Proteomics of hot-wet and cold-dry temperaments proposed in Iranian traditional medicine: a Network-based Study

Evaluation of relationship between memory and temperament in 18-28 years old students

Background

Mizaj (Temperament) is a concept to express individual differences in Persian medicine and according to this theory, there is a relationship between Mizaj type and the abilities of different body organs. This cross-sectional study aimed to investigate the relationship between the type of Mizaj and the memory score (Quotient).

Methods

The target population was the 18 to 38 years old students of Babol University of Medical Sciences. Mojahedi's Mizaj questionnaire (MMQ) was used for determining the whole Mizaj. The physical Persian version of Wechsler Memory Scale III (WMS III) was used to assess memory score. The collected data were analyzed by SPSS Version 22 and the chi square (x2) and t-test were run and p- value 0.05 was considered as significant difference.

Results

Forty-two of participants were females and 18 were males. The average age of them was 23.6 (21-27). The average of Memory Quotient (MQ) was 122.1 ± 5.7. The average of MQ in warm Mizaj was 125.46 ± 1.2 and in cold Mizaj was 118.79 ± 6.5. The difference between two groups is statistically significant (p< 0.001). The average of MQ in dry Mizaj was 124.16 ± 2.67 and in wet Mizaj was 118.40 ± 7.64. The difference between two groups is statistically significant (P= 0.005).

Conclusion

The results showed there are significant relationship between memory score and warm/cold Mizaj and dry /wet Mizaj. It means students with warm or dry Mizaj had better memory score than students with cold or wet Mizaj. This relation was also detected between subtypes of memory and Mizaj expect between working memory and dry/wet Mizaj. These results are in accordance with theories in PM which indicate people with warm Mizaj and dry Mizaj have better memory and people with cold Mizaj and wet Mizaj have weaker memory and are more at risk of memory dysfunction.

Effects of Dietary Modification Based on Complementary and Alternative Iranian Medicine in Patients with Secondary-Progressive Multiple Sclerosis: A Randomized Controlled Clinical Trial

Objectives: To evaluate the efficacy of dietary modifications based on complementary and alternative Iranian medicine (CAIM) in patients with secondary-progressive multiple sclerosis (SPMS). Design: In this randomized controlled trial, 70 SPMS patients were randomized to receive either a moderate-nature diet based on Persian medicine (as intervention) or usual diet plus health-related diet recommendations (as control) for 2 months. Serum high-sensitivity C-reactive protein (hs-CRP), erythrocyte sedimentation rate (ESR), Expanded Disability Status Scale (EDSS), Modified Fatigue Impact Scale (MFIS), State-Trait Anxiety Inventory (STAI), Global Pain Scale (GPS), Gastrointestinal Symptom Rating Scale (GSRS), anthropometric measurements, and quality of life (QOL) were assessed at baseline and end of trial. Analysis of covariance was performed, and the results were adjusted for potential confounders using SPSS v.14. Results: All participants completed the study for 2 months. There were significant improvements across the mean changes of hs-CRP (-0.1 ± 0.2 mg/L for intervention vs. -0.01 ± 0.13 mg/L for control; padjusted = 0.012), MFIS (-11.0 ± 11.8 vs. -0.7 ± 9.9; padjusted <0.001), GSRS (-19.9 ± 16.3 to 1.2 ± 17.5; padjusted <0.001), GPS (padjusted = 0.032), and QOL (padjusted <0.05). No significant difference was observed across the ESR, EDSS, STAI, and anthropometric measurements. Conclusion: Dietary modifications based on CAIM may improve inflammation and clinical manifestations in SPMS patients. Nonetheless, further trials are required to confirm these findings. Clinical Trial Registration: IRCT20181113041641N2.

The Network between Heart and Liver from the View of Persian Medicine Versus Conventional Medicine

BACKGROUND

Liver and heart are two important organs in the human body, whose function strongly affects other organs. On the other hand, these two main organs affect each other due to common metabolic pathways. Therefore, a disorder in any of them can lead to disease in other organs. Today, using the network medicine perspective, these complex connections can be easily mapped and discovered. From the Persian medicine viewpoint, links are formed based on the material causes of diseases, while from the conventional medicine viewpoint, they are mostly formed due to metabolites, genes, and pathways.

