Epigenetic regulation of transcription and cellular development

Epigenetic machinery can regulate different biological processes via different mechanisms. In this thesis, we explore the effects of the epigenetic system on transcription and how it can differ during cellular development in different human cell lines models, with focus on hematopoiesis. Paper I, aimed to identify new roles for different epigenetic regulators in myeloid differentiation. We performed a CRISPR-Cas9 screen that targeted 1092 epigenetic factors in a model for myeloid differentiation, with the objective to uncover novel roles for regulatory factors that are important for differentiation in hematopoiesis. In our analysis, the chromodomain helicase DNA-binding 2 (CHD2) showed a crucial impact on megakaryocytic differentiation in the K-562 cell line model. In paper II, our aim was to identify the roles of different PHC subunits in Polycomb repressive complex 1 during hematopoiesis. Data mining from publicly available datasets showed opposite expression pattern between each PHC subunit. PHC1 is higher expressed in early stages of myelopoiesis that is opposite to PHC2, and PHC3, which expression increasing with differentiation. PHC1-3 was knocked down individually, using siRNA in the myeloblast cell line KG-1. RNA-sequencing analysis after knock down for each specific PHC subunit, showed how PHC1, 2 and 3 play different roles during development and myeloid differentiation. In paper III, we used the FANTOM5 database for transcription start sites (TSS) in a wide variety of primary cells. The study mapped the usage of alternative TSS that leads to exclusion of coding sequence, and exclusion of annotated protein domains. We demonstrated a dynamic usage of alternative TSS and their potential regula- tory roles in different cell lineages and development stages. We investigated the role of alternative TSSs for KDM2B in the Jurkat T-cell lineage and their potential functional consequences. In paper IV, our aim was to study the dynamics of 3D chromatin structure in rela- tion to the circadian rhythm. We demonstrated that chromosomal fiber interactions are organized by PARP1- CTCF activity. We showed how the 3D genome structure can influence circadian rhythm machinery and how the transcription activation and silencing are under oscillation

TFUZZY-OF: a new method for routing protocol for low-power and lossy networks load balancing using multi-criteria decision-making

The internet of things (IoT) based on a network layer perspective includes low-power and lossy networks (LLN) that are limited in terms of power consumption, memory, and energy usage. The routing protocol used in these networks is called routing over low-power and lossy networks (RPL). Therefore, the IoT networks include smart objects that need multiple routing for their interconnections which makes traffic load balancing techniques indispensable to RPL routing protocol. In this paper, we propose a method based on fuzzy logic and the technique for the order of prioritization by similarity to the ideal solution (TOPSIS) as a well-known multi-criteria decision-making method to solve the load balancing problem by routing metrics composition. For this purpose, a combination of both link and node routing metrics namely hop count, expected transmission count, and received signal strength indicator is used. The results of simulations show that this method can increase the quality of services in terms of packet delivery ratio and average end-to-end delay

Investigating the Relationship among the Quality of Married Life, Internet Addiction, and Mindfulness in Women with Breast Cancer: The Mediating Role of Sexual Satisfaction

Background: Cyberspace has attracted sizeable audience thanks to its broad range of topics, diverse content, and audio and visual attractions. However, Internet addiction is believed to be a salient phenomenon as the consequence of improper use of cyberspace, which leads to mental and personality-related disorders. The present research aimed to investigate the mediating role of sexual satisfaction in the correlation among the quality of married life, Internet addiction, and mindfulness in patients with breast cancer.Methods: This is a descriptive correlational study. The statistical population herein comprised all the women with breast cancer in Tehran, Iran in 2022, out of whom a sample of 250 was conveniently selected. The research tools included the Revised Dyadic Adjustment Scale, the Internet Addiction Test, the Kentucky Inventory of Mindfulness Skills, and the Index of Sexual Satisfaction. The research model was evaluated with structural equation modeling in AMOS-25 and SPSS version 27.Results: Based on the obtained results, the mean and standard deviation (SD) of quality of married life, Internet addiction, mindfulness, and sexual satisfaction were 47.90±6.71, 59.18±8.88, 53.09±8.73, and 66.25±7.14, respectively. The results revealed the significance of all the direct paths (P<0.001), except for the path of mindfulness to the quality of married life. The indirect paths from Internet addiction to the quality of married life mediated by sexual satisfaction (P=0.010), and the association between mindfulness and the quality of married life mediated by sexual satisfaction (P=0.015) were also significant. Furthermore, the final model was found to have good fit (RMSEA=0.027).Conclusions: The research model herein had a desirable fit. It is an appropriate model, according to which different programs can be developed and designed in order to improve the quality of married life of patients with breast cancer

