Archives of Advances in Biosciences

There is an idiom that “biophysicist is who discusses about biology when meets physicist, talks about physics when meets biologist and says joke when meets another biophysicist”. This idiom points to multidisciplinary nature of biophysics but what really is the biophysics? And who is the biophysicist?  Biophysics was  defined as: "that branch of knowledge that applies the principles of physics and chemistry and the methods of mathematical analysis and computer modeling to understand how the mechanisms of biological systems work” in homepage of Biophysical Society[1]. Biophysics may be thought of as the central circle in a two-dimensional array of overlapping circles, which include physics, chemistry, physiology, and general biology.[2]Two wings of Biophysics are Biology and physics. Organisms are made of biomaterials, which can be studied by physical laws, since physical principles and laws hold from microscopic level to macroscopic level. Biophysicist selects a part of biological problems that are pliable to interpret by physical principles and then formulate hypotheses that can be tested by experiment². Historically, bioluminescence can be considered among the earliest biophysical phenomena. The modern biophysics appeared by discovering of molecular structure of myoglobin and deoxyribonucleic acid (DNA). There is no doubt that Biophysics as a multidisciplinary science covers wide spectrum of subjects as follows: Instrumental biophysics, Radiation Biophysics and radiobiology, Structural biology, Physiological biophysics, bio-cybernetics, Membrane Biophysics, Molecular biophysics, Bioenergetics, Mathematical and theoretical biophysics and Biophysical Chemistry.And the final question, do you still believe the above idiom about the biophysicist?

[1] http://www.biophysics.org/

[2] http://www.britannica.com/

The factors such as disease can disrupt homeostasis, resulting in perturbations of endogenous biochemicals that are involved in key metabolic profiles. Metabonomics is useful technique to quantitative description of endogenous metabolites present in a biological sample such as urine, plasma and tissue. High resolution ¹H nuclear magnetic resonance (NMR)-based metabonomics is a technique used to analyze and interpret multivariate metabolic data that correlate with changes of physiological conditions. Before any explanation for metabolite data, preprocessing the spectroscopic data is essential. In this paper, we show scaling effects in metabonomics investigation of patients diagnosed with Crohn's and Celiac disease. two techniques of scaling were applied as follows: mean centering and auto scaling. Results reveal that the mean centering is more useful to segregate patients from healthy subjects in the data set of Crohn's and Celiac disease.

The Pain is the most common complaint in various diseases. Postoperative pain is common complication and spatially in elderly patient because of exacerbation of heard and vessel was impotents. The aim of this study was evaluation of the effect of low-dose IV dexamethasone on postoperative pain in patients with lumbar discectomy.  In a clinical trial that studied in neurosurgery wards of Shohada and Imam Reza hospitals affiliated to the Tabriz University of Medical Sciences on patients underwent lumbar discectomy, the effect of low-dose IV dexamethasone on postoperative pain was evaluated. 80 patients divided in 2 equal groups, we used IV morphine (present routine treatment) in group A and IV morphine in addition to 8mg IV dexamethasone in group B, for reducing post lumbar discectomy pain. 21 patients in group A, & 22 in group B were male and 19 patients in group A & and 18 in group B were female (P=0.823). Mean age of patients in groups A and B was 39.32 and 39.22 years, respectively (P=0.945). Mean of pain score (VAS) at 6 hours post-operation in group A and B was 6.97 and 6.75, respectively (P=0.065). VAS at 12, 18 or 24 hours post-operation in both groups didn't differ significantly, too (P>0.05). We didn't observe any significant reduction in post lumbar discectomy pain after adding 8 mg dexamethasone into morphine. Regarding other studies, it seems that higher doses of dexamethasone should be used to achieve a significant pain reduction.