MATERIALS AND METHODS

In this article, we first investigated the recent articles of conventional medicine that examine the relationship between heart and liver in the important databases. Then, we checked out the sources of Persian medicine and finally, using the RStudio software used in network medicine for text mining, we drew the communication network centered on heart and liver and their mutual causes from the perspective of Persian Medicine.

RESULTS

Examining the network connection between the heart and the liver showed that the definitions based on Persian medicine, which are based on the material causes of diseases, are very compatible with the genes, metabolites and pathways between these two organs.

CONCLUSION

Understanding these concepts can be helpful in detecting the co-occurrence of diseases of these two organs, as well as predicting the possible occurrence of related diseases between the heart and liver, and ultimately in better treatment.

Introduction: Hot and Cold Theory, the Path Towards Personalized Medicine

In traditional medicines, the concept of "hot and cold theory" or temperament evolved based on thousands of years of precise observation of individuals' differences to provide efficacious personalized treatments. Based on the hot and cold theory, human body organs have extensive interactions forming a complex system in a dynamic equilibrium named temperament, Dosha, constitution, or Mizaj. This equilibrium is different between individuals and is affected by genetics, environment, and lifestyle. Deviation from this balance state on the coldness-hotness spectrum can predispose one to various diseases. The goal of prevention and treatment is to maintain or revive the body system's status towards that person's original equilibrium.

"Human as an Embodied Spirit": A Proposed Conceptual Model for Nursing Based on Iranian Mysticism and Wisdom

Most nursing models are developed based on Western philosophy. The conceptual model of "human as an embodied spirit" based on Iranian mysticism and wisdom is presented in this article. This conceptual model was developed in 2 phases: first, using a derivation process, the concepts of the model were developed. Next, in a synthesis process, the conceptual model was constructed. Definitions and descriptions of each of the concepts of the model-the constitution of the physical body, the composition of graded soul, knowledge-based interventions, love-based interventions, balance, and harmony-and the relations between these concepts are presented in the article. This model gives equal value to the art and the science of nursing and integrates all dimensions of human being and related health problems in such a way that they can be explained and approached as a continuum. The next step is the testing of this model followed by the development of guidelines for education and practice.

The TCM prescription Ma-xing-shi-gan-tang inhibits Streptococcus pneumoniae pathogenesis by targeting pneumolysin

ETHNOPHARMACOLOGICAL RELEVANCE

Ma-xing-shi-gan-tang (MXSGT), which is documented in the Treatise on Febrile Diseases and is a therapeutic drug, is a well-known classic prescription in China and has been widely studied. Previous studies have shown that MXSGT has various pharmacological activities, including anti-influenza virus activity, and ameliorates microvascular hyperpermeability and inflammatory reactions. However, no study has reported the effect of MXSGT in the treatment of bacterial pneumonia.

AIM OF THE STUDY

In this study, the potential inhibition of MXSGT against the virulence of S. pneumoniae by targeting PLY was investigated.

MATERIALS AND METHODS

First, HPLC analysis was used to determine the main components of MXSGT. Then PLY protein was constructed and used for hemolysis assay and western blot to test the ability of MXSGT to inhibit PLY activity, production and widowed characteristics. The growth curve of S. pneumoniae was drawled with or without MXSGT treatment. In addition, the inhibition of MXSGT against PLY-mediated A549 cell death was examined by cytotoxicity assay. Finally, the mouse experiment was used to verify the effect of MXSGT on mouse lungs.

RESULTS

This work has discovered that MXSGT, a TCM prescription, is an effective inhibitor of PLY, an important virulence factor that is essential for S. pneumoniae pathogenicity. MXSGT inhibits the oligomerization of PLY without affecting S. pneumoniae growth and PLY production. In addition, experimental MXSGT treatment was effective against S. pneumoniae infection both in vitro and in vivo.

