Biological Networks

Networks of coordinated interactions among biological entities govern a myriad of biological functions that span a wide range of both length and time scales—from ecosystems to individual cells and from years to milliseconds. For these networks, the concept “the whole is greater than the sum of its parts” applies as a norm rather than an exception. Meanwhile, continued advances in molecular biology and high-throughput technology have enabled a broad and systematic interrogation of whole-cell networks, allowing the investigation of biological processes and functions at unprecedented breadth and resolution—even down to the single-cell level. The explosion of biological data, especially molecular-level intracellular data, necessitates new paradigms for unraveling the complexity of biological networks and for understanding how biological functions emerge from such networks. These paradigms introduce new challenges related to the analysis of networks in which quantitative approaches such as machine learning and mathematical modeling play an indispensable role. The Special Issue on “Biological Networks” showcases advances in the development and application of in silico network modeling and analysis of biological systems

Quantitative performance metrics for robustness in circadian rhythms

Motivation: Sensitivity analysis provides key measures that aid in unraveling the design principles responsible for the robust performance of biological networks. Such metrics allow researchers to investigate comprehensively model performance, to develop more realistic models, and to design informative experiments. However, sensitivity analysis of oscillatory systems focuses on period and amplitude characteristics, while biologically relevant effects on phase are neglected. Results: Here, we introduce a novel set of phase-based sensitivity metrics for performance: period, phase, corrected phase and relative phase. Both state- and phase-based tools are applied to free-running Drosophila melanogaster and Mus musculus circadian models. Each metric produces unique sensitivity values used to rank parameters from least to most sensitive. Similarities among the resulting rank distributions strongly suggest a conservation of sensitivity with respect to parameter function and type. A consistent result, for instance, is that model performance of biological oscillators is more sensitive to global parameters than local (i.e. circadian specific) parameters. Discrepancies among these distributions highlight the individual metrics' definition of performance as specific parametric sensitivity values depend on the defined metric, or output. Availability: An implementation of the algorithm in MATLAB (Mathworks, Inc.) is available from the authors. Contact: [email protected] Supplementary information: Supplementary Data are available at Bioinformatics onlin

Model design choices impact biological insight: Unpacking the broad landscape of spatial-temporal model development decisions.

Computational models enable scientists to understand observed dynamics, uncover rules underlying behaviors, predict experimental outcomes, and generate new hypotheses. There are countless modeling approaches that can be used to characterize biological systems, further multiplied when accounting for the variety of model design choices. Many studies focus on the impact of model parameters on model output and performance; fewer studies investigate the impact of model design choices on biological insight. Here we demonstrate why model design choices should be deliberate and intentional in context of the specific research system and question. In this study, we analyze agnostic and broadly applicable modeling choices at three levels-system, cell, and environment-within the same agent-based modeling framework to interrogate their impact on temporal, spatial, and single-cell emergent dynamics. We identify key considerations when making these modeling choices, including the (i) differences between qualitative vs. quantitative results driven by choices in system representation, (ii) impact of cell-to-cell variability choices on cell-level and temporal trends, and (iii) relationship between emergent outcomes and choices of nutrient dynamics in the environment. This generalizable investigation can help guide the choices made when developing biological models that aim to characterize spatial-temporal dynamics

A geodatabase of blood pressure level and the associated factors including lifestyle, nutritional, air pollution, and urban greenspace

OBJECTIVES: Hypertension is a prevalent chronic disease globally. A multifaceted combination of risk factors is associated with hypertension. Scientific literature has shown the association among individual and environmental factors with hypertension, however, a comprehensive database including demographic, environmental, individual attributes and nutritional status has been rarely studied. Moreover, an integrated spatial-epidemiological approach has been scarcely researched. Therefore, this study aims to provide and describe a geodatabase including individual-based and socio-environmental data related to people living in the city of Mashhad, Iran in 2018. DATA DESCRIPTION: The database has been extracted from the PERSIAN Organizational Cohort study in Mashhad University of Medical Sciences. The data note includes three shapefiles and a help file. The shapefile format is a digital vector storage format for storing geometric location and associated attribute information. The first shapefile includes the data of population, air pollutants and amount of available green space for each census block of the city. The second shapefile consists of aggregated blood pressure data to the census blocks of the city. The third shapefile comprises the individual characteristics data (i.e., demographic, clinical, and lifestyle). Finally, the fourth file is a guide to the previous data files for users