The value of clinical use of tumor markers CEA and CA15-3 for early detection of recurrent breast cancer still is a controversial. This study was investigated relationship between tumor markers CEA and CA15-3 and recurrence breast cancer. Data regarding 147 women who had breast cancer were entered into the study. Patients were reviewed for 120 months after treatment. Maximum time for relapse was considered a 6 months. Results were showed recurrence cancer in 20% of diagnosed patients. All of them in diagnosis time had a higher of normal tumor markers (CA<3, CA15-3<30).These observations indicated that CA15-3 is a sensitive tumor marker for diagnosis especially for recurrent breast cancer.

Bacteria use a chemical language to communicate with each other which enables them to synchronize gene expression as a result of cell density. This special language which is called quorum sensing (QS) is based on producing and sensing the small signals and eventually leads them to perceive when a minimum population unit is reached. On the contrary, quorum sensing blockade (quorum quenching) has been recently grabbed scientists attention as a promising tool in controlling bacterial pathogens which utilize N-acyl homoserine lactone (AHL) to regulate their virulence factor production. Biodegradation of AHL molecules is an efficient way in QS interrupting which normally happens in the natural environment. In this survey, the effect of Bacillus cereus UT26 strain as an efficient quorum quencher on degrading both signal molecules (C4-HSL and 3oxoC12-HSL) of Pseudomonas aeruginosa was investigated. The strain strongly degraded both AHLs and hereby inhibited pyocyanin production in the lab condition. Moreover, co-culture experiments revealed that quorum quenching activity has an important role in interaction between different bacterial species; since the wild type (wt) strain of B. cereus UT26 reached 1000 fold higher growth yield comparing aiiA mutant strain of  which has lost quorum quenching activity by a site directed mutation in AiiA lactonase gene.

Saprophitic Pseudomonas species are root-colonizing bacteria that can improve plant health. Efficient exploitation of these bacteria in agriculture requires knowledge of traits that enhance ecological performance in the rhizosphere. Some Pseudomonas fluorescens strains present biocontrol properties, protecting the roots of some plant species against plant pathogens. These bacteria induce systemic resistance in the host plant, so it can better resist attack by a true pathogen. The bacteria outcompete other (pathogenic) soil microbes, e.g., by siderophores, giving a competitive advantage at scavenging for iron. The bacteria produce compounds antagonistic to other soil microbes, such as phenazine - type antibiotics or hydrogen cyanide. In this study  the changes in the protein profile of P. fluorescens strain UTPF68, involved in the multiple interactions between plant (tomato) and an antagonistic agent (Trichoderma atroviride strain P1) investigated. Two-dimensional electrophoresis was used to analyze separately collected proteins from each one, two or three partner interactions. The results about differential produced spots in Pseudomonas proteome in each collation, showed that 18 differential spots became visible as new, 16 spots were absent, 17 spots were up-regulated and 1 spot was down-regulated, when Tomato-Pseudomonas (TP) condition was compared with control Pseudomonas alone (P). Also more than 84 differential spots were accumulated in proteome of Pseuodomonas due to the presence of Trichoderma, as new, absent, increased and decreased spots. By comparison of conditions revealed 2 protein spots that detected by MS, have newly expressed in present of Plant and Trichoderma. These proteins corresponded to arginine deiminase of P. putida GB-1 and Chaperonin GroEL protein of P. putida S16 that their expressions associated to stress condition.The results indicated that the presence of Plant and Trichoderma induces major changes in the protein profile of Pseudomonas.