CONCLUSION

These findings directly demonstrate the potential mechanism of the Chinese herbal formula MXSGT in the treatment of pneumococcal disease and provide additional evidence for promotion of the wide use of MXSGT in the clinic.

IrGO: Iranian traditional medicine General Ontology and knowledge base

Background

Iranian traditional medicine, also known as Persian Medicine, is a holistic school of medicine with a long prolific history. It describes numerous concepts and the relationships between them. However, no unified language system has been proposed for the concepts of this medicine up to the present time. Considering the extensive terminology in the numerous textbooks written by the scholars over centuries, comprehending the totality of concepts is obviously a very challenging task. To resolve this issue, overcome the obstacles, and code the concepts in a reusable manner, constructing an ontology of the concepts of Iranian traditional medicine seems a necessity.

Construction and content

Makhzan al-Advieh, an encyclopedia of materia medica compiled by Mohammad Hossein Aghili Khorasani, was selected as the resource to create an ontology of the concepts used to describe medicinal substances. The steps followed to accomplish this task included (1) compiling the list of classes via examination of textbooks, and text mining the resource followed by manual review to ensure comprehensiveness of extracted terms; (2) arranging the classes in a taxonomy; (3) determining object and data properties; (4) specifying annotation properties including ID, labels (English and Persian), alternative terms, and definitions (English and Persian); (5) ontology evaluation. The ontology was created using Protégé with adherence to the principles of ontology development provided by the Open Biological and Biomedical Ontology (OBO) foundry.

Utility and discussion

The ontology was finalized with inclusion of 3521 classes, 15 properties, and 20,903 axioms in the Iranian traditional medicine General Ontology (IrGO) database, freely available at http://ir-go.net/. An indented list and an interactive graph view using WebVOWL were used to visualize the ontology. All classes were linked to their instances in UNaProd database to create a knowledge base of ITM materia medica.

Conclusion

We constructed an ontology-based knowledge base of ITM concepts in the domain of materia medica to help offer a shared and common understanding of this concept, enable reuse of the knowledge, and make the assumptions explicit. This ontology will aid Persian medicine practitioners in clinical decision-making to select drugs. Extending IrGO will bridge the gap between traditional and conventional schools of medicine, helping guide future research in the process of drug discovery.

Association of temperament with genetic polymorphisms in SOD1, GSTM1 and GSTT1 genes

Due to its accessibility, efficacy, and affordability, traditional medicine (TM) is the main source of health services for many people in the world. Nevertheless, in spite of its benefits, there are still many issues about the principles of TM which demand further declaration. One of the essential principles of Iranian traditional medicine (ITM) is temperament (mizaj), which efficiently applied in diagnosis and therapy of illnesses. In this study we aimed to explore the association of GSTM1/T1, and SOD1 50 bp Ins/Del polymorphisms with combined groups of temperament. The study was conducted in 217 healthy males from Fars province, southern Iran. The self-reported mizaj questionnaire was applied to identify the participants’ temperament. Then individuals with temperate, warm/moist, and warm/dry temperament were entered in the study. To determine the genotype of GSTM1, GSTT1, and SOD1, the polymerase chain reaction (PCR)-based method was performed. As the results of χ² analysis showed, the frequency of GSTT1, GSTM1, and SOD1 polymorphisms in temperate group was not significantly differ from that in each of warm/moist and warm/dry groups. Further research with larger samples are suggested to clarify the association between temperament and biomolecular features.

The Value of 'Traditionality': The Epistemological and Ethical Significance of Non-western Alternatives in Science

After a brief review of the relationship between science and value, this paper introduces the value of 'traditionality' as a value in the pure and applied sciences. Along with other recognized values, this value can also contribute to formulating hypotheses and determining theories. There are three reasons for legitimizing the internal role of this value in science: first, this value can contribute to scientific progress by presenting more diverse hypotheses; second, the value of external consistency in science entails this value; and third, this value helps to eliminate some of the adverse social and cultural effects of Western science in non-Western societies. 'Traditionality' is an extrinsic epistemic value, according to the first two reasons, and at the same time, is an ethical value, according to the last reason. Also, the ethics of belief is adopted to further confirm the ethical role of this value. Finally, this paper discusses three potential criticisms that can be levelled against this idea and responds to each of them.

