Search results for: Babak Dindar Safa

Authors: Rasouli Divkalaee Zeinab, Kalteh Safa, Roudbari Aliakbar

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Introduction: Medical waste can lead to the generation and transmission of many infectious and contagious diseases due to the presence of pathogenic agents, thereby necessitating the need for special management to collect, decontaminate, and finally dispose of such products. This study aimed to design a centralized health care (medical) waste management program for the cities of Semnan, Mahdishahr, and Shahmirzad. Methods: This descriptive-analytical study was conducted for six months in the cities of Semnan, Mahdishahr, and Shahmirzad. In this study, the quantitative and qualitative characteristics of the generated wastes were determined by taking samples from all medical waste production centers. Then, the equipment, devices, and machines required for separate collection of the waste from the production centers and for their subsequent decontamination were estimated. Next, the investment costs, current costs, and working capital required for collection, decontamination, and final disposal of the wastes were determined. Finally, the payment for proper waste management of each category of medical waste-producing centers was determined. Results: 1021 kilograms of medical waste are produced daily in the cities of Semnan, Mahdishahr, and Shahmirzad. It was estimated that a 1000-liter autoclave, a machine for collecting medical waste, four 60-liter bins, four 120-liter bins, and four 1200-liter bins were required for implementing the study plan. Also, the estimated total annual medical waste management costs for Semnan City were determined (23,283,903,720 Iranian Rials). Conclusion: The study results showed that establishing a proper management system for medical wastes generated in the three studied cities will cost between 334,280 and 1,253,715 Iranian Rials in fees for the medical centers. The findings of this study provided comprehensive data regarding medical wastes from the generation point to the landfill site, which is vital for the government and the private sector.

Keywords: clinics, decontamination, management, medical waste

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Authors: Babak Nemat Shahrbabaki, Arezo Fallahi, Masoomeh Hashemian

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Introduction: Health and safety are basic components of civil right. Health care systems in different countries were influenced by political, economic and cultural circumstances. In order to health services to people, these systems are organized with different forms, methods such as: prevention, treatment and rehabilitation and in this among, public satisfaction with the services provided is important. This study aimed to determine client satisfaction with family physician and relationship with physician’ demographic variables in health care centers of Jiroft county, Iran. Methods: This is a descriptive-analytical study. The collective data tool was a self-made questionnaire with two parts. The first part comprised demographic characteristics, and the second part contained 11 items for the assessment of satisfaction with family physician from different aspects. In addition, questionnaire, reliability and validity were confirmed. Random simple sampling method was used to determine samples. 234 people referred to the health centers filled questionnaire. The data were analyzed using SPSS software, and inferential statistical analysis was performed. Findings: The majority of the study population were women, married, and aged between 18 and 62 years (mean= 30.09±10.71). Total average satisfaction score was 42.63±3.68. Overall satisfaction averages were 9.47% very high, 30.04% high, 33.09% moderate, 15.12% low, and 12.28% very low. Except lodge on of family physician none of physician’ demographic variables did not effect on satisfaction index. Discussion & Conclusion: The Results showed that mean of satisfaction indexes of family physicians was high and lodge on of family physician effected on this index. Informing people about the main goals of family-doctor program will help to promote the quality of program and increase people satisfaction.

Keywords: family physician program, satisfaction, health-care centers, client

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Authors: Arezoo Fallahi, Fateme Aslibigi, Parvaneh Taymoori, Babak Nematshahrbabaki

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Background and Aims: Cancer of the cervix, one of cancer-related death, is the second most common cancer in women worldwide. It develops over time but it is one of the most preventable types of cancer and there is the available proper screening program for its preventing. Since Pap smear test is vital to prevent and control of disease but women do not accomplish it regularly. Therefore, this study was aimed to explore women's needs referring to health care centers for doing Pap smear test. Material and methods: In this study, an inductive qualitative method with content analysis approach was used. This survey was done in varamin city (is located capital of Iran) in year 2014. Through the purposive sampling 15 women's view of point referring to health care centers of for doing Pap smear test was surveyed. Inclusion criteria were: 20-50 years old married women, having experience Pap smear test and attendance to participate in the Study. Recorded semi- structured interviews were typed and analyzed through of content analysis method. To obtain trustworthiness and rigor of the data, the criteria of credibility, dependability, confirmability and transferability was used. Results: During the data analysis, four main categories of “role of health care team”, “role of organizations”, “social support” and “policies and administration system” were developed. The participants emphasized on making motivational rules and coordination among organizations to do behaviors related to women health. Conclusion: The findings of study showed that doing Pap smear test are attributed to appropriate and intimate interactions with health professionals, family support, encouraging legislation and policies and coordination and notification of organizations. Therefore, designers and stockholders of policies and health system should more consider to growth and involve other organizations toward women's health.

Keywords: qualitative approach, pap smear test, women, health care centers

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Authors: Nima Safaei, Arezoo Masoud, Babak Safaei

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In recent years, there has been a growing emphasis on the role of urban planning in walking capability and the effects of individual and socioeconomic factors on the physical activity levels of city dwellers. Although considerable number of studies are conducted about walkability and for identifying the effective factors in walking mode choice in developed countries, to our best knowledge, literature lacks in the study of factors affecting choice of walking mode in developing countries. Due to the high importance of health aspects of human societies and in order to make insights and incentives for reducing traffic during rush hours, many researchers and policy makers in the field of transportation planning have devoted much attention to walkability studies; they have tried to improve the effective factors in the choice of walking mode in city neighborhoods. In this study, effective factors in walkability that have proven to have significant impact on the choice of walking mode, are studied at the same time in work trips. The data for the study is collected from the employees in their workplaces by well-instructed people using questionnaires; the statistical population of the study consists of 117 employed people who commute daily from work to home in Rasht city of Iran during the beginning of spring 2015. Results of the study which are found through the linear regression modeling, show that people who do not have freedom of choice for choosing their living locations and need to be present at their workplaces in certain hours have lower levels of walking. Additionally, unlike some of the previous studies which were conducted in developed countries, coincidental effects of Body Mass Index (BMI) and the income level of employees, do not have a significant effect on the walking level in work travels.