Receiver Operating Characteristics (ROC) curves have numerous applications for identifying a cut-off point in diagnostic tests. Nonetheless, given that sometimes two cut-off points have to be specified simultaneously, the ROC curve can be used to identify such points. The Volume under the ROC Surface (VUS) serves as a criterion for the accuracy of diagnostic tests. One of the unfortunate outcomes in pregnancy is pre-term delivery; it has been noted that an increase in the level of hemoglobin in the first trimester of pregnancy could result in preterm delivery in weeks 34 to 37 and that an ongoing hemoglobin increase could result in the delivery of a premature fetus before the 34th week of pregnancy. In this regard, in order to separate three groups of on-time delivery, pre-term delivery and immature delivery two cut-off points have to be identified, simultaneously. A suitable measure to identify such points is the ROC surface. In the current study, the hemoglobin information of the first trimester of pregnancy and delivery time of 623 pregnant ladies referring to Milad Hospital in Tehran in 2009-2010 was obtained. ROC surface was adopted to draw two ideal cut-off points for the first trimester of pregnancy. The optimal points for hemoglobin of the first trimester computed with the ROC surface were 12.54 and 13.2. While a hemoglobin rate less than 12.54 indicated an on-time delivery, a rate between the two cut-off points referred to pre-term delivery and hemoglobin more than 13.2 showed a premature fetus. The three-dimensional ROC surface is a useful tool that can visually summarize the ability of a biological marker to classify individuals between more than two groups.

The present research is an attempt to describe the quantity and quality of publication trends of media literacy based on Scopus reports. The population under study was composed of 510 documents on media literacy published through 2011. The results were analyzed based on date of publication, type of document, language of the documents, source of publications, subject areas, authors and their affiliations, and the countries involved in developing the articles. Citation indicators formed the second phase of investigation in the present study. With a negligible amount of fluctuation, the number of publications on media literacy has increased steadily over the years, with the greatest number occurring in 2011.  The analysis of data based on document types indicated that, of the 510 documents, 330 were articles (64.70%), 85 were reviews (16.66%), and 64 were conference papers (12.54%). 446 documents (84.45%) were published in English and the rest presented in other languages. The United States with 190 documents (37.25%), the United Kingdom with 43 documents (8.43%), and Australia with 14 documents (2.74%) were the most represented countries, with the most prolific authors known as Austin, Hobbs, and Cheung. Thematically, the greatest number of documents were produced in Social Sciences with 360 documents (70.57%), followed by Medicine with 92 documents (18.03%). The largest number of documents has been published in Comunicar followed by American Behavioral Scientist, and Simile.  The most cited articles from 1996 up to 2011 included 22 documents on the H-index zone. Analysis of the results of H-index zone by subject categories indicated that most documents on h-index zone belonged to social sciences and Medicine areas. Psychology had the most influence on media literacy, as was shown by the ratio of most cited documents to total number of documents on media literacy in any of the subject categories. The results highlight the multidisciplinary nature of media literacy. As for the H-index zone, 16 documents (73.91%) belonged to the United States. Overall, the United States, with 190 (37.25%) publications (out of a total of 510), had an important role in enhancing the quantity and quality of the media literacy literature

Plant-based drugs are regarded promising recently. Scrophularia has been shown various biological activities such as antimicrobial, antitumor and anti-inflammatory properties. According to pervious researches, bacteria are becoming resistant to some kinds of antibiotics, so it is prominent to find more reliable sources against them. Here Staphylococcus aureus as a common type of Gram- positive bacteria has been chosen for this in vitro study. After culturing this bacterium, it was treated with various dosages of Scrophularia striata seed aqueous extract and tetracycline, and then its antibacterial effect was assessed by spectrophotometery method based on bacteria population alteration after 24h incubation. In order to investigate probable side effects of the seed extract its effect on human fibroblast cells has been studied. MTT assay was applied for cell survival determination of human fibroblast cells after 24h. Findings indicate that bacterial population has been declined between 1 to 20 μg mL^-1 dosages of the extract, which 5 μg mL^-1 isthe most effective dosage without containing any cytotoxic effect on human fibroblast cells. In fact extract not only has no antiproliferation properties but also has evoked cell profileration, so it can be consider as a cell growth factor. Tetracycline, on the contrary, showed its potent impact merely in highest dosages with noticeable side effects. It can be concluded that, Scrophularia striata could be possibly a promising antibiotic which shows significant antibacterial properties, and with lesser side effects.