A new taxonomic backbone for the infrageneric classification of the species‐rich genus Silene (Caryophyllaceae)

The systematization of species in plant taxonomy based on the phylogenetic relationships among them are of utmost importance and also very challenging in large genera. In those, phylogenetic results often may suggest substantially different relationships than previous classifications, and call for large‐scale taxonomic revisions. Delimitation of the genus Silene has been and is still somewhat controversial, and recent molecular phylogenetic studies have settled several monophyletic groups that differ substantially from previous taxonomies. The infrageneric taxonomy of Silene s.str. has not been updated as a whole taking the phylogenetic information into account. In this study, we review previous phylogenetic results based on multiple loci, and conducted comprehensive gene tree analyses based on the nrDNA ITS and cpDNA rps16 regions for 1586 and 944 samples representing 415 and 397 species, respectively, including Silene and its allies, as well as a species tree analysis including 262 samples representing 243 species. We sampled representatives from all 44 sections recognized in the most recent global revision of the genus. The results support the recognition of three subgenera, i.e., S. subg. Behenantha, S. subg. Lychnis and S. subg. Silene, which is partly in agreement with previous molecular phylogenetic findings and contradicts all previous traditional classifications. Silene sect. Atocion, with a few annual species showing a narrow distribution range in the eastern Mediterranean, is treated as incertae sedis because of its uncertain phylogenetic position, possibly due to exceptionally high substitution rates. Silene subg. Lychnis, weakly supported as sister to the other subgenera, splits into three main clades and includes four sections. Silene subg. Behenantha, which forms a possible sister group in relation to S. subg. Silene, is poorly resolved basally and includes a large number of mostly small clades recognized as 18 sections. In S. subg. Silene, 11 sections are recognized, among which four are broadly circumscribed: S. sect. Auriculatae, S. sect. Sclerocalycinae, S. sect. Silene and S. sect. Siphonomorpha. Silene sect. Acutifoliae and S. sect. Portenses are described here as new taxa, whereas new status or new combinations are proposed for S. sect. Anotites, S. sect. Muscipula, S. sect. Petrocoma, S. sect. Pulvinatae, S. sect. Sclerophyllae and S. sect. Uebelinia. Five new combinations and two new names are proposed for taxa in Silene formerly assigned to Lychnis and Uebelinia. The correct infrageneric nomenclature compatible with the new infrageneric system is provided along with synonymy and type citations. Shortcomings of this study, such as the lack of a morphological diagnostic key and sparse sampling of some large sections, are listed and discussed.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/156144/5/tax12230.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156144/4/tax12230-sup-0006-Supinfo06.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156144/3/tax12230-sup-0001-Supinfo01.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156144/2/tax12230-sup-0007-FigureS1.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156144/1/tax12230_am.pd

Obesity and Gastroesophageal Reflux: Quantifying the Association Between Body Mass Index, Esophageal Acid Exposure, and Lower Esophageal Sphincter Status in a Large Series of Patients with Reflux Symptoms

Obesity and gastroesophageal reflux disease (GERD) are increasingly important health problems. Previous studies of the relationship between obesity and GERD focus on indirect manifestations of GERD. Little is known about the association between obesity and objectively measured esophageal acid exposure. The aim of this study is to quantify the relationship between body mass index (BMI) and 24-h esophageal pH measurements and the status of the lower esophageal sphincter (LES) in patients with reflux symptoms. Data of 1,659 patients (50% male, mean age 51 ± 14) referred for assessment of GERD symptoms between 1998 and 2008 were analyzed. These subjects underwent 24-h pH monitoring off medication and esophageal manometry. The relationship of BMI to 24-h esophageal pH measurements and LES status was studied using linear regression and multiple regression analysis. The difference of each acid exposure component was also assessed among four BMI subgroups (underweight, normal weight, overweight, and obese) using analysis of variance and covariance. Increasing BMI was positively correlated with increasing esophageal acid exposure (adjusted R 2 = 0.13 for the composite pH score). The prevalence of a defective LES was higher in patients with higher BMI (p &lt; 0.0001). Compared to patients with normal weight, obese patients are more than twice as likely to have a mechanically defective LES [OR = 2.12(1.63–2.75)]. An increase in body mass index is associated with an increase in esophageal acid exposure, whether BMI was examined as a continuous or as a categorical variable; 13% of the variation in esophageal acid exposure may be attributable to variation in BMI