Problem of Foreign Body in GI Tract

Most foreign bodies pass through the gastrointestinal tract uneventful. We report of a case of inadvertently ingested foreign body, which by endoscopy simulated a polyp and on biopsy reported as cancer, so the patient underwent an unnecessary major operation. This report emphasizes the importance of resemblance of foreign bodies with gastrointestinal neoplasm, and endoscopists, surgeons and pathologists should consider this entity in their daily practice

Gaussian mixture models and machine learning predict megakaryocytic growth and differentiation potential ex vivo

The ability to analyze single cells via flow cytometry has resulted in a wide range of biological and medical applications. Currently, there is no established framework to compare and interpret time-series flow cytometry data for cell engineering applications. Manual analysis of temporal trends is time-consuming and subjective for large-scale datasets. We resolved this bottleneck by developing TEmporal Gaussian Mixture models (TEGM), an unbiased computational strategy to quantify and predict temporal trends of developing cell subpopulations indicative of cellular phenotype. TEGM applies Gaussian mixture models and gradient boosted trees for cell engineering applications. TEGM enables the extraction of subtle features, such as the dispersion and rate of change of surface marker expression for each subpopulation over time. These critical, yet hard-to-discern, features are fed into machine-learning algorithms that predict underlying cell classes. Our framework can be flexibly applied to conventional flow cytometry sampling schemes, and allows for faster and more consistent processing of time-series flow cytometry data. Please click Additional Files below to see the full abstract

Using Gaussian mixture models and machine learning to predict donor- dependent megakaryocytic cell growth and differentiation potential ex vivo

The ability to analyze single cells via flow cytometry has resulted in a wide range of biological and medical applications. Currently, there is no established framework to compare and interpret time-series flow cytometry data for cell engineering applications. Manual analysis of temporal trends is time-consuming and subjective for large-scale datasets. We resolved this bottleneck by developing TEmporal Gaussian Mixture models (TEGM), an unbiased computational strategy to quantify and predict temporal trends of developing cell subpopulations indicative of cellular phenotype.. Please click Additional Files below to see the full abstract

Evaluation of E-cadherin (CDH1) gene polymorphism related to gastric cancer in Kurdish population

Abstract: Helicobacter pylori (H.pylori) infection induces inflammation in gastric mucosa that may progress to gastric cancer that causes of much mortality. This cancer is a multistage process involved changes in environmental, genetic and epigenetic factors. Polymorphism in promoter of CDH1 gene is associated with reduced E-cadherin protein expression. Gastric cancer is associated with multiple changes nucleotides in CDH1 gene. Aimed: We were evaluating -160 (C>A) CDH1 gene polymorphism associations with gastric cancer in Kurdish population. Methods: A total of 306 biopsies taken from corpus of 144 gastric cancer patients and 162 nonulcer dyspepsia patients were classified as H.pylori-infected and H.pylori-uninfected. All diagnoses confirmed pathologically and molecularly. Polymorphism in -160(C>A) CDH1 was evaluated by PCR-RFLP. Results: Polymorphism of -160 (C>A) CDH1 in H.pylori-uninfected and H.pylori-infected groups were not associated with gastric cancer (p > 0.05). Also there was not relationship between -160(C>A) CDH1 genotypes and H.pylori infection susceptibility (p > 0.05). We found significant relationship between CC genotype and survival time among gastric cancer patients (p = 0.01). Conclusion: -160(C>A) CDH1 polymorphism may regardless of presence or absence of H.pylori, don’t influences gastric cancer sensibility in Kurdish population. In other hand CC genotype, as a good trait, increases period of life for Kurdish cancer patients

Expression of IL-18 cytokine mRNA in gastric mucosa tissue of patients with H. pylori infection in Chahar Mahal and Bakhtiari