Accurate interpretation of radiographic images is dependent on viewing conditions. Recently the number of radiology departments has been increased so it needs to use a workstation for reporting. The aim of this study was assess monitor performance and the effect of viewing conditions on object detection. This investigation aimed to quantify the effects of changes in box brightness and ambient light level on reader performance. Radiographs of the contrast-details phantom were taken in multiple exposures and were viewed by six observers. The viewing test was performed in 50,100 and 150 lux of ambient light in compound with 1000,1500 and 2000 cd m^-2 box brightness. The percentage of uniformity was also 85. The results were analyzed by SPSS software. Low contrast visibility generally increased when the ambient light was 100 lux. The greatest performance was obtained in 2000 cd m^-2 brightness and 15% non uniformity in mentioned ambient lighting. Reader performance not affected by ambient light and view box luminance although it seems those factors influenced on detection of low-contrast features in some studies.

Many commonly used statistical methods require that the population distribution be nearly normal. Unfortunately, in some papers the one-sample Kolmogorov-Smirnov test has been used for testing normality while the assumptions of applying this test are not satisfied. To conduct this test, it is assumed that the population distribution is fully specified. In practical situation where the mean and SD of population distribution is not specified in advance, one can use a modification of the K-S test for checking the normality assumption which is called, Lilliefors test. In this paper, we explain the method of computing this test with some common statistical softwares such as SPSS, S-PLUS, R and StatXact and utilize a dermatology dataset from Skin Research Center of Shohada-e-Tajrish hospital to illustrate how the use of the one-sample K-S (with the mean and SD estimated from the sample) instead of its modification can be misleading in practice. We also use Monte Carlo simulation to compare the approximate power of the one-sample K-S test (with the estimated population mean and SD) with Lilliefors test in some common specified continuous distributions. The result indicates that one should not use the one-sample K-S test for assessing the normality assumption in practical situation.

Fruity teas are popular due to variety in sensory properties as well as their nutritional and therapeutical characteristics. Recently, the worldwide researches related to fruity teas have been considerably developed. In this work, effects of fruit type (apple, quince and pear) and brewing time (10 or 20 min) on some nutritional properties (Mg, Fe and Ca contents, sugars and protein percent) as well as on the sensory attributes of final products were investigated. No chemical preservative, flavoring gents and colorants were added for preparation of the samples. At the end of 10 min brewing, the highest extraction rates of Mg and protein, Fe and sugars, and Ca were observed for pear, apple, and quince, respectively. At the end of 20 min brewing, the greatest extraction rates of Mg and protein, sugars, and Ca were related to the pear, apple, and quince, respectively. Increasing the time of brewing up to 10 min although did not noticeably affect the extraction rate of nutrients from dried fruits (especially for protein content), significantly influence the sensory characteristics (flavor and color) of final products; so that those prepared by 20 min brewing had higher acceptability. Among the fruity teas produced by 20 min brewing, apple had the best sensory acceptability from flavor and color points of view. After that, pear tea from taste and quince tea from color standpoints were realized as the best samples.

Effects of homogenization sequence (before or after heating) and homogenization pressure (0, 50, or 150 bar) were studied on the certain textural properties of milk-based creamy dessert including hardness, surface tension and syneresis. Also, the microstructure of the treatments was analyzed using scanning electron microscopy (SEM). Homogenization at 50 bar after heating led to the highest hardness, whilst unhomogenized and homogenized treatments at 150 bar before heating resulted in the lowest hardness.  Using pressure of 50 and 150 bar after heating led to the highest and lowest surface tension, respectively. While the highest syneresis was observed when unhomogenized treatment applied, the lowest syneresis was obtained using primarily the treatments with homogenization after heating and then the treatments with homogenization before heating. Finally, good correlation was observed between the textural and rheological results and the micrographs of microstructure obtained from SEM method