Keywords: BMI, linear regression, transportation, walking, work trips

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Authors: Babak Bahri, Fatemeh Yassaee Meybodi, Changiz Eslahchi

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In the pursuit of effective cancer therapies, the exploration of combinatorial drug regimens is crucial to leverage synergistic interactions between drugs, thereby improving treatment efficacy and overcoming drug resistance. However, identifying synergistic drug pairs poses challenges due to the vast combinatorial space and limitations of experimental approaches. This study introduces ClusterSyn, a machine learning (ML)-powered framework for classifying anti-cancer drug synergy scores. ClusterSyn employs a two-step approach involving drug clustering and synergy score prediction using a fully connected deep neural network. For each cell line in the training dataset, a drug graph is constructed, with nodes representing drugs and edge weights denoting synergy scores between drug pairs. Drugs are clustered using the Markov clustering (MCL) algorithm, and vectors representing the similarity of drug pairs to each cluster are input into the deep neural network for synergy score prediction (synergy or antagonism). Clustering results demonstrate effective grouping of drugs based on synergy scores, aligning similar synergy profiles. Subsequently, neural network predictions and synergy scores of the two drugs on others within their clusters are used to predict the synergy score of the considered drug pair. This approach facilitates comparative analysis with clustering and regression-based methods, revealing the superior performance of ClusterSyn over state-of-the-art methods like DeepSynergy and DeepDDS on diverse datasets such as Oniel and Almanac. The results highlight the remarkable potential of ClusterSyn as a versatile tool for predicting anti-cancer drug synergy scores.

Keywords: drug synergy, clustering, prediction, machine learning., deep learning

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Authors: Babak Nemat

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Background and Purpose: Non-alcoholic fatty liver is one of the most common liver disorders, which, as the most important cause of death from liver disease, has unpleasant consequences and complications. The aim of this study was to investigate the effect of an educational intervention based on a health belief model to prevent non-alcoholic fatty liver among women. Materials and Methods: This experimental study was performed among 110 women referring to comprehensive health service centers in Malayer City, west of Iran, in 2023. Using the available sampling method, 110 participants were divided into experimental and control groups. The data collection tool included demographic characteristics and a questionnaire based on the health belief model. In the experimental group, three one-hour training sessions were conducted in the form of pamphlets, lectures, and group discussions. Data were analyzed using SPSS software version 21, by correlation tests, paired t-tests, and independent t-tests. Results: The mean age of participants was 38.07±6.28 years, and most of the participants were middle-aged, married, housewives with academic education, middle-income, and overweight. After the educational intervention, the mean scores of the constructs include perceived sensitivity (p=0.01), perceived severity (p=0.01), perceived benefits (p=0.01), guidance for internal (p=0.01), and external action (p=0.01), and perceived self-efficacy (p=0.01) in the experimental group were significantly higher than the control group. The score of perceived barriers in the experimental group decreased after training. The perceived obstacles score in the test group decreased after the training (15.2 ± 3.9 v.s 11.2 ± 3.3, (p<0.01). Conclusion: The findings of the study showed that the design and implementation of educational programs based on the constructs of the health belief model can be effective in preventing women from developing higher levels of non-alcoholic fatty liver.

Keywords: non-alcoholic fatty liver, health belief model, education, women

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Authors: Babak Mirzashahi, Arvin Najafi, Pejman Mansouri, Mahmoud Farzan

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Background: The most effective treatment of posterior cruciate ligament (PCL) tears and the consequence of untreated PCL injuries remain controversial. Objectives: The aim of this study is to assess outcomes of fixation of tibial posterior cruciate ligament (PCL) avulsion fractures via a modified technique. Patients and Methods: From January, 2009 to March, 2012, there were 45 cases of PCL tibial avulsion fractures that were referred to our hospital and were managed through a modified open posterior approach. Fixation of Tibial PCL avulsion fractures were fixed by means of a lag screw and washer placed through our modified open posterior approach. Range of motion was begun on the first postoperative day. Clinical stability, range of motion, gastrocnemius muscle strength, radiographic investigation, and patient’s overall quality of life was analyzed at final follow up visit. Results: The average of overall musculoskeletal functional evaluation scores was 15 (range 3–35). All patients achieved union of their fracture and had clinically stable knees at the latest follow-up. The mean preoperative Lysholm score for 15 knees was 62 ± 8 (range, 50-75); the mean postoperative Lysholm score was 92± 7 (range, 75-101). A significant difference in Lysholm scores between preoperative and final follow-up evaluations was found (P < .05). At first-year follow-up, 42 (93%) patients revealed a difference of less than 10 mm in thigh circumference between their injured and healthy knees. Conclusions: The management of displaced large PCL avulsion fractures with placement of a cancellous lag screw with washer by means of the modified open posterior approach leads to satisfactory clinical, radiographic, and functional results and reduces the operation time and less blood loss. Level of evidence: IV.

