IMMAN : an R/Bioconductor package for Interolog protein network reconstruction, mapping and mining analysis

Background: Reconstruction of protein-protein interaction networks (PPIN) has been riddled with controversy for decades. Particularly, false-negative and - positive interactions make this progress even more complicated. Also, lack of a standard PPIN limits us in the comparison studies and results in the incompatible outcomes. Using an evolution-based concept, i.e. interolog which refers to interacting orthologous protein sets, pave the way toward an optimal benchmark. Results: Here, we provide an R package, IMMAN, as a tool for reconstructing Interolog Protein Network (IPN) by integrating several Protein-protein Interaction Networks (PPINs). Users can unify different PPINs to mine conserved common networks among species. IMMAN is designed to retrieve IPNs with different degrees of conservation to engage prediction analysis of protein functions according to their networks. Conclusions: IPN consists of evolutionarily conserved nodes and their related edges regarding low false positive rates, which can be considered as a gold standard network in the contexts of biological network analysis regarding to those PPINs which is derived from.Peer reviewe

Multi-Criteria Evaluation of the Vulnerability of the Urban Water Supply Network Against Biological Attacks

The water supply network is one of the most critical infrastructures of human societies, which could cause illness or death in many consumers due to its expanding nature. Water pollution is one of the ways of spreading biological pollutants among the population, which is known as bioterrorism today. Biological contamination usually occurs with the use of pathogens and biotoxins. Therefore, recognizing the vulnerable stages of the water supply network against various pollutants is of particular importance. In this research, in the first stage, a selection of five pathogens (Bacillus anthracis, Cryptosporidiosis, Francisella tularensis, Vibrio cholerae, Shigella) that are more likely to pollute water sources have been made. Thus, employing each component of the water supply system (including raw water source (dam)), Raw water storage tank, water treatment plant, treated water transmission line, treated water tanks, and distribution network (30 scenarios) were defined. In the next step, using multi-criteria group decision-making and employing three main criteria (vulnerability of each water supply stage, the amount of contaminant damage power, the amount of contaminant risk in each of the water supply stages) and their sub-criteria, the weight of each criterion was determined from the perspective of decision-makers by utilizing GFDM software. After analyzing the scenarios, the risk level of each scenario was ranked. Scenario 26 created the most risk, which consists of introducing the pathogen Bacillus anthracis into the distribution network. The entry of contamination into the distribution network due to high availability and lack of subsequent treatment steps, as well as the slight chance of preventing the contaminant from reaching consumers, can cause many diseases and deaths. Furthermore, it has a high resistance against chloride and is stable in water, so the entry of this contaminant into the distribution network can be dangerous. Considering the existing conditions, recognizing and calculating the risk of different scenarios can lead to readiness and increase the speed of action in response to possible biological attacks

Occupational Health Problems and Safety Conditions among Small and Medium-Sized Enterprises: A Cross-sectional Study in Shiraz, Iran

Background: Small and medium-sized enterprises (SMEs) include a large part of manufacturing jobs and play an important role in developing national economics and employment. Objectives: The present study aimed to investigate occupational health problems and safety conditions among SMEs in Shiraz, Iran. Methods: This cross-sectional study was carried out on 711 SMEs, including 371 small enterprises (fewer than 25 workers) and 340 medium enterprises (25–99 workers), in Shiraz, Iran. The participants were selected randomly among the workplaces under the coverage of social security insurance. The researcher-made questionnaire, which consisted of demographic characteristics, the frequency rate of occupational accidents, and exposure to workplace harmful agents, were distributed among participants. Findings: The results showed there were significantly more physical and chemical harmful agents in medium enterprises compared to small ones (P < 0.001). However, the frequency rate of accidents in small enterprises was significantly higher than in medium enterprises (P < 0.001). Also, there was no significant difference between the studied enterprises in ergonomic hazards, except for awkward posture, whose frequency rate was significantly higher in small enterprises (P < 0.05). Finally, among the reported symptoms, the prevalence of eye, skin, ear, and respiratory symptoms was significantly higher in medium enterprises compared to small enterprises (P < 0.05). Conclusions: Occupational health and safety (OHS) regulations in medium enterprises have led to improved OHS conditions compared to small enterprises. Therefore, small enterprises should be included in OHS regulations

Simultaneous inhibition of Sirtuin 3 and cholesterol homeostasis targets acute myeloid leukemia stem cells by perturbing fatty acid β-oxidation and inducing lipotoxicity