Bile duct ligation (BDL) is shown to induce cholestasis-related liver function impairments as well as consequent cognitive dysfunctions (i.e. impaired learning and memory formation). This study investigates the effects of cholestasis (14, 21 and 28 days post bile duct ligation) on spatial and non-spatial novelty detection, using a non-associative task. Male mice weighing 30-35 g were used. Cholestasis was induced by ligation of the main bile duct using two ligatures and transecting the duct at the midpoint between them. Open field paradigm was employed to assess the spatial and non-spatial memories retention. Our data showed that cholestasis (28 days after bile duct ligation) decrease and increased duration time of displace and non-displace objects respectively, indicating spatial memory deficit. Moreover, this intervention (28 days after bile duct ligation) decreased and did not alter duration time of substitute and non-substitute objects respectively, suggesting non-spatial memory deficit. Moreover, the data postulated that 14 and 21 days post bile duct ligation both spatial and non-spatial memories did not alter. Our results suggested that cholestasis (28 but not 14 and 21 days post bile duct ligation) impaired spatial and non-spatial memory in the mice.

Evidence is emerging for the association of polymorphisms in PRODH gene and increased risk of schizophrenia. In this project, peripheral blood sampling was obtained from 175 schizophrenia patients that their diseases were confirmed by psychiatrists. 185 healthy individuals were considered as control group. The related tests were administered on the basis of PCR-RFLP. In the continuation, statistical analysis was made on the basis of obtained genotypes from two groups of healthy and patient groups using SPSS16.0 software. The administration of this project aims at investigating the hypothesis that proline dehydrogenase gene, as one of the most important genes involved in schizophrenia incidence which is proved in various populations [outside Iran], may also be involved in incidence of schizophrenia in Iran. This study has analyzed one single nucleotide polymorphism in the PRODH gene, including 757C/T in the incidence of this disease in the given statistical population.

According to our results, SNP 757 C/T may be effective in incidence of the disease since P value was < 0.01. Ultimately, our results suggest that outbreak of mutation in PRODH gene in our population can be one of causes of increasing risk of Schizophrenia in this population.

Schizophrenia is a mental disorder painful with prevalence of about 1% in the world.  Nowadays, there is no experimental test aiding the accurate diagnosis of schizophrenic patients but recently quantitative determination of some serum proteins led to many investigations on the roles of these in neuropsychiatric.In the present study, our aim is to quantitative determination ApoA1 and IgM between 134 schizophrenic patients and 127 healthy control persons. Schizophrenia patients were selected from the Tehran Razi hospital.  The age (p=0.53) and sex distributions of schizophrenic patients were similar to those of control persons. We measured ApoA1 and IgM levels by immunoturbidimetry method. P<0.05 was considered significant.  ApoA1 showed a significant decrease in serum (p=0.00) and IgM to be significantly increased (p=0.00).Furthermore, female patients showed an increase IgM more than males. These results for ApoA1 and IgM support other reports.  Decrease ApoaA1 confirmed the relationship of lipid metabolism in schizophrenia patients, also increase IgM evaluate the impact of treatment. This report can help to identify disease markers and treatment such as immunoglobulin therapy or regulate lipid metabolism. It can be imagined that immunoglobulin therapy more effective in the female patients than male and need to expa

Breast cancer within incident of one million new cases each year has become one of the most common malignancies and leading cause of death among females. This disease is comprised of about 18% of women cancers. The availability of early detection and improved treatments may decrease the mortality rates which reflected in the United States and many other western countries. Breast cancer in over the past 20 years may also have contributed to the Increasing age, nulliparity, positive family history of breast cancer, and use of menopausal hormone therapy were positively risk factors associated with breast cancer. Therefore, studying this malignity is prominent due to its mortality world wild. Evaluation and study of different aspects of breast cancer have been established during past decays which, in this review, it is presented and discussed.

