Enumerating all the spanning trees in an un-oriented graph - A novel approach

2010 ◽  
Author(s):  
Cristian E. Onete ◽  
Maria Cristina C. Onete
Keyword(s):  
Spanning Trees ◽  
Oriented Graph ◽  
Novel Approach

scholarly journals MicrobeTrace: Retooling Molecular Epidemiology for Rapid Public Health Response

2020 ◽  
Author(s):  
Ellsworth M. Campbell ◽  
Anthony Boyles ◽  
Anupama Shankar ◽  
Jay Kim ◽  
Sergey Knyazev ◽  
...  
Keyword(s):  
Public Health ◽  
Molecular Epidemiology ◽  
Spanning Trees ◽  
Healthcare Providers ◽  
Contact Tracing ◽  
Surveillance Systems ◽  
Multiple Sources ◽  
Public Health Response ◽  
Link Type ◽  
Novel Approach

AbstractMotivationOutbreak investigations use data from interviews, healthcare providers, laboratories and surveillance systems. However, integrated use of data from multiple sources requires a patchwork of software that present challenges in usability, interoperability, confidentiality, and cost. Rapid integration, visualization and analysis of data from multiple sources can guide effective public health interventions.ResultsWe developed MicrobeTrace to facilitate rapid public health responses by overcoming barriers to data integration and exploration in molecular epidemiology. Using publicly available HIV sequences and other data, we demonstrate the analysis of viral genetic distance networks and introduce a novel approach to minimum spanning trees that simplifies results. We also illustrate the potential utility of MicrobeTrace in support of contact tracing by analyzing and displaying data from an outbreak of SARS-CoV-2 in South Korea in early 2020.Availability and ImplementationMicrobeTrace is a web-based, client-side, JavaScript application (https://microbetrace.cdc.gov) that runs in Chromium-based browsers and remains fully-operational without an internet connection. MicrobeTrace is developed and actively maintained by the Centers for Disease Control and Prevention. The source code is available at https://github.com/cdcgov/[email protected]

scholarly journals MicrobeTrace: Retooling molecular epidemiology for rapid public health response

2021 ◽  
Vol 17 (9) ◽  
pp. e1009300 ◽  
Author(s):  
Ellsworth M. Campbell ◽  
Anthony Boyles ◽  
Anupama Shankar ◽  
Jay Kim ◽  
Sergey Knyazev ◽  
...  
Keyword(s):  
Public Health ◽  
Molecular Epidemiology ◽  
Spanning Trees ◽  
Healthcare Providers ◽  
Contact Tracing ◽  
Surveillance Systems ◽  
Multiple Sources ◽  
Public Health Response ◽  
Link Type ◽  
Novel Approach

Outbreak investigations use data from interviews, healthcare providers, laboratories and surveillance systems. However, integrated use of data from multiple sources requires a patchwork of software that present challenges in usability, interoperability, confidentiality, and cost. Rapid integration, visualization and analysis of data from multiple sources can guide effective public health interventions. We developed MicrobeTrace to facilitate rapid public health responses by overcoming barriers to data integration and exploration in molecular epidemiology. MicrobeTrace is a web-based, client-side, JavaScript application (https://microbetrace.cdc.gov) that runs in Chromium-based browsers and remains fully operational without an internet connection. Using publicly available data, we demonstrate the analysis of viral genetic distance networks and introduce a novel approach to minimum spanning trees that simplifies results. We also illustrate the potential utility of MicrobeTrace in support of contact tracing by analyzing and displaying data from an outbreak of SARS-CoV-2 in South Korea in early 2020. MicrobeTrace is developed and actively maintained by the Centers for Disease Control and Prevention. Users can email [email protected] for support. The source code is available at https://github.com/cdcgov/microbetrace.

scholarly journals A novel approach to understanding Parkinsonian cognitive decline using minimum spanning trees, edge cutting, and magnetoencephalography

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Olivier B. Simon ◽  
Isabelle Buard ◽  
Donald C. Rojas ◽  
Samantha K. Holden ◽  
Benzi M. Kluger ◽  
...  
Keyword(s):  
Gene Expression Analysis ◽  
Spanning Trees ◽  
Minimum Spanning Tree ◽  
High Dimensional Data ◽  
Null Distribution ◽  
High Dimensional ◽  
Neural Connectivity ◽  
Cross Sectional ◽  
Novel Approach ◽  
Wide Range

AbstractGraph theory-based approaches are efficient tools for detecting clustering and group-wise differences in high-dimensional data across a wide range of fields, such as gene expression analysis and neural connectivity. Here, we examine data from a cross-sectional, resting-state magnetoencephalography study of 89 Parkinson’s disease patients, and use minimum-spanning tree (MST) methods to relate severity of Parkinsonian cognitive impairment to neural connectivity changes. In particular, we implement the two-sample multivariate-runs test of Friedman and Rafsky (Ann Stat 7(4):697–717, 1979) and find it to be a powerful paradigm for distinguishing highly significant deviations from the null distribution in high-dimensional data. We also generalize this test for use with greater than two classes, and show its ability to localize significance to particular sub-classes. We observe multiple indications of altered connectivity in Parkinsonian dementia that may be of future use in diagnosis and prediction.