Assessment the studies on the concept of Mizaj (temperament) in Persian Medicine

Introduction Mizaj or temperament is a main concept in Persian Medicine (PM), which the process of diagnosis, treatment and preventive prescriptions are developed based on it. In this study, the articles written on the concept of Mizaj were reviewed. Method Credited electronic resources, including Pubmed, Scopus, Cochrane Library and web-of-science were searched using keywords Temperament, Mizaj, Mizadj, Midzaj and Mezaj (with the concept of Mizaj in Persian and/or Greek medicine). Search results were limited to English articles, published in 1995-2017. The articles in which temperament had the psychoanalytic aspect or was based on Ayurveda or Chinese/Korean medicine were removed. A team of four PM experts evaluated the method and the results. Results Among the total of 32 articles were published in this field, 14 were review articles, 2 were on animal subject, 14 were on human subject and 2 were surveys for designing questionnaire for people's Mizaj assessment. Most of review studies were just new versions of ancient Persian texts translated into English and the innovations on the subject were few. Studies on animal subject and developing questionnaires were also limited. In some human studies, use of standard questionnaires and homogenous methodology in Mizaj assessment was not considered. Conclusions It seems that studies on temperaments have increased in the past few years but are still at the forefront. In human studies a homogenous method for evaluating temperament has not been used and some of them failed to address the main concept of Mizaj in PM. Therefore, it is necessary to use the original category of Mizaj and to design standard method.

Unsupervised Learning and Multipartite Network Models: A Promising Approach for Understanding Traditional Medicine

The ultimate goal of precision medicine is to determine right treatment for right patients based on precise diagnosis. To achieve this goal, correct stratification of patients using molecular features and clinical phenotypes is crucial. During the long history of medical science, our understanding on disease classification has been improved greatly by chemistry and molecular biology. Nowadays, we gain access to large scale patient-derived data by high-throughput technologies, generating a greater need for data science including unsupervised learning and network modeling. Unsupervised learning methods such as clustering could be a better solution to stratify patients when there is a lack of predefined classifiers. In network modularity analysis, clustering methods can be also applied to elucidate the complex structure of biological and disease networks at the systems level. In this review, we went over the main points of clustering analysis and network modeling, particularly in the context of Traditional Chinese medicine (TCM). We showed that this approach can provide novel insights on the rationale of classification for TCM herbs. In a case study, using a modularity analysis of multipartite networks, we illustrated that the TCM classifications are associated with the chemical properties of the herb ingredients. We concluded that multipartite network modeling may become a suitable data integration tool for understanding the mechanisms of actions of traditional medicine.

UNaProd: A Universal Natural Product Database for Materia Medica of Iranian Traditional Medicine

BACKGROUND

Iranian traditional medicine (ITM) is a holistic medical system that uses a wide range of medicinal substances to treat disease. Reorganization and standardization of the data on ITM concepts is a necessity for optimal use of this rich source. In an initial step towards this goal, we created a database of ITM materia medica. Main Body. Primarily based on Makhzan al-Advieh, which is the most recent encyclopedia of materia medica in ITM with the largest number of monographs, a database of natural medicinal substances was created using both text mining methods and manual editing. UNaProd, a Universal Natural Product database for materia medica of ITM, is currently host to 2696 monographs, from herbal to animal to mineral compounds in 16 diverse attributes such as origin and scientific name. Currently, systems biology, and more precisely systems medicine and pharmacology, can be an aid in providing rationalizations for many traditional medicines and elucidating a great deal of knowledge they can offer to guide future research in medicine.