Celiac disease (CD) is an immune-mediated disorder resulting in nutrient malabsorption now thought to have a prevalence of 1:100 in the Iranian population.Symptoms of CD are included diarrhea, abdominal pain, steatorrhea, bloating, cramps, flatulence, weight loss, weakness and short stature. In addition to presenting symptoms, patients are also at increased risk of metabolic bone disease, lymphoma (enteropathy-associated with T-cell) and other malignancies in different parts of the body such as gastric, esophageal, bladder, breast and brain. There appears to be a strong genetic component to this disease. In this short review we provided the historical, clinical and genetic aspects of this disease and highlight numerous findings from recent molecular immunology studies.

Osteoporosis as a skeletal disorder characterize by compromised bone strength predisposing a person to an increased risk of fracture. All people should be encouraged to take efforts to prevent bone loss and fractures. Nutrition is one of several factors that can be modified to reduce osteoporosis risk. The purpose of this review article is assessment the role of the other nutrients the exception of calcium and vitamin D on bone health and prevention of osteoporosis.The search was undertaken in three databases (PubMed, google scholar and science direct) for publications from 2005 onwards using key words as follows. Initial searches yielded approximately 2467 results. After considering additional exclusion criteria, 33 clinical trial and meta- analysis papers remained.According to investigations, high intake of dietary protein increase bone resorption and calcium excretion and low protein intake can prevent calcium absorption and decrease strength and bone mass. Omega-3 supplementation also can decrease bone resorption and α-linleic acid (for men and women) and arashidonic acid (in men) and isoflavones can significantly diminish the risk of hip fracture. Adequate intake of some nutrients like zinc, vitamin A, boron and manganese in bone formation and copper, fluoride and strontium in bone mineralization have positive effects. However, high intake of vitamin A and fluoride result in hip fracture incretion. Vitamin K (in form of K₂) along with calcium and vitamin D induce bone fracture decrease. If intake of phosphate, iron and sodium be more than the recommended values, they may present negative effects on bone mineralization.In conclusion, risk of osteoporosis incidence may be diminished with an adequate and balanced diet containing variety of foods to meet needs and a healthy lifestyle. Nutrition education and training the other preventive factors should be carrying out in childhood to achieve the peak bone mass in youth and aging.

As recent advancements in biology shows, the molecular machines specially proteins, RNA and complex molecules play the main role of the so called cell functionality. It means a very big part of the system biology is concerned with the interactions of such molecular components. Drug industries and research institutes are trying hard to better understand the concepts underlying these interactions and are highly dependent on the issues regarding these molecular elements. However the costs for such projects are so high and in many cases these projects will be funded by governments or profit making companies. With this in mind it has to be said that the techniques like stimulation are always a very good candidate to decrease such costs and to provide scientists with a bright future of the project results before undergoing costly experiments. However the costs involved projects that determine an approximation for the problem is not that much high but they are also costly. So it is of utmost importance to invent special techniques for the concept of stimulation that can also decrease the project costs and also predict much accurately. Since the system biology and proteomics as the study of the proteins and their functions are in the center of consideration for the purpose of drug discovery, understanding the cell functionalities and the underlying causes behind diseases; so we need advance software and algorithms that can predict the structure of the molecular components and to provide researchers with the computational tools to analyze such models. In this paper we make review of the importance of molecular modeling, its limitations and applications.

Diabetes mellitus is one of the most common chronic diseases in nearly all countries. It is difficult to treat and expensive to manage. The development of type 2 diabetes is strongly related to lifestyle factors, thus it might be a preventable disease. Observational studies and intervention trials have shown that physical activity, weight loss and dietary intake including whole grain, dietary fiber and dietary fat are important in delaying and preventing type 2 diabetes. The aim of this review is to gather current information from epidemiologic and clinical trial studies on dietary and lifestyle practices for reducing the risk of type 2 diabetes. The review focuses on the macro and micronutrients, food items and dietary patterns which have been identified as significant in the prevention and management of type 2 diabetes. Also, the role of physical activity and weight loss are presented.