Keywords: posterior cruciate ligament, tibial fracture, lysholm knee score, patient outcome assessment

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Authors: Arezoo Fallahi, Siamak Derakhshan, Parvaneh Taymoori, Babak Nematshahrbabaki

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Background: Osteoporosis, the most common metabolic bone disease, is an important health care issue. Not only the cost of disease is high but also is one of the causes of disability and mortality and effect on quality of life. Although self-care is effective on disease, s control and treatment but still effective factors on self-care of patient, s viewpoint have not been survey. The aim of this study was to explore effective factors on self-care in women with osteoporosis. Materials and methods: This study was done by conventional content analysis approach in year 2014. Through purposeful sampling 15 women referred to bone mass densitometry centers participated in this study. Inclusion criteria were: Women older than 50 years old with osteoporosis, final diagnosis of osteoporosis for over six –month period, T-score index below -2.5 (lower back or hip), drug use by patients with a physician’s prescription, ability in speaking and attending to participate in the study. Data was collected by face to face and group semi-structure deep interviews and analyzed via content analysis method. To support of rigor of data, criteria credibility, confirmability and transferability were used. Results: during data analysis five categories developed: “hope and disability in the face of illness”, “mutual roles of physician”, “role of family” and “administrative centers and organizations”. To perform self-care behaviors, the participations of this study emphasized on pay attention to their own healthy, regarding patients' rights by physician, pay attention to women's health by men, and the role of media especially radio and television. Conclusion: the finding of the study showed that women’s responsibility with osteoporosis for their health is not a factor but it is multifactorial. Increasing life expectancy in patients, attention to patients needs by physician, increasing health promotion programs in the media and enhancing role of family may provide conditions and infrastructure to empowerment women in doing self-care behavior.

Keywords: women, osteoporosis, self-care, content analysis

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Authors: Zahra Abdi, Roghayeh Alipour, Babak Farahi Ghasraboonasr

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Introduction: Diabetes is a serious medical condition that requires constant care. People with type 2 diabetes may also be likely to experience dry, itchy skin and poor wound healing. Some people with diabetes will have a skin problems at some time in their lives and for those not yet diagnosed with diabetes, a skin problem can be an indication of the disease. our purpose was to assess the capability and knowledge of students of Shiraz University of Medical Sciences about prevent from skin complications in diabetes type 2. Methods: In this descriptive cross-sectional study, knowledge of 360 students of Shiraz University of Medical Sciences was evaluated about different ways to avoid skin complications in diabetes type 2. Data were analyzed by spss19.(P<0.05) was considered significant. Results: 360 students of Shiraz University of Medical Sciences participated in this study. 45% of students agree with the effect of Moisturize skin daily, If Diabetics have sensitive skin, choose a fragrance-free, dye-free moisturizer that won’t irritate skin. 52% believe that Protect skin from sun can be so useful, Sun exposure is drying and aging. Use sunscreen with SPF 30 or higher whenever you’re outside. Wear gloves when doing yardwork to protect the skin on your hands. 62% of students strongly agree with Carefully clean any cuts and scrapes, If diabetics notice any sign of infection skin that’s red, swollen, or warm to the touch, or has a foul-smelling drainage or pus should consulting with a doctor immediately. Diabetics should be careful about any injury that takes longer than normal to heal and they should consulting with doctor about them too. 72% of students believe that diabetics should be diligent about daily foot care. Clean and moisturize feet each day and check each foot closely, top and bottom, for wounds even a tiny cut, blisters, or cracked skin. Conclusions: The risk of getting these diabetes complications can be lessened by controlling blood sugar. Skin complications can cause serious consequences. Taking care of skin is so important and using these tips are remarkable effective and help diabetics to look after their skin easier.

Keywords: skin complications, diabetes type 2, Shiraz University of Medical Sciences, diabetics

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Authors: Babak Rezaei, Arash Zargar Shoushtari

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Kangan anticline is located in the Coastal Fars area, southwest of Nar and west of west Assaluyeh anticlines and north of Kangan harbor in Boushehr province. The Kangan anticline is nearly asymmetric and with 55Km long and 6Km wide base on structural map of Kangan Formation. The youngest and the oldest Formations on surface are Bakhtiyari (Pliocene) and Sarvak (Cenomanian) respectively. The highest dip angles of 30 and 40 degree were observed in north and south flanks of Kangan anticline respectively and two reverse faults cut these flanks parallel to structure strike. Existence of sweet gas in Kangan Fm. and Upper Dalan in this structure is confirmed with probable Silurian shales origin. Main facies belts in these formations include super tidal and intertidal flat, lagoon, oolitic-bioclastic shoals and open marine sub environments that expand in a homoclinal and shallow water carbonate ramp under the arid climates. Digenetic processes studies, indicates the influence of all digenetic environments (marine, meteoric, burial) in the reservoir succession. These processes sometimes has led to reservoir quality improvement (such as dolomitization and dissolution) but in many instances reservoir units has been destroyed (such as compaction, anhydrite and calcite cementation). In this study, petrophysical evaluation is made in Kangan and upper Dalan formations by using well log data of five selected wells. Probabilistic method is used for petrophysical evaluation by applying appropriate soft wares. According to this evaluation the lithology of Kangan and upper Dalan Formations mainly consist of limestone and dolomite with thin beds of Shale and evaporates. In these formations 11 Zones with different reservoir characteristic have been identified. Based on wire line data analyses, in some part of these formations, high porosity can be observed. The range of porosity (PHIE) and water saturation (Sw) are estimated around 10-20% and 20-30%, respectively.

Keywords: microfacies, electrofacies, petrophysics, diagenese, gas fields

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Authors: Ezat Vahidian, Babak Eshrati

