-class is split with a substantial proportion of households opting for private schools. On the other hand, opting out from public health is only prevalent among wealthy households, and even within that group the share of households who are paying for a private health insurance is much smaller than the share of households who opt for private education. For both policy domains, however, we find that people who use private services have worse evaluations of public services, express less support for the public provision of those services, and more generally, are less supportive of redistribution compared to people inside the public systems. We discuss the implications of these descriptive statistics for the sustainability of the public provision of services and the social contract.
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Slaughter-Acey, Jaime, Kathryn Behrens, Amy M. Claussen, Timothy Usset, Carrie Neerland, Sameerah Bilal-Roby, Huda Bashir, et al. Social and Structural Determinants of Maternal Morbidity and Mortality: An Evidence Map. Agency for Healthcare Research and Quality (AHRQ), December 2023. http://dx.doi.org/10.23970/ahrqepccer264.

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Objective. The purpose was to review available evidence of risk factors associated with maternal morbidity and mortality in the United States during the prenatal and postpartum periods to inform a National Institutes of Health Pathways to Prevention Workshop: Identifying Risks and Interventions to Optimize Postpartum Health, held November 29–December 1, 2022. Data sources. We searched MEDLINE®, CINAHL®, and the Social Sciences Citation Index through November 2022. Review methods. We searched for observational studies examining exposures related to social and structural determinants of health and at least one health or healthcare-related outcome for pregnant and birthing people. We extracted basic study information and grouped studies by social and structural determinants of health domains and maternal outcomes. We prioritized studies according to study design and rigor of analytic approaches to address selection bias based on the ROBINS-E. We summarize all included studies and provide additional descriptions of direction of association between potential risk exposures and outcomes. Results. We identified 8,378 unique references, with 118 included studies reporting social and structural determinants of health associated with maternal health outcomes. Studies covered risk factors broadly, including identity and discrimination, socioeconomic, violence, trauma, psychological stress, structural/institutional, rural/urban, environment, comorbidities, hospital, and healthcare use factors. However, the risk factors we identified represent only a subset of potential social and structural determinants of interest. We found an unexpectedly large volume of research on violence and trauma relative to other potential exposures of interest for pregnant people. Outcome domains included maternal mortality, severe maternal morbidity, hypertensive disorders, gestational diabetes, cardio/metabolic disorders, weathering (the physiological effect of premature aging caused by chronic stressful experiences), depression, other mental health or substance use disorders, and cost/healthcare use outcomes. Depression/other mental health outcomes represented a large proportion of medical outcomes captured. Risk of bias was high, and rarely did studies report the excess risk attributable to a specific exposure. Conclusions. Identifying risk factors pregnant and birthing people face is vitally important. Limited depth and quality of available research within each social and structural determinant of health impeded our ability to outline specific pathways, including risk factor interdependence. While more recently published literature showed a trend toward increased rigor, future research can emphasize techniques that estimate the causal impacts of risk factors. Improved reporting in studies, along with organized and curated catalogues of maternal health exposures and their presumed mechanisms, would make it easier to examine exposures in the future. In the longer term, the field could be advanced by datasets designed to more fully capture the data required to robustly examine racism and other social and structural determinants of health, in combination with their intersections and feedback loops with other biologic/medical risk factors.
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