CONCLUSIONS

A database of materia medica is a stepping stone in creating a systems pharmacology platform of ITM that encompasses the relationships between the drugs, their targets, and diseases. UNaProd is hyperlinked to IrGO and CMAUP databases for Mizaj and molecular features, respectively, and it is freely available at http://jafarilab.com/unaprod/.

Integrated use of bioinformatic resources reveals that co-targeting of histone deacetylases, IKBK and SRC inhibits epithelial-mesenchymal transition in cancer

With the advent of high-throughput technologies leading to big data generation, increasing number of gene signatures are being published to predict various features of diseases such as prognosis and patient survival. However, to use these signatures for identifying therapeutic targets, use of additional bioinformatic tools is indispensible part of research. Here, we have generated a pipeline comprised of nearly 15 bioinformatic tools and enrichment statistical methods to propose and validate a drug combination strategy from already approved drugs and present our approach using published pan-cancer epithelial-mesenchymal transition (EMT) signatures as a case study. We observed that histone deacetylases were critical targets to tune expression of multiple epithelial versus mesenchymal genes. Moreover, SRC and IKBK were the principal intracellular kinases regulating multiple signaling pathways. To confirm the anti-EMT efficacy of the proposed target combination in silico, we validated expression of targets in mesenchymal versus epithelial subtypes of ovarian cancer. Additionally, we inhibited the pinpointed proteins in vitro using an invasive lung cancer cell line. We found that whereas low-dose mono-therapy failed to limit cell dispersion from collagen spheroids in a microfluidic device as a metric of EMT, the combination fully inhibited dissociation and invasion of cancer cells toward cocultured endothelial cells. Given the approval status and safety profiles of the suggested drugs, the proposed combination set can be considered in clinical trials.

An insight to HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) pathogenesis; evidence from high-throughput data integration and meta-analysis

BACKGROUND

Human T-lymphotropic virus 1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) is a progressive disease of the central nervous system that significantly affected spinal cord, nevertheless, the pathogenesis pathway and reliable biomarkers have not been well determined. This study aimed to employ high throughput meta-analysis to find major genes that are possibly involved in the pathogenesis of HAM/TSP.

RESULTS

High-throughput statistical analyses identified 832, 49, and 22 differentially expressed genes for normal vs. ACs, normal vs. HAM/TSP, and ACs vs. HAM/TSP groups, respectively. The protein-protein interactions between DEGs were identified in STRING and further network analyses highlighted 24 and 6 hub genes for normal vs. HAM/TSP and ACs vs. HAM/TSP groups, respectively. Moreover, four biologically meaningful modules including 251 genes were identified for normal vs. ACs. Biological network analyses indicated the involvement of hub genes in many vital pathways like JAK-STAT signaling pathway, interferon, Interleukins, and immune pathways in the normal vs. HAM/TSP group and Metabolism of RNA, Viral mRNA Translation, Human T cell leukemia virus 1 infection, and Cell cycle in the normal vs. ACs group. Moreover, three major genes including STAT1, TAP1, and PSMB8 were identified by network analysis. Real-time PCR revealed the meaningful down-regulation of STAT1 in HAM/TSP samples than AC and normal samples (P = 0.01 and P = 0.02, respectively), up-regulation of PSMB8 in HAM/TSP samples than AC and normal samples (P = 0.04 and P = 0.01, respectively), and down-regulation of TAP1 in HAM/TSP samples than those in AC and normal samples (P = 0.008 and P = 0.02, respectively). No significant difference was found among three groups in terms of the percentage of T helper and cytotoxic T lymphocytes (P = 0.55 and P = 0.12).

CONCLUSIONS

High-throughput data integration disclosed novel hub genes involved in important pathways in virus infection and immune systems. The comprehensive studies are needed to improve our knowledge about the pathogenesis pathways and also biomarkers of complex diseases.

Traditional, complementary and alternative medicine in children constipation: a systematic review

OBJECTIVES

This review aims to evaluate the efficacy and safety of complementary and alternative medicine methods for constipation in the pediatric population.