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Introduction: Elder abuse, a very complex issue with diverse definitions and names, has been very slow to capture the public eye and public policy since it is manifested at many levels. It requires the involvement of different types of professionals. While elder abuse is not a new phenomenon, the speed of population ageing world-wide is likely to lead to an increase in its incidence and prevalence. Elder abuse has devastating consequences for older persons such as poor quality of life, psychological distress, and loss of property and security. It is also associated with increased mortality and morbidity. Elder abuse is a problem that manifests itself in both rich and poor countries and at all levels of society. Purpose: The purpose of this study is to determine the prevalence of elder abuse and effects of social factor on it in Markazi Province. Materials and methods: The society of the study was all of the elders in Markazi Province that were available by geographical address in the table of rural and urban household societies. The study was cross sectional and multi phases in sampling the first one was classification according rural and urban area and the second one was cluster sampling with equal cluster. Estimation of samples were 472 persons and increased by design effect to 1110 persons. Collection data was done by questionnaire and analyzed by SPSS and chi 2 exam. Results: This study showed 70 persons were abused (42/8% male and 57/2% female) mean of ages was 74/7 years. 64% were marred and 31% were widows. There were not any significant meaningful association between elder abuse and area of living (pv=0.299),occupation (p.v=0.104), education (pv=0.358) and age (P.value=0.104) there were significant meaningful association between physical impairment (pv=0.08), and movement impairment (P.value=0.008). Conclusion: Results verify that maltreatment occurred in the aged persons. Analysis of data indicated that elder abuse exist in every socioeconomic group with any context of education in urban area and rural area and in men and women. Prevalence of elder abuse was 6.3% (70 persons) that verify the data of developed countries with limited sample.

Keywords: elder abuse, education, occupation, area of living

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Authors: Zeineb Baatout, Safa Teka, Nejmeddine Jaballah, Nawfel Sakly, Xiaonan Sun, Mustapha Majdoub

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Currently, the economic interests linked to the development of bio-based materials make biomass one of the most interesting areas for science development. We are interested in the β-cyclodextrin (β-CD), one of the popular bio-sourced macromolecule, produced from the starch via enzymatic conversion. It is a cyclic oligosaccharide formed by the association of seven glucose units. It presents a rigid conical and amphiphilic structure with hydrophilic exterior, allowing it to be water-soluble. It has also a hydrophobic interior enabling the formation of inclusion complexes, which support its application for the elaboration of electrochemical and optical sensors. Nevertheless, the solubility of β-CD in water makes its use as sensitive layer limit and difficult due to their instability in aqueous media. To overcome this limitation, we chose to precede by modification of the hydroxyl groups to obtain hydrophobic derivatives which lead to water-stable sensing layers. Hence, a series of benzylated β-CDs were synthesized in basic aqueous media in one pot. This work reports the synthesis of a new family of substituted amphiphilic β-CDs using a green methodology. The obtained β-CDs showed different degree of substitution (DS) between 0.85 and 2.03. These organic macromolecular materials were soluble in common organic volatile solvents, and their structures were investigated by NMR, FT-IR and MALDI-TOF spectroscopies. Thermal analysis showed a correlation between the thermal properties of these derivatives and the benzylation degree. The surface properties of the thin films based on the benzylated β-CDs were characterized by contact angle measurements and atomic force microscopy (AFM). These organic materials were investigated as sensitive layers, deposited on quartz crystal microbalance (QCM) gravimetric transducer, for humidity sensor at room temperature. The results showed that the performances of the prepared sensors are greatly influenced by the benzylation degree of β-CD. The partially modified β-CD (DS=1) shows linear response with best sensitivity, good reproducibility, low hysteresis, fast response time (15s) and recovery time (17s) at higher relative humidity levels (RH) between 11% and 98% in room temperature.

Keywords: β-cyclodextrin, green synthesis, humidity sensor, quartz crystal microbalance

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Authors: Amir Gerayeli, Babak Moradi

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The continuously declining oil reservoirs and reservoirs aging have created a huge demand for utilization of Enhanced Oil Recovery (EOR) methods recently. Primary and secondary oil recovery methods have various limitations and are not practical for all reservoirs. Therefore, it is necessary to use chemical methods to improve oil recovery efficiency by reducing oil and water surface tension, increasing sweeping efficiency, and reducing displacer phase viscosity. One of the well-known methods of oil recovery is Alkaline-Surfactant-Polymer (ASP) flooding that shown to have significant impact on enhancing oil recovery. As some of the biggest oil reservoirs including those of Iran’s are fractional reservoirs with substantial amount of trapped oil in their fractures, the use of Alkaline-Surfactant-Polymer (ASP) flooding method is increasingly growing, the method in which the impact of several parameters including type and concentration of the Alkaline, Surfactant, and polymer are particularly important. This study investigated the use of Nano particles to improve Enhanced Oil Recovery (EOR). The study methodology included performing several laboratory tests on drill cores extracted from Karanj Oil field Asmary Formation in Khuzestan, Iran. In the experiments performed, Sodium dodecyl benzenesulfonate (SDBS) and 1-dodecyl-3-methylimidazolium chloride ([C12mim] [Cl])) were used as surfactant, hydrolyzed polyacrylamide (HPAM) and guar gum were used as polymer, Sodium hydroxide (NaOH) as alkaline, and Silicon dioxide (SiO2) and Magnesium oxide (MgO) were used as Nano particles. The experiment findings suggest that water viscosity increased from 1 centipoise to 5 centipoise when hydrolyzed polyacrylamide (HPAM) and guar gum were used as polymer. The surface tension between oil and water was initially measured as 25.808 (mN/m). The optimum surfactant concentration was found to be 500 p, at which the oil and water tension surface was measured to be 2.90 (mN/m) when [C12mim] [Cl] was used, and 3.28 (mN/m) when SDBS was used. The Nano particles concentration ranged from 100 ppm to 1500 ppm in this study. The optimum Nano particle concentration was found to be 1000 ppm for MgO and 500 ppm for SiO2.