Mapping local patterns of childhood overweight and wasting in low- and middle-income countries between 2000 and 2017

A double burden of malnutrition occurs when individuals, household members or communities experience both undernutrition and overweight. Here, we show geospatial estimates of overweight and wasting prevalence among children under 5 years of age in 105 low- and middle-income countries (LMICs) from 2000 to 2017 and aggregate these to policy-relevant administrative units. Wasting decreased overall across LMICs between 2000 and 2017, from 8.4% (62.3 (55.1–70.8) million) to 6.4% (58.3 (47.6–70.7) million), but is predicted to remain above the World Health Organization’s Global Nutrition Target of <5% in over half of LMICs by 2025. Prevalence of overweight increased from 5.2% (30 (22.8–38.5) million) in 2000 to 6.0% (55.5 (44.8–67.9) million) children aged under 5 years in 2017. Areas most affected by double burden of malnutrition were located in Indonesia, Thailand, southeastern China, Botswana, Cameroon and central Nigeria. Our estimates provide a new perspective to researchers, policy makers and public health agencies in their efforts to address this global childhood syndemic

Improvement of Flexible Design Matrix in Sparse Bayesian Learning for Multi Task fMRI Data Analysis

peer reviewedDetecting the active regions of the brain during cognitive functions is one of the important problems in cognitive neuroscience and disorder diagnosis. One of the promising approaches to solve this problem is to use General Linear Model (GLM) in functional Magnetic Resonance Imaging (fMRI) data. The main difficulty of the GLM method is to determine a flexible design matrix to model mentioned problem appropriately. In this paper, an approach to the critical construction of a flexible design matrix for precise detection of active regions of the brain, according to response in synthetic fMRI data based on GLM is presented. Should the design matrix is accurate, the next detection algorithm can extract a correct response from a very low signal to noise ratio (SNR); therefore, the presented design matrix is flexible to eschew over fitting and capture unfamiliar slow drifts. Using a sparse Bayesian learning method, some specific regressors are selected for flexible design matrix. Results show clearly prominent performance of suggested algorithm rather than conventional t-test methods and other conventional Bayesian analysis of fMRI data

The Role of Language in Processing Various Characters in Bahram Beyzai’s Play: One Thousand and First Night

Language is one of the main components of narrative (both short story and play), the significance of which is irrefutable in narrative literature. Since most events occur within and through language in drama, studying elements of language is quite effective in the analysis of the discourse of characters. Characters communicate and bond with each other through language in a play; thus; the present study aims at the analysis and critical reading of Bahram Beyzai’s One Thousand and First Night, as one of the leading playwrights of Iran, in following realms: discourse system and structure of the play, it’s variety and tasks, features and functions, and characterization techniques which are realized through language. To do so, the present study scrutinizes the characters of the play in terms of speech and language usage and the effect of language on characterization and the flourishment of personae. Manfred Pfister’s Theory and Analysis of Drama has been applied as the main theoretical tools for studying various functions of language, such as referential function, expressive, rhetorical, speech-maker, meta-linguistic, and poetic

Electrochemical, Structural and Nano Tribological Behavior of Ni-W-PTFE Nanocomposite Coatings Prepared by Tartrate Bath

WOS: 000378559300073A tartrate nickel plating bath has been used to prepare nickel-tungsten (Ni-W) dispersed PTFE composite coatings with four different PTFE contents (0, 4, 8 and 20 gl(-1)). The coatings are characterized using of Field-Emission Scanning Electron Microscopy (SEM), Energy Dispersive X-ray Analysis (EDAX) and X-ray Diffractrometry (XRD). XRD results indicate that the PTFE particle changed the surface texture significantly. The nano tribological behavior of the nano composite coating was estimated by contact mode of AFM. Electrochemical performance of the nanocomposite depositions was evaluated using potentiodynamic polarization and electrochemical impedance spectroscopy (EIS). The results show that the Ni-W/PTFE nanocomposite films exhibit better electrochemical and tribological performance than the Ni-W coating. The corrosion rate and surface roughness decreased about 50 and 5 times less than bare coating in optimum condition 8 gl(-1) PTFE