EVIDENCE ACQUISITION

Medical literature search was performed in several databases for a variety of Traditional, Complementary and Alternative Medicine in childhood constipation. Databases included Web of Science, Scopus, Embase, Cochrane Library, PubMed, ScienceDirect, Google scholar and a number of Persian databases including IranDoc, Magiran and SID. No time limitation was determined. Clinical trials or case series that had evaluated the effectiveness of CAM therapies in functional constipation of 1-18 year old children were included. Papers not in English or Persian language were excluded. Related articles were screened independently by two reviewers according to their titles and abstracts. A data extraction form was filled in for each eligible paper. Quality assessment of eligible documents was also performed.

RESULTS

30 studies were included, comprising 27 clinical trials and 3 case series. Ten documents were on herbal medicine, nine on traditional medicine, ten on manual therapies and one on homeopathy. Except for two herbal and one reflexology interventions, all studies reported positive effects on childhood constipation, with the majority being statistically significant. As the number of studies in each method was limited, we could not perform a meta-analysis.

CONCLUSION

The scarcity of research on the efficacy and safety of different types of complementary and alternative medicine methods in children with constipation necessitates conducting more studies in each field. Graphical abstract.

Predicting Meridian in Chinese traditional medicine using machine learning approaches

Plant-derived nature products, known as herb formulas, have been commonly used in Traditional Chinese Medicine (TCM) for disease prevention and treatment. The herbs have been traditionally classified into different categories according to the TCM Organ systems known as Meridians. Despite the increasing knowledge on the active components of the herbs, the rationale of Meridian classification remains poorly understood. In this study, we took a machine learning approach to explore the classification of Meridian. We determined the molecule features for 646 herbs and their active components including structure-based fingerprints and ADME properties (absorption, distribution, metabolism and excretion), and found that the Meridian can be predicted by machine learning approaches with a top accuracy of 0.83. We also identified the top compound features that were important for the Meridian prediction. To the best of our knowledge, this is the first time that molecular properties of the herb compounds are associated with the TCM Meridians. Taken together, the machine learning approach may provide novel insights for the understanding of molecular evidence of Meridians in TCM.

Advances in biomarker detection: Alternative approaches for blood-based biomarker detection

In the clinical setting, a blood sample is typically the starting point for biomarker search and discovery. Mass spectrometry (MS) is a highly sensitive and informative method for characterizing a very wide range of metabolites and proteins and is therefore a potentially powerful tool for biomarker discovery. However, the physicochemical characteristics of blood coupled with very large ranges of protein and metabolite concentrations present a significant technical obstacle for resolving and quantifying putative biomarkers by MS. Blood fractionation procedures are being developed to reduce the proteome/metabolome complexity and concentration ranges, allowing a greater diversity of analytes, including those at very low concentrations, to be quantified. In this chapter, several strategies for enriching and/or isolating specific blood components are summarized, including methods for the analysis of low and high molecular weight compounds, usually neglected in this type of assays, extracellular vesicles, and peripheral blood mononuclear cells (PBMCs). For each method, relevant practical information is presented for effective implementation.

The necessity for integrating traditional, complementary, and alternative medicine into medical education curricula in Iran

BACKGROUND

The use of traditional and complementary medicine (T&CM) is increasing in both developed and developing countries. The school of Persian medicine (PM) in Iran is a comprehensive medical school that is rich in history and has its own special principles, elements, philosophy, and diagnostic and treatment options. Many complementary therapy modalities are also popular and in demand among patients and physicians. The aim of this paper is to provide logic for the policymakers in Iranian medical education to make changes in medical education curricula, particularly on integrating T&CM.

METHODS

We reviewed the global experience in teaching T&CM to medical students, and highlighting the strengths of PM, described why it is necessary to integrate T&CM into general medicine curricula in Iran.

RESULTS

PM is a traditional system of medicine that dates back about 7000 years. Although there are few studies about the safety and effectiveness of PM, research into it has recently been accelerated. There is a suitable opportunity for integrating T&CM with conventional medicine. Physicians should be familiar with T&CM to avoid any contraindications, interactions, and unwanted effects.