Keywords: alkaline-surfactant-polymer, ionic liquids, relative permeability, reduced surface tension, tertiary enhanced oil recovery, wettability change

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Authors: Ali Kamal M. Sami, Safa Almukhtar, Alaa Al-Krush, Ismael Hama-Amin Akha Weas, Ruqaya Ahmed Alqais

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Introduction and Objectives Lower urinary tract symptoms (LUTS) are common among men with benign prostatic hyperplasia (BPH). The combination of 5 alpha-reductase inhibitors and alpha-blockers has been used as a conservative treatment of male LUTS secondary to BPH. Nanotechnology structured water magnalife is a type of water that is produced by modulators and specific frequency and energy fields that transform ordinary water into this Nanowater. In this study, we evaluated the use of Nano-water with the conservative treatment and to see if it improves the outcome and gives better results in those patients with LUTS/BPH. Material and methods For a period of 3 months, 200 men with International Prostate Symptom Score (IPSS)≥13, maximum flow rate (Qmax)≤ 15ml/s, and prostate volume > 30 and <80 ccs were randomly divided into two groups. Group A 100 men were given Nano-water with the (tamsulosindutasteride) and group B 100 men were given ordinary bottled water with the (tamsulosindutasteride). The water bottles were unlabeled and were given in a daily dose of 20ml/kg body weight. Dutasteride 0.5mg and tamsulosin 0.4 mg daily doses. Both groups were evaluated for the IPSS, Qmax, Residual Urine (RU), International Index of Erectile Function–Erectile Function (IIEF-EF) domain at the beginning (baseline data), and at the end of the 3 months. Results Of the 200 men with LUTS who were included in this study, 193 men were followed, and 7 men dropped out of the study for different reasons. In group A which included 97 men with LUTS, IPSS decreased by 16.82 (from 20.47 to 6.65) (P<0.00001) and Qmax increased by 5.73 ml/s (from 11.71 to 17.44) (P<0.00001) and RU <50 ml in 88% of patients (P<0.00001) and IIEF-EF increased to 26.65 (from 16.85) (P<0.00001). While in group B, 96 men with LUTS, IPSS decreased by 8.74(from 19.59 to 10.85)(P<0.00001) and Qmax increased by 4.67 ml/s(from 10.74 to 15.41)(P<0.00001), RU<50 ml in 75% of patients (P<0.00001), and IIEF-EF increased to 21(from 15.87)(P<0.00001). Group A had better results than group B. IPSS in group A decreased to 6.65 vs 10.85 in group B(P<0.00001), also Qmax increased to 17.44 in group A vs 15.41 in group B(P<0.00001), group A had RU <50 ml in 88% of patients vs 75% of patients in group B(P<0.00001).Group A had better IIEF-EF which increased to 26.65 vs 21 in group B(P<0.00001). While the differences between the baseline data of both groups were statistically not significant. Conclusion The use of nanotechnology structured water magnalife gives a better result in terms of LUTS and scores in patients with BPH. This combination is showing improvements in IPSS and even in erectile function in those men after 3 months.

Keywords: nano water, lower urinary tract symptoms, benign prostatic hypertrophy, erectile dysfunction

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Authors: Nadine khadraoui, Rym Essid, Olfa Tabbene, Imen Chniba, Safa Boujemaa, Selim Jallouli, Nadia Fares, Behija Mlik, Boutheina Ben Abdelmoumen Mardassi

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Background and aim: Mycoplasma hominis is an opportunistic pathogen that can cause various gynecological infections such cervicitis, infertility, and, less frequently, extra-genital infections. Previous studies on the antimicrobial susceptibility of Mycoplasma hominis Tunisian strains have highlighted a significant resistance, even multi-resistance, to the most used antibiotic in the therapy of consequential infections. To address this concern, the present study aimed for the alternative of phytotherapy. Peganum harmala seed extract was tested as an antibacterial agent against multidrug-resistant M.hominis clinical strains. Material and Methods: Peganum harmala plant was collected from Ain Sebaa, Tabarka, North West region of Tunisia in April 2018, air-dried, grounded and extracted by different solvents.The crude methanolic extract was further partitioned with n-HEX, DCM, EtOAC and n-BuOl. Antibacterial activity was evaluated against M. hominis ATCC 23114 and 20 M. hominis clinical strains.The antimycoplasmal activity was tested by the microdilution method, and MIC values were determined. Phytochemical analysis and hemolytic activity on human erythrocytes were also performed. The active fraction was then subjected to purification, and the chemical identification of the active compound was investigated. Results: Among the tested fractions, the n-BuOH extract was the most active fraction since it exhibited an inhibitory effect against M. hominis ATCC 23114 and 80% of the tested clinical strains with MIC between 125 and 1000 µg/ml. The phytochemical analysis of the n-BuOH revealed its metabolic abundance in polyphenols, flavonoids and condensed tannin with levels of 257.37 mg AGE/g, 172.27 mg EC/g and 58.27 mg EC/g, respectively. In addition, P. harmala n-BuOH extract exhibited potent bactericidal activity against all M. hominis isolates with CMB values ranging between 125 and 4000 µg/ml. Further, the active fraction exhibited weak cytotoxicity effect at active concentrations when tested on human erythrocytes. The active compound was identified by gas chromatography–mass spectrometry as an indole alkaloid harmaline. Conclusion: In summary, Peganum harmala extract demonstrated an interesting anti-mycoplasmal activity against M. hominis Tunisian strains. Therefore, it could be considered as a potential candidate for the treatment of consequential infections. However, further studies are necessary to evaluate its mechanism of action in mycoplasmas.

