Roots, Extrema and Inflection Points by using Taylor Regression Procedure

Christopoulos, Demetris

doi:10.2139/ssrn.2521403

Cited by 5 publications

(3 citation statements)

References 3 publications

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“…The R statistical software (v4.0.2) was used to calculate and rank Pearson correlation coefficients between fitness scores of CIC and each targeted gene. The inflection point of the positive coefficient curve was calculated using the R package RootsExtremalnflections (vl.2.1) (Christopoulos 2019). A pair of genes was considered co-essential if the BH-adjustedp- p value was < 0.05 and the coefficient was > 0.178 (the inflection point).…”

Section: Methodsmentioning

confidence: 99%

Multi-omic analysis of CIC’s functional networks reveals novel interaction partners and a potential role in mitotic fidelity

Chittaranjan

Song

Chan

et al. 2019

Preprint

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Background: CIC is a transcriptional repressor inactivated by loss-of-function mutations in several cancer types, including gliomas, lung cancers, and gastric adenocarcinomas. CIC alterations and/or loss of CIC activity have been associated with poorer outcomes and more aggressive phenotypes across cancer types, which is consistent with the notion that CIC functions as a tumour suppressor across a wide range of contexts.Results: Using mammalian cells lacking functional CIC, we found that CIC deficiency was associated with chromosome segregation (CS) defects, resulting in chromosomal instability and aneuploidy. These CS defects were associated with transcriptional dysregulation of spindle assembly checkpoint and cell cycle regulators. We also identified novel CIC interacting proteins, including core members of the SWI/SNF complex, and showed that they cooperatively regulated the expression of genes involved in cell cycle regulation. Finally, we showed that loss of CIC and ARID1A cooperatively increased CS defects and reduced cell viability. Conclusions:Our study ascribes a novel role to CIC as an important regulator of the cell cycle and demonstrates that loss of CIC can lead to chromosomal instability and aneuploidy in human and murine cells through defects in CS, providing insight into the underlying mechanisms of CIC's increasingly apparent role as a "pan-cancer" tumour suppressor.

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Section: Methodsmentioning

confidence: 99%

Multi-omic analysis of CIC’s functional networks reveals novel interaction partners and a potential role in mitotic fidelity

Chittaranjan

Song

Chan

et al. 2019

Preprint

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“…The Taylor regression procedure was applied to obtain the inflection point of the 𝐺𝐺 ̂𝑠𝑠 -𝐵𝐵𝐵𝐵 ̂ curve (Christopoulos, 2017).…”

Section: 𝐺𝐺 ̂𝑠𝑠 -𝐵𝐵𝐵𝐵 ̂ -Curvementioning

confidence: 99%

Conservative or non-conservative strategy to advance breeding generation? A case study inEucalyptus benthamiiusing spatial variation and competition model

Araújo

Rocha

Estopa³

et al. 2023

Silvae Genetica

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The greatest challenge faced when breeding populations of forest species is to achieve the right equilibrium among genetic gain and no loss of the effective population size. Thus this study aims to define the best thinning strategy to compose a seed orchard of Eucalyptus benthamii to obtain genetic gain maintaining the effective population size. The population of E. benthamii studied consisted of 28 open-pollinated progenies. The diameter at breast height (DBH) and height (H) parameters were determined three years after planting. Measurement data were analyzed and compared using four different mathematical models (with and without competition effect and spatial variation). Strategies considering genetic gain and effective population size were simulated considering the number of families, the number of individuals between families, and the total number of individuals. The mathematical model accounting for the competition effect had the best fit for DBH whereas the model accounting for the environmental variation effect presented the best fit for H. The ranking of BLUPs grouped the families into three clusters (best, intermediate/average, worst/poor families). The strategy that maintains 40 % of the individuals, generates a genetic gain of 13 % in DBH and 8 % in total height while maintaining an effective population size greater than 92 for booth traits.

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“…Accuracy (objective performance) was treated as a nonlinear function of the SOA and the point of the fastest increase in accuracy, corresponding to the inflection point is the access threshold to conscious processing, characterizing the transition between unconscious (i.e., subliminal and/or preconscious processing in the existence of the lack of awareness) and conscious processing (Del Cul, Baillet, & Dehaene, 2007). To obtain access threshold to conscious processing (inflection point) for both each person and each group, we used nonlinear regression to estimate the objective performance as a function of SOA using Taylor regression estimator which is available in the RootsExtremaInflections package of R (Christopoulos, 2014) and can work for discrete and noisy values. In this method, Taylor polynomial of a smooth function f around a point ρ is used:…”

Section: Behavioral Datamentioning

confidence: 99%

Delayed access to conscious processing in multiple sclerosis: Reduced cortical activation and impaired structural connectivity

Silemek

Ranjeva

Audoin

et al. 2021

Human Brain Mapping

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Although multiple sclerosis (MS) is frequently accompanied by visuo-cognitive impairment, especially functional brain mechanisms underlying this impairment are still not well understood. Consequently, we used a functional MRI (fMRI) backward masking task to study visual information processing stratifying unconscious and conscious in MS. Specifically, 30 persons with MS (pwMS) and 34 healthy controls (HC) were shown target stimuli followed by a mask presented 8-150 ms later and had to compare the target to a reference stimulus. Retinal integrity (via optical coherence tomography), optic tract integrity (visual evoked potential; VEP) and whole brain structural connectivity (probabilistic tractography) were assessed as complementary structural brain integrity markers. On a psychophysical level, pwMS reached conscious access later than HC (50 vs. 16 ms, p < .001). The delay increased with disease duration (p < .001, β = .37) and disability (p < .001, β = .24), but did not correlate with conscious information processing speed (Symbol digit modality test, β = .07, p = .817). No association was found for VEP and retinal integrity markers. Moreover, pwMS were characterized by decreased brain activation during unconscious processing compared with HC. No group differences were found during conscious processing. Finally, a complementary structural brain integrity analysis showed that a reduced fractional anisotropy in corpus callosum and an impaired connection between right insula and primary visual areas was related to delayed conscious access in pwMS. Our study revealed slowed conscious access to visual stimulus material in MS and a complex pattern of functional and structural alterations coupled to unconscious processing of/delayed conscious access to visual stimulus material in MS.

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Roots, Extrema and Inflection Points by using Taylor Regression Procedure

Cited by 5 publications

References 3 publications

Multi-omic analysis of CIC’s functional networks reveals novel interaction partners and a potential role in mitotic fidelity

Multi-omic analysis of CIC’s functional networks reveals novel interaction partners and a potential role in mitotic fidelity

Conservative or non-conservative strategy to advance breeding generation? A case study inEucalyptus benthamiiusing spatial variation and competition model

Delayed access to conscious processing in multiple sclerosis: Reduced cortical activation and impaired structural connectivity

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