CONCLUSION

Traditional medicine is part of Iran's heritage and, thus, needs special attention. Familiarization of physicians with T&CM can help them choose the best treatment options for their patients. To integrate T&CM into the medical education curricula of Iran, a two-credit course has been proposed for implementation across the country.

A systematic survey of centrality measures for protein-protein interaction networks

Background

Numerous centrality measures have been introduced to identify “central” nodes in large networks. The availability of a wide range of measures for ranking influential nodes leaves the user to decide which measure may best suit the analysis of a given network. The choice of a suitable measure is furthermore complicated by the impact of the network topology on ranking influential nodes by centrality measures. To approach this problem systematically, we examined the centrality profile of nodes of yeast protein-protein interaction networks (PPINs) in order to detect which centrality measure is succeeding in predicting influential proteins. We studied how different topological network features are reflected in a large set of commonly used centrality measures.

Results

We used yeast PPINs to compare 27 common of centrality measures. The measures characterize and assort influential nodes of the networks. We applied principal component analysis (PCA) and hierarchical clustering and found that the most informative measures depend on the network’s topology. Interestingly, some measures had a high level of contribution in comparison to others in all PPINs, namely Latora closeness, Decay, Lin, Freeman closeness, Diffusion, Residual closeness and Average distance centralities.

Conclusions

The choice of a suitable set of centrality measures is crucial for inferring important functional properties of a network. We concluded that undertaking data reduction using unsupervised machine learning methods helps to choose appropriate variables (centrality measures). Hence, we proposed identifying the contribution proportions of the centrality measures with PCA as a prerequisite step of network analysis before inferring functional consequences, e.g., essentiality of a node.

Electronic supplementary material

The online version of this article (10.1186/s12918-018-0598-2) contains supplementary material, which is available to authorized users.

Valproic acid inhibits the protective effects of stromal cells against chemotherapy in breast cancer: Insights from proteomics and systems biology

Interaction between tumor and stromal cells is beginning to be decoded as a contributor to chemotherapy resistance. Here, we aim to take a system-level approach to explore a mechanism by which stromal cells induce chemoresistance in cancer cells and subsequently identify a drug that can inhibit such interaction. Using a proteomic dataset containing quantitative data on secretome of stromal cells, we performed multivariate analyses and found that bone-marrow mesenchymal stem cells (BM-MSCs) play the most protective role against chemotherapeutics. Pathway enrichment tests showed that secreted cytokines from BM-MSCs activated 4 signaling pathways including Janus kinase-signal transducer and activator of transcription, phosphatidylinositol 3-kinase-protein kinase B, and mitogen-activated protein kinase, transforming growth factor-β in cancer cells collectively leading to nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kB) transcription factor activation. Based on the data from integrated Library of Integrated Network-Based Cellular Signatures (iLINCs) program, we found that among different drugs, valproic acid (VA) affected the expression of 34 genes within the identified pathways that are activated by stromal cells. Our in vitro experiments confirmed that VA inhibits NF-kB activation in cancer cells. In addition, analyzing gene expression data in patients taking oral VA showed that this drug decreased expression of antioxidant enzymes culminating in increased oxidative stress in tumor cells. These results suggest that VA confines the protective role of stromal cells by inhibiting the adaptation mechanisms toward oxidative stress which is potentiated by stromal cells. Since VA is an already prescribed drug manifesting anticancer effects, this study provides a mechanistic insight for combination of VA with chemotherapy in the clinical setting.

Reliability and validity assessment of gastrointestinal dystemperaments questionnaire: a novel scale in Persian traditional medicine

Background

Development of a questionnaire based on the resources of Persian traditional medicine seems necessary. One of the problems faced by practitioners of traditional medicine is the different opinions regarding the diagnosis of general temperament or temperament of member. One of the reasons is the lack of validity tools, and it has led to difficulties in training the student of traditional medicine and the treatment of patients. The differences in the detection methods, have given rise to several treatment methods.

Objective

The present study aimed to develop a questionnaire and standard software for diagnosis of gastrointestinal dystemperaments.