Keywords: mycoplasma hominis, peganum harmala, antibioresistance, phytotherapy, phytochemical analysis

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Authors: Babak Sadeghi, Rony Snyders, Marie-Paule.Delplancke-Ogletree

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Nitrogen fixation (NF) is one of the crucial industrial processes. Many attempts have been made in order to artificially fix nitrogen, and among them, the Haber-Bosch’s (H-B) process is widely used. However, it presents two major drawbacks: huge fossil feedstock consumption and noticeable greenhouse gases emission. It is, therefore, necessary to develop alternatives. Plasma technology, as an inherent “green” technology, is considered to have a great potential for reducing the environmental impacts and improving the energy efficiency of the NF process. In this work, we have studied the catalyst assisted microwave plasma for NF application. Heterogeneous catalysts of MoO₃, with various loads 0, 5, 10, 20, and 30 wt%, supported on γ-alumina were prepared by conventional wet impregnation. Crystallinity, surface area, pore size, and microstructure were obtained by X-ray diffraction (XRD), Brunauer–Emmett–Teller (BET) adsorption isotherm, Scanning electron microscopy (SEM), and Transmission electron microscopy (TEM). The XRD patterns of calcined alumina confirm the γ- phase. Characteristic picks of MoO₃ could not be observed for low loads (< 20 wt%), likely indicating a high dispersion of metal oxide over the support. The specific surface area along with pores size are decreasing with increasing calcination temperature and MoO₃ loading. The MoO₃ loading does not modify the microstructure. TEM and SEM results for loading inferior to 20 wt% are coherent with a monolayer of MoO₃ on the support as proposed elsewhere. For loading of 20 wt% and more, TEM and Electron diffraction (ED) show nanocrystalline ₃-D MoO₃ particles. The catalytic performances of these catalysts were investigated in the post-discharge of a microwave plasma for NOx formation from N₂/O₂ mixtures. The plasma is sustained by a surface wave launched in a quartz tube via a surfaguide supplied by a 2.45 GHz microwave generator in pulse mode. In-situ identification and quantification of the products were carried out by Fourier-transform infrared spectroscopy (FTIR) in the post-discharge region. FTIR analysis of the exhausted gas reveal NO and NO₂ bands in presence of catalyst while only NO band were assigned without catalyst. On the other hand, in presence of catalyst, a 10% increase of NOₓ formation and of 20% increase in energy efficiency are observed.

Keywords: γ-Al2O₃-MoO₃, µ-waveplasma, N2 fixation, Plasma-catalysis, Plasma diagnostic

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Authors: Boutheina Ben Abdelmoumen Mardassi, Salim Chibani, Safa Boujemaa, Amaury Vaysse, Julien Guglielmini, Elhem Yacoub

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Background and aim: Mycoplasma hominis (MH) is a pathogenic bacterium belonging to the Mollicutes class. It causes a wide range of gynecological infections and infertility among adults. Recently, we have explored for the first time the phylodistribution of Tunisian M. hominis clinical strains using an expanded MLST. We have demonstrated their distinction into two pure lineages, which each corresponding to a specific pathotype: genital infections and infertility. The aim of this project is to gain further insight into the evolutionary dynamics and the specific genetic factors that distinguish MH pathotypes Methods: Whole genome sequencing of Mycoplasma hominis clinical strains was performed using illumina Miseq. Denovo assembly was performed using a publicly available in-house pipeline. We used prokka to annotate the genomes, panaroo to generate the gene presence matrix and Jolytree to establish the phylogenetic tree. We used treeWAS to identify genetic loci associated with the pathothype of interest from the presence matrix and phylogenetic tree. Results: Our results revealed a clear categorization of the 62 MH clinical strains into two distinct genetic lineages, with each corresponding to a specific pathotype.; gynecological infections and infertility[AV1] . Genome annotation showed that GC content is ranging between 26 and 27%, which is a known characteristic of Mycoplasma genome. Housekeeping genes belonging to the core genome are highly conserved among our strains. TreeWas identified 4 virulence genes associated with the pathotype gynecological infection. encoding for asparagine--tRNA ligase, restriction endonuclease subunit S, Eco47II restriction endonuclease, and transcription regulator XRE (involved in tolerance to oxidative stress). Five genes have been identified that have a statistical association with infertility, tow lipoprotein, one hypothetical protein, a glycosyl transferase involved in capsule synthesis, and pyruvate kinase involved in biofilm formation. All strains harbored an efflux pomp that belongs to the family of multidrug resistance ABC transporter, which confers resistance to a wide range of antibiotics. Indeed many adhesion factors and lipoproteins (p120, p120', p60, p80, Vaa) have been checked and confirmed in our strains with a relatively 99 % to 96 % conserved domain and hypervariable domain that represent 1 to 4 % of the reference sequence extracted from gene bank. Conclusion: In summary, this study led to the identification of specific genetic loci associated with distinct pathotypes in M hominis.

Keywords: mycoplasma hominis, infertility, gynecological infections, virulence genes, antibiotic resistance

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Authors: Atefeh Abdollahi, Maryam Bahreini, Babak Choobi Anzali, Fatemeh Rasooli

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Introduction: Triage becomes the main part of organization of care in Emergency department (ED)s. It is used to describe the sorting of patients for treatment priority in ED. The accurate triage of injured patients has reduced fatalities and improved resource usage. Besides, the nurses’ knowledge and skill are important factors in triage decision-making. The ability to define an appropriate triage level and their need for intervention is crucial to guide to a safe and effective emergency care. Methods: This is a prospective cross-sectional study designed for emergency nurses working in four public university hospitals. Five triage workshops have been conducted every three months for emergency nurses based on a standard triage Emergency Severity Index (ESI) IV slide set - approved by Iranian Ministry of Health. Most influential items on triage performance were discussed through brainstorming in workshops which then, were peer reviewed by five emergency physicians and two head registered nurses expert panel. These factors that might distract nurse’ attention from proper decisions included patients’ past medical diseases, the natural tricks of triage and system failure. After permission had been taken, emergency nurses participated in the study and were given the structured questionnaire. Data were analysed by SPSS 21.0. Results: 92 emergency nurses enrolled in the study. 30 % of nurses reported the past history of chronic disease as the most influential confounding factor to ascertain triage level, other important factors were the history of prior admission, past history of myocardial infarction and heart failure to be 20, 17 and 11 %, respectively. Regarding the concept of difficulties in triage practice, 54.3 % reported that the discussion with patients and family members was difficult and 8.7 % declared that it is hard to stay in a single triage room whole day. Among the participants, 45.7 and 26.1 % evaluated the triage workshops as moderately and highly effective, respectively. 56.5 % reported overcrowding as the most important system-based difficulty. Nurses were mainly doubtful to differentiate between the triage levels 2 and 3 according to the ESI VI system. No significant correlation was found between the work record of nurses in triage and the uncertainty in determining the triage level and difficulties. Conclusion: The work record of nurses hardly seemed to be effective on the triage problems and issues. To correct the deficits, training workshops should be carried out, followed by continuous refresher training and supportive supervision.