Background: H. pylori infection is associated with gastritis and marked infiltration of the gastric mucosa by inflammatory cells secreting of several cytokines that contribute to maintain and expand the local inflammation. Different clinical expressions of the infection may reflect different patterns of cytokine expression. Interleukin (IL)-1β, tumor necrosis factor (TNF)-α, IL-17, IL-23, and IL-18 have been reported to be involved in H. pylori-induced gastric mucosal inflammation, but the details and relation to different patterns of inflammation remain unclear. Materials and Methods: Analysis of IL-18 RNA transcripts was performed by real-time PCR. Total RNA was extracted from gastric biopsies of 56 H. pylori-infected patients, 50 H. pylori-negative patients with gastritis, by biozol reagent according to the manufacturer's instructions. CDNA was synthesized from 1 mg of total RNA using First Strand cDNA Synthesis Kit (fermentas) and 3 μL cDNA was amplified by PCR using the 2x Rotor-Gene Probe PCR Master Mix (QIAGEN) and specific primers for each cytokine and β-actin. Results: IL-18 mRNA expression was significantly increased in biopsies of H. pylori-infected patients compared to H. pylori-uninfected individuals. Conclusion: IL-18 may play an important role in the inflammatory response and promoting gastric Th1 responses to H. pylori colonization, and may ultimately influence the outcome of H. pylori-associated diseases that arise within the context of gastritis

The Moderating Role of Islamic Lifestyle in the Relationship between Cognitive Emotion Regulation and Mobile Dependency in Kermanshah’s Adolescent Girls in 2017