Methods

The present research is a tool developing study which included 8 stages of developing the items, determining the statements based on items, assessing the face validity, assessing the content validity, assessing the reliability, rating the items, developing a software for calculation of the total score of the questionnaire named GDS v.1.1, and evaluating the concurrent validity using statistical tests including Cronbach’s alpha coefficient, Cohen’s kappa coefficient.

Results

Based on the results, 112 notes including 62 symptoms were extracted from resources, and 58 items were obtained from in-person interview sessions with a panel of experts. A statement was selected for each item and, after merging a number of statements, a total of 49 statements were finally obtained. By calculating the score of statement impact and determining the content validity, respectively, 6 and 10 other items were removed from the list of statements. Standardized Cronbach’s alpha for this questionnaire was obtained 0.795 and its concurrent validity was equal to 0.8.

Conclusion

A quantitative tool was developed for diagnosis and examination of gastrointestinal dystemperaments. The developed questionnaire is adequately reliable and valid for this purpose. In addition, the software can be used for clinical diagnosis.

Identification and Analysis of Rice Yield-Related Candidate Genes by Walking on the Functional Network

Rice (Oryza sativa L.) is one of the most important staple foods in the world. It is possible to identify candidate genes associated with rice yield using the model of random walk with restart on a functional similarity network. We demonstrated the high performance of this approach by a five-fold cross-validation experiment, as well as the robustness of the parameter r. We also assessed the strength of associations between known seeds and candidate genes in the light of the results scores. The candidates ranking at the top of the results list were considered to be the most relevant rice yield-related genes. This study provides a valuable alternative for rice breeding and biology research. The relevant dataset and script can be downloaded at the website: http://lab.malab.cn/jj/rice.htm.

Association of glutathione S-transferase M1 and T1 polymorphisms and temperament

Mizaj (Temperament) is one of the basic concepts of Iranian Traditional Medicine (ITM), which has great importance in diagnosis and treatment of diseases, as well as maintaining the ideal healthy state of an individual. However, very little is known about the biological mechanisms of mizaj dependence treatment in practical ITM. This study was aimed to evaluate any association between the mizaj and glutathione S-transferase M1 (GSTM1) and T1 (GSTT1) polymorphisms in healthy people. The samples included 247 healthy males from Fars province, southern Iran. The mizaj was determined using a self-reported mizaj identification scale. Subjects with equilibrium or any of four simple mizajes (warm, cold, moist, and dry) were included in the study. The GSTM1 and GSTT1 genotypes were determined using a polymerase chain reaction (PCR)-based method. No any differences in the frequency of GSTM1/T1 polymorphism between equilibrium and each of other mizaj groups were found. However, when equilibrium, moist, and dry groups were pooled and as a "medium warmness" group were compared to the warm group, the frequency of GSTT1-null in the warm group was significantly higher compare to that in the medium warmness group. Also, the combination genotypes of GSTM1 and GSTT1 was associated with the warmness; that is, individuals with combination of GSTM1 positive and GSTT1 null were more susceptible to have a warm temperament. This study indicated that the mizaj could be affected by GSTM1/T1 genes, although further research with larger samples is needed to reach full conclusions.

Historical root of precision medicine: an ancient concept concordant with the modern pharmacotherapy

Pharmacogenomics and pharmacoproteomics are new sciences that their goal is achieving therapeutics with maximum results and minimal side effects for each individual due to the pattern of his genome and proteome.

Although they considered new and high technology sciences but in distant past, Persian sages like Avicenna also knew about importance of “personalized medicine” and used specific patterns to detect individual differences in order to select suitable medication.

Based on experience and analogy they divided individuals into different categories considering characteristics like body color, body temperature, sleep-awake pattern and skeletal structure.

They also paid attention to effect of environmental conditions such as climate, job and the change of seasons on the influence of medication.

Considering the low cost and ease of use of these experiences, it seems that researching their opinions can uncover the historical roots of modern pharmacoproteomics and can possibly infuse new ideas in this field.