Keywords: assessment, education, nurse, triage

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Authors: Brad Fox

Abstract:

Between something and nothing, a bit of both, neither/nor, a figment of the imagination, the womb of the universe - questions of what matter is, where it exists and what it means continue to surge up from the bottom of our concepts and theories. This paper looks at divergences and convergences, intimations and mistranslations, in a lineage of thought that begins with Plato’s Timaeus, travels through Arabic Spain and Syria, finally to end up in the language of science. Up to the 13th century, philosophers in Christian France based such inquiries on a questionable and fragmented translation of the Timaeus by Calcidius, with a commentary that conflated the Platonic concept of khora (‘space’ or ‘void’) with Aristotle’s hyle (‘primal matter’ as derived from ‘wood’ as a building material). Both terms were translated by Calcidius as silva. For 700 years, this was the only source for philosophers of matter in the Latin-speaking world. Bernard Silvestris, in his Cosmographia, exemplifies the concepts developed before new translations from Arabic began to pour into the Latin world from such centers as the court of Toledo. Unlike their counterparts across the Pyrenees, 13th century philosophers in Muslim Spain had access to a broad vocabulary for notions of primal matter. The prolific and visionary theologian, philosopher, and poet Muhyiddin Ibn Arabi could draw on the Ikhwan Al-Safa’s 10th Century renderings of Aristotle, which translated the Greek hyle as the everyday Arabic word maddah, still used for building materials today. He also often used the simple transliteration of hyle as hayula, probably taken from Ibn Sina. The prophet’s son-in-law Ali talked of dust in the air, invisible until it is struck by sunlight. Ibn Arabi adopted this dust - haba - as an expression for an original metaphysical substance, nonexistent but susceptible to manifesting forms. Ibn Arabi compares the dust to a phoenix, because we have heard about it and can conceive of it, but it has no existence unto itself and can be described only in similes. Elsewhere he refers to it as quwwa wa salahiyya - pure potentiality and readiness. The final portion of the paper will compare Bernard and Ibn Arabi’s notions of matter to the recent ontology developed by theoretical physicist and philosopher Karen Barad. Looking at Barad’s work with the work of Nils Bohr, it will argue that there is a rich resonance between Ibn Arabi’s paradoxical conceptions of matter and the quantum vacuum fluctuations verified by recent lab experiments. The inseparability of matter and meaning in Barad recall Ibn Arabi’s original response to Ibn Rushd’s question: Does revelation offer the same knowledge as rationality? ‘Yes and No,’ Ibn Arabi said, ‘and between the yes and no spirit is divided from matter and heads are separated from bodies.’ Ibn Arabi’s double affirmation continues to offer insight into our relationship to momentary experience at its most fundamental level.

Keywords: Karen Barad, Muhyiddin Ibn Arabi, primal matter, Bernard Silvestris

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Authors: Nozar Kishi, Babak Kamrani, Filmon Habte

Abstract:

Natural hazards such as earthquakes and tropical storms, are very frequent and highly destructive in Japan. Japan experiences, every year on average, more than 10 tropical cyclones that come within damaging reach, and earthquakes of moment magnitude 6 or greater. We have developed stochastic catastrophe models to address the risk associated with the entire suite of damaging events in Japan, for use by insurance, reinsurance, NGOs and governmental institutions. KCC’s (Karen Clark and Company) catastrophe models are procedures constituted of four modular segments: 1) stochastic events sets that would represent the statistics of the past events, hazard attenuation functions that could model the local intensity, vulnerability functions that would address the repair need for local buildings exposed to the hazard, and financial module addressing policy conditions that could estimates the losses incurring as result of. The events module is comprised of events (faults or tracks) with different intensities with corresponding probabilities. They are based on the same statistics as observed through the historical catalog. The hazard module delivers the hazard intensity (ground motion or wind speed) at location of each building. The vulnerability module provides library of damage functions that would relate the hazard intensity to repair need as percentage of the replacement value. The financial module reports the expected loss, given the payoff policies and regulations. We have divided Japan into regions with similar typhoon climatology, and earthquake micro-zones, within each the characteristics of events are similar enough for stochastic modeling. For each region, then, a set of stochastic events is developed that results in events with intensities corresponding to annual occurrence probabilities that are of interest to financial communities; such as 0.01, 0.004, etc. The intensities, corresponding to these probabilities (called CE, Characteristics Events) are selected through a superstratified sampling approach that is based on the primary uncertainty. Region specific hazard intensity attenuation functions followed by vulnerability models leads to estimation of repair costs. Extensive economic exposure model addresses all local construction and occupancy types, such as post-linter Shinand Okabe wood, as well as concrete confined in steel, SRC (Steel-Reinforced Concrete), high-rise.