سابقه و هدف: استفاده از تلفن همراه در سال‌های اخیر به جزء جدایی‌ناپذیر زندگی تبدیل شده است. با وجود کاربردهای مفید تلفن همراه، استفاده‌ی بیش‌ازحد و مداوم از آن موجب وابستگی و آسیب به افراد می‌شود. پژوهش حاضر با هدف بررسی نقش سبک زندگی اسلامی در رابطه‌ی بین تنظیم شناختی-هیجانی و وابستگی به تلفن همراه در دختران نوجوان انجام شد. روش کار: این پژوهش مطالعه‌یی توصیفی-مقطعی و از نوع همبستگی بود. جامعه‌ی آماری پژوهش شامل کلیه‌ی دانش‌آموزان دختر سطح دومِ دور‌ه‌ی متوسطه‌ی شهر کرمانشاه بود که 400 نفر از آنان با روش نمونه‌گیری تصادفی خوشه‌ییِ چندمرحله‌یی انتخاب شدند. برای جمع‌آوری داده‌ها، آزمون‌شونده‌ها به مقیاس‌های نقش سبک زندگی اسلامی (LLST)، تنظیم شناختی/هیجانی (CERQ) و استفاده‌ی آسیب‌زا از تلفن همراه (COS) پاسخ دادند. برای تحلیل داده‌ها از مدل‌یابی معادلات ساختاری استفاده شد. در این پژوهش همه‌ی موارد اخلاقی رعایت شده است و نویسندگان مقاله هیچ‌گونه تضاد منافعی گزارش نکرده‌اند. یافته‌ها: یافته‌ها نشان داد که تنظیم شناختی/هیجانی و سبک زندگی اسلامی پیش‌بینی‌کننده‌های خوبی برای اعتیاد به تلفن همراه محسوب می‌شوند. همچنین، بر اساس یافته‌های مدل‌یابی معادلات ساختاری روابط علّی معنادار و مثبت بین تنظیم شناختی/هیجانی، سبک زندگی اسلامی و اعتیاد به تلفن همراه وجود داشت و نقش سبک زندگی اسلامی در رابطه‌ی بین تنظیم شناختی/هیجانی و اعتیاد به تلفن همراه تأیید شد. نتیجه‌گیری: نتایج نشان‌دهنده‌ی این است که به‌کارگیری سبک زندگی اسلامی، راهبرد مقابله‌یی با تنظیم شناختی/هیجانیِ منفی است که به پیشگیری از اعتیاد به تلفن همراه منجر خواهد شد. استناد مقاله به این صورت است: RostamiNasab-DolatAbad Z, Ehsanpour F, Mohammadkhani M, Shariatmadar-Tehrani A, Bagheri-Mahyari N. The Moderating Role of Islamic Lifestyle in the Relationship between Cognitive Emotion Regulation and Mobile Dependency in Kermanshah’s Aadolescent Girls in 2017. Journal of Pizhūhish dar dīn va salāmat. 2019;5(3):84-95. https://doi.org/10.22037/jrrh.v5i3.18951Background and Objective: The use of mobile phones has recently become an indispensable part of life. Although mobile phones have several advantages, their excessive use can make individuals prone to dependence. The aim of this study was to investigate the moderating role of Islamic lifestyle in the relationship between cognitive emotion regulation and mobile dependency in adolescent girls. Methods: The present study is a descriptive cross-sectional study of correlation type. The statistical population of the study consisted of all secondary school girl students in Kermanshah. Four hundred individuals were selected through multistage cluster random sampling. To collect data, subjects responded to Islamic lifestyle standards (LLST), cognitive/emotional regulation questionnaire (CERQ) and mobile phone harm survey (COS). In order to analyze the data, structural equation modeling was used. In this study, all the ethical considerations have been observed and no conflict of interest was reported by the authors. Results: The results showed that cognitive/emotional adjustment and Islamic lifestyle are considered good predictors of mobile dependency. Also, based on the findings of structural equation modeling, there are significant and positive causal relationships between cognitive/emotional adjustment, Islamic lifestyle and mobile dependency. Moreover, the mediating role of Islamic lifestyle in the relationship between cognitive/emotional adjustment and mobile dependency was confirmed. Conclusion: The findings suggest that the use of Islamic lifestyle as a coping strategy in people with negative cognitive/emotional adjustment will prevent cell phone addiction.   Please cite this article as: RostamiNasab-DolatAbad Z, Ehsanpour F, Mohammadkhani M, Shariatmadar-Tehrani A, Bagheri-Mahyari N. The Moderating Role of Islamic Lifestyle in the Relationship between Cognitive Emotion Regulation and Mobile Dependency in Kermanshah’s Aadolescent Girls in 2017. Journal of Pizhūhish dar dīn va salāmat. 2019;5(3):84-95. https://doi.org/10.22037/jrrh.v5i3.18951خلفية البحث وأهدافه: إن إستخدام الهاتف الجوال قد تحول في السنوات الأخيرة الى جزء غير منفصل عن الحياة اليومية. بالرغم من الاستخدامات المفيدة للهاتف الجوال فإن الاستخدام الزائد عن الحاجة والمستمر له يؤدي الى التعلق به والى أضرار تصيب الافراد. ان التحقيق الحاضر تم القيام به بهدف دراسة دور نمط الحياة الاسلامية فيما يتعلق بالعلاقة ما بين تنظيم المعرفة-الاثارة والتعلق بالهاتف الجوال عند الفتايات. منهجية البحث: التحقيق الحاضر هو دراسة توصیفية-مرحلية ومن النوع التضامني. المجتمع الاحصائي في هذا التحقيق يشمل كافة التلميذات من المستوى الثاني للمرحلة الثانوية التعليمية بمدينة كرمانشاه حيث تم أختيار 400 تلميذة من بين هؤلاء بأسلوب أخذ العينة العنقودية العشوائية على عدة مراحل. من اجل تجميع المعلومات فقد أجاب الافراد المختبرون على مقاييس نمط الحياةالاسلامية (LLST)، تنظيم المعرفة/الاثارة (CERQ) والاستخدام المضر للهاتف الجوال (COS). وتم تفسير المعلومات عبر الاستفادة من العثور على النموذج من خلال المعادلات البنيوية. تمت مراعاة جمیع الموارد الاخلاقية في هذا البحث؛ فإن مؤلفي البحث لم يشيروا إلى اي تضارب في المصالح. الكشوفات: أظهرت الكشوفات ان تنظيم المعرفة/الاثارة ونمط الحياة الاسلامية يعتبران عنصرين جيدين لتوقع الادمان على الهاتف الجوال. وكذلك استنادا الى الكشوفات في العثور على النموذج من خلال المعادلات البنيوية هناك علاقة إيجابية ذات دلالة إحصائية بين تنظيم المعرفة/الاثارة، نمط الحياة الاسلامية والادمان على الهاتف الجوال. وتم تأييد دور نمط الحياة الاسلامية في العلاقة ما بين تنظيم المعرفة/الاثارة والادمان على الهاتف الجوال. الاستنتاج: لقد دلت النتائج على ان استخدام نمط الحياة الاسلامية، استراتيجية المواجهة مع تنظيم المعرفة/الاثارة هو أمر سلبي سوف يؤدي الى الوقاية من االادمان على الهاتف الجوال.   يتم استناد المقالة على الترتيب التالي: RostamiNasab-DolatAbad Z, Ehsanpour F, Mohammadkhani M, Shariatmadar-Tehrani A, Bagheri-Mahyari N. The Moderating Role of Islamic Lifestyle in the Relationship between Cognitive Emotion Regulation and Mobile Dependency in Kermanshah’s Aadolescent Girls in 2017. Journal of Pizhūhish dar dīn va salāmat. 2019;5(3):84-95. https://doi.org/10.22037/jrrh.v5i3.1895