An integer sequence and standard monomials

2018 ◽  
Vol 17 (02) ◽  
pp. 1850037
Author(s):  
Ajay Kumar ◽  
Chanchal Kumar
Keyword(s):  
Spanning Trees ◽  
Monomial Ideal ◽  
Oriented Graph ◽  
Barycentric Subdivision ◽  
Parking Functions ◽  
Minimal Free Resolution ◽  
Ideal Formula ◽  
Laplace Matrix ◽  
Integer Sequence ◽  
Standard Monomials

For an (oriented) graph [Formula: see text] on the vertex set [Formula: see text] (rooted at [Formula: see text]), Postnikov and Shapiro (Trans. Amer. Math. Soc. 356 (2004) 3109–3142) associated a monomial ideal [Formula: see text] in the polynomial ring [Formula: see text] over a field [Formula: see text] such that the number of standard monomials of [Formula: see text] equals the number of (oriented) spanning trees of [Formula: see text] and hence, [Formula: see text], where [Formula: see text] is the truncated Laplace matrix of [Formula: see text]. The standard monomials of [Formula: see text] correspond bijectively to the [Formula: see text]-parking functions. In this paper, we study a monomial ideal [Formula: see text] in [Formula: see text] having rich combinatorial properties. We show that the minimal free resolution of the monomial ideal [Formula: see text] is the cellular resolution supported on a subcomplex of the first barycentric subdivision [Formula: see text] of an [Formula: see text] simplex [Formula: see text]. The integer sequence [Formula: see text] has many interesting properties. In particular, we obtain a formula, [Formula: see text], with [Formula: see text] for [Formula: see text], [Formula: see text] and [Formula: see text] for [Formula: see text], similar to [Formula: see text].

Copper-dependent ATP7B up-regulation drives the resistance of TMEM16A-overexpressing head-and-neck cancer models to platinum toxicity

2019 ◽  
Vol 476 (24) ◽  
pp. 3705-3719 ◽  
Author(s):  
Avani Vyas ◽  
Umamaheswar Duvvuri ◽  
Kirill Kiselyov
Keyword(s):  
Oxidative Stress ◽  
Head And Neck ◽  
Transcriptional Activation ◽  
Platinum Resistance ◽  
Mrna Levels ◽  
Strong Positive Correlation ◽  
Platinum Compounds ◽  
Copper Chelation ◽  
Novel Approach ◽  
Cancer Models

Platinum-containing drugs such as cisplatin and carboplatin are routinely used for the treatment of many solid tumors including squamous cell carcinoma of the head and neck (SCCHN). However, SCCHN resistance to platinum compounds is well documented. The resistance to platinum has been linked to the activity of divalent transporter ATP7B, which pumps platinum from the cytoplasm into lysosomes, decreasing its concentration in the cytoplasm. Several cancer models show increased expression of ATP7B; however, the reason for such an increase is not known. Here we show a strong positive correlation between mRNA levels of TMEM16A and ATP7B in human SCCHN tumors. TMEM16A overexpression and depletion in SCCHN cell lines caused parallel changes in the ATP7B mRNA levels. The ATP7B increase in TMEM16A-overexpressing cells was reversed by suppression of NADPH oxidase 2 (NOX2), by the antioxidant N-Acetyl-Cysteine (NAC) and by copper chelation using cuprizone and bathocuproine sulphonate (BCS). Pretreatment with either chelator significantly increased cisplatin's sensitivity, particularly in the context of TMEM16A overexpression. We propose that increased oxidative stress in TMEM16A-overexpressing cells liberates the chelated copper in the cytoplasm, leading to the transcriptional activation of ATP7B expression. This, in turn, decreases the efficacy of platinum compounds by promoting their vesicular sequestration. We think that such a new explanation of the mechanism of SCCHN tumors’ platinum resistance identifies novel approach to treating these tumors.

Collecting Words: A Clinical Example of a Morphology-Focused Orthographic Intervention

2020 ◽  
Vol 51 (3) ◽  
pp. 544-560 ◽  
Author(s):  
Kimberly A. Murphy ◽  
Emily A. Diehm
Keyword(s):  
Written Language ◽  
Morphological Knowledge ◽  
English Orthography ◽  
Word Level ◽  
Novel Approach ◽  
Language Pathology ◽  
The One ◽  
Critical Intervention ◽  
Reading And Spelling ◽  
Reading And Spelling Difficulties

Purpose Morphological interventions promote gains in morphological knowledge and in other oral and written language skills (e.g., phonological awareness, vocabulary, reading, and spelling), yet we have a limited understanding of critical intervention features. In this clinical focus article, we describe a relatively novel approach to teaching morphology that considers its role as the key organizing principle of English orthography. We also present a clinical example of such an intervention delivered during a summer camp at a university speech and hearing clinic. Method Graduate speech-language pathology students provided a 6-week morphology-focused orthographic intervention to children in first through fourth grade ( n = 10) who demonstrated word-level reading and spelling difficulties. The intervention focused children's attention on morphological families, teaching how morphology is interrelated with phonology and etymology in English orthography. Results Comparing pre- and posttest scores, children demonstrated improvement in reading and/or spelling abilities, with the largest gains observed in spelling affixes within polymorphemic words. Children and their caregivers reacted positively to the intervention. Therefore, data from the camp offer preliminary support for teaching morphology within the context of written words, and the intervention appears to be a feasible approach for simultaneously increasing morphological knowledge, reading, and spelling. Conclusion Children with word-level reading and spelling difficulties may benefit from a morphology-focused orthographic intervention, such as the one described here. Research on the approach is warranted, and clinicians are encouraged to explore its possible effectiveness in their practice. Supplemental Material https://doi.org/10.23641/asha.12290687

Abstract #709: E-Consults: A Novel Approach to Increase Access to Subspecialty Care in Endocrinology

2015 ◽  
Vol 21 ◽  
pp. 128
Author(s):  
Kaniksha Desai ◽  
Halis Akturk ◽  
Ana Maria Chindris ◽  
Shon Meek ◽  
Robert Smallridge ◽  
...  
Keyword(s):  
Novel Approach
Sign in / Sign up

Export Citation Format

Share Document