Outcomes for patients with acute myeloid leukemia (AML) remain poor due to the inability of current therapeutic regimens to fully eradicate disease-initiating leukemia stem cells (LSC). Previous studies have demonstrated that oxidative phosphorylation (OXPHOS) is an essential process that is targetable in LSC. Sirtuin 3 (SIRT3), a mitochondrial deacetylase with a multi-faceted role in metabolic regulation, has been shown to regulate OXPHOS in cancer models; however, it has not yet been studied in the context of LSC. Thus, we sought to identify if SIRT3 is important for LSC function. Using RNAi and a SIRT3 inhibitor (YC8-02), we demonstrate that SIRT3 is a critical target for the survival of primary human LSC but is not essential for normal human hematopoietic stem and progenitor cell function. In order to elucidate the molecular mechanisms by which SIRT3 is essential in LSC we combined transcriptomic, proteomic, and lipidomic approaches, showing that SIRT3 is important for LSC function through the regulation of fatty acid oxidation (FAO) which is required to support OXPHOS and ATP production in human LSC. Further, we discovered two approaches to further sensitize LSC to SIRT3 inhibition. First, we found that LSC tolerate the toxic effects of fatty acid accumulation induced by SIRT3 inhibition by upregulating cholesterol esterification. Disruption of cholesterol homeostasis sensitizes LSC to YC8-02 and potentiates LSC death. Second, SIRT3 inhibition sensitizes LSC to the BCL-2 inhibitor venetoclax. Together, these findings establish SIRT3 as a regulator of lipid metabolism and potential therapeutic target in primitive AML cells

OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood Conservation

Orthology relations can be used to transfer annotations from one gene (or protein) to another. Hence, detecting orthology relations has become an important task in the post-genomic era. Various genomic events, such as duplication and horizontal gene transfer, can cause erroneous assignment of orthology relations. In closely-related species, gene neighborhood information can be used to resolve many ambiguities in orthology inference. Here we present OrthoGNC, a software for accurately predicting pairwise orthology relations based on gene neighborhood conservation. Analyses on simulated and real data reveal the high accuracy of OrthoGNC. In addition to orthology detection, OrthoGNC can be employed to investigate the conservation of genomic context among potential orthologs detected by other methods. OrthoGNC is freely available online at http://bs.ipm.ir/softwares/orthognc and http://tinyurl.com/orthoGNC

New Heuristics for Rooted Triplet Consistency

Rooted triplets are becoming one of the most important types of input for reconstructing rooted phylogenies. A rooted triplet is a phylogenetic tree on three leaves and shows the evolutionary relationship of the corresponding three species. In this paper, we investigate the problem of inferring the maximum consensus evolutionary tree from a set of rooted triplets. This problem is known to be APX-hard. We present two new heuristic algorithms. For a given set of m triplets on n species, the FastTree algorithm runs in O(m + α(n)n2) time, where α(n) is the functional inverse of Ackermann’s function. This is faster than any other previously known algorithms, although the outcome is less satisfactory. The Best Pair Merge with Total Reconstruction (BPMTR) algorithm runs in O(mn3) time and, on average, performs better than any other previously known algorithms for this problem

OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood Conservation

10.1016/j.gpb.2017.07.002GENOMICS PROTEOMICS & BIOINFORMATICS156361-37

The Prevalence of Unsafe Behaviors in Iranian Workers: A Sys-tematic Review and Meta-Analysis

Background: Unsafe behaviors are the cause of 80% of accidents. However, there has also been no worldwide review and meta-analysis of the prevalence of workers’ unsafe behaviors. Therefore, the present study aimed to investigate and estimate the prevalence of unsafe behaviors among Iranian workers using a systematic review and meta-analysis study. Methods: This systematic review and meta-analysis were conducted from Nov to Dec 2018. The researchers searched Medline/PubMed, Scopus, Embase, Science Direct, and Google Scholar for international articles and four Iranian databases (Scientific Information Database, MagIran, IranMedex, and IranDoc) for Persian articles. The method of reporting this study was based on the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analysis) checklist. Results: Overall, 235 articles from databases were imported to EndNote library. Final screening of the included studies produced a total of 38 studies. Based on the random-effect model, the prevalence of total unsafe behaviors, non-use or inappropriate use of personal protective equipment, and inappropriate work posture was 40.37% (CI 95% = 35.8-44.9), 27.79% (CI 95% = 21.2-34.3), and 14.87% (CI 95% = 10.7-18.9). There was no statistically significant relationship between unsafe behaviors and mean age, mean of work experiences, and year of study. Conclusion: The prevalence of unsafe behaviors among Iranian workers was relatively high and the most common behaviors were non-use or inappropriate use of PPE; one of the most important causes for this behavior is lack of training, inappropriate working conditions, and lack of positive attitude towards safety. Therefore, further studied are required to investigate the causes of these unsafe behaviors

Prevalence of self-reported work-related illness and injuries among building construction workers, Shiraz, Iran

The construction industry is one of the largest and most hazardous industries in the world, which has a direct role in the development of countries. The purpose of this study was to investigate the prevalence of self-reported workrelated illness and injuries among construction workers in Shiraz, Iran. 850 randomly selected workers from 2450 construction sites completed a self-statement questionnaire regarding the prevalence of self-reported work-related illness and injuries (WRIIs), in Shiraz, Iran. The association of WRII with demographic variables were studied. The overall prevalence rate of occupational injuries was 31 %. Musculoskeletal disorders (53.3 %), eye diseases (34.1 %) and skin diseases (30.1 %) have been the most prevalent work-related illnesses among construction workers, respectively. The prevalence of WRIIs among construction workers was significantly associated with age, education, marriage, work experience, safety training programs and number of workers in the workplace as well as employment status. Considering the high prevalence of WRIIs among construction workers, more stringent occupational safety and health interventions are recommended in construction workplaces