Keywords: typhoon, earthquake, Japan, catastrophe modelling, stochastic modeling, stratified sampling, loss model, ERM

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Authors: Samson Munn, Virginia H. Kim, Huija Chen, Sean Maldonado, Michelle Kim, Paul Koscheski, Babak N. Kalantari, Gregory Eckel, Albert Lee

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In terms of screening mammography quality, neither the portion of reports that advise call-back imaging that should be bilateral versus unilateral nor how much the unilateral call-backs may appropriately diverge from 50–50 (left versus right) is known. Many factors may affect detection laterality: display arrangement, reflections preferentially striking one display location, hanging protocols, seating positions with respect to others and displays, visual field cuts, health, etc. The call-back bilateral fraction may reflect radiologist experience (not in our data) or confidence level. Thus, laterality and bilaterality of call-backs advised in screening mammography reports could be worthy quality metrics. Here, laterality data did not reveal a concern until drilling down to individuals. Bilateral screening mammogram report recommendations by five breast imaging, attending radiologists at Harbor-UCLA Medical Center (Torrance, California) 9/1/15--8/31/16 and 9/1/16--8/31/17 were retrospectively reviewed. Recommended call-backs for bilateral versus unilateral, and for left versus right, findings were counted. Chi-square (χ²) statistic was applied. Year 1: of 2,665 bilateral screening mammograms, reports of 556 (20.9%) recommended call-back, of which 99 (17.8% of the 556) were for bilateral findings. Of the 457 unilateral recommendations, 222 (48.6%) regarded the left breast. Year 2: of 2,106 bilateral screening mammograms, reports of 439 (20.8%) recommended call-back, of which 65 (14.8% of the 439) were for bilateral findings. Of the 374 unilateral recommendations, 182 (48.7%) regarded the left breast. Individual ranges of call-backs that were bilateral were 13.2–23.3%, 10.2–22.5%, and 13.6–17.9%, by year(s) 1, 2, and 1+2, respectively; these ranges were unrelated to experience level; the two-year mean was 15.8% (SD=1.9%). The lowest χ² p value of the group's sidedness disparities years 1, 2, and 1+2 was > 0.4. Regarding four individual radiologists, the lowest p value was 0.42. However, the fifth radiologist disfavored the left, with p values of 0.21, 0.19, and 0.07, respectively; that radiologist had the greatest number of years of experience. There was a concerning, 93% likelihood that bias against left breast findings evidenced by one of our radiologists was not random. Notably, very soon after the period under review, he retired, presented with leukemia, and died. We call for research to be done, particularly by large departments with many radiologists, of two possible, new, quality metrics in screening mammography: laterality and bilaterality. (Images, patient outcomes, report validity, and radiologist psychological confidence levels were not assessed. No intervention nor subsequent data collection was conducted. This uncomplicated collection of data and simple appraisal were not designed, nor had there been any intention to develop or contribute, to generalizable knowledge (per U.S. DHHS 45 CFR, part 46)).

Keywords: mammography, screening mammography, quality, quality metrics, laterality

Procedia PDF Downloads 140

Authors: Alexander Harrison Greer, Edward King, Elijah Lee, Safa Obuz, Ruhao Sun, Aditya Sardesai, Toby Ma, Daniel Chow, Bryce Broadus, Calvin Costner, Troy Barnes, Biagio DeSimone, Yeshwin Sankuratri, Yiheng Chen, Holly Golecki

Abstract:

Although a relatively new field, soft robotics is experiencing a rise in applicability in the secondary school setting through The Soft Robotics Toolkit, shared fabrication resources and a design competition. Exposing students outside of university research groups to this rapidly growing field allows for development of the soft robotics industry in new and imaginative ways. Soft robotic actuators have remained difficult to implement in classrooms because of their relative cost or difficulty of fabrication. Traditionally, a two-part molding system is used; however, this configuration often results in delamination. In an effort to make soft robotics more accessible to young students, we aim to develop a simple, single-mold method of fabricating soft robotic actuators from common household materials. These actuators are made by embedding a soluble polymer insert into silicone. These inserts can be made from hand-cut polystyrene, 3D-printed polyvinyl alcohol (PVA) or acrylonitrile butadiene styrene (ABS), or molded sugar. The insert is then dissolved using an appropriate solvent such as water or acetone, leaving behind a negative form which can be pneumatically actuated. The resulting actuators are seamless, eliminating the instability of adhering multiple layers together. The benefit of this approach is twofold: it simplifies the process of creating a soft robotic actuator, and in turn, increases its effectiveness and durability. To quantify the increased durability of the single-mold actuator, it was tested against the traditional two-part mold. The single-mold actuator could withstand actuation at 20psi for 20 times the duration when compared to the traditional method. The ease of fabrication of these actuators makes them more accessible to hobbyists and students in classrooms. After developing these actuators, they were applied, in collaboration with a ceramics teacher at our school, to a glove used to transfer nuanced hand motions used to throw pottery from an expert artist to a novice. We quantified the improvement in the users’ pottery-making skill when wearing the glove using image analysis software. The seamless actuators proved to be robust in this dynamic environment. Seamless soft robotic actuators created by high school students show the applicability of the Soft Robotics Toolkit for secondary STEM education and outreach. Making students aware of what is possible through projects like this will inspire the next generation of innovators in materials science and robotics.

Keywords: pneumatic actuator fabrication, soft robotic glove, soluble polymers, STEM outreach

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Authors: Safa Ladhari, Alireza Saidi, Phuong Nguyen-Tri

Abstract:

During health crises, such as COVID-19, using disposable protective equipment (PEs) (masks, gowns, etc.) causes long-term problems, increasing the volume of hazardous waste that must be handled safely and expensively. Therefore, producing textiles for antimicrobial and reusable materials is highly desirable to decrease the use of disposable PEs that should be treated as hazardous waste. In addition, if these items are used regularly in the workplace or for daily activities by the public, they will most likely end up in household waste. Furthermore, they may pose a high risk of contagion to waste collection workers if contaminated. Therefore, to protect the whole population in times of sanitary crisis, it is necessary to equip these materials with tools that make them resilient to the challenges of carrying out daily activities without compromising public health and the environment and without depending on them external technologies and producers. In addition, the materials frequently used for EPs are plastics of petrochemical origin. The subject of the present work is replacing petroplastics with bioplastic since it offers better biodegradability. The chosen polymer is polyhydroxybutyrate (PHB), a family of polyhydroxyalkanoates synthesized by different bacteria. It has similar properties to conventional plastics. However, it is renewable, biocompatible, and has attractive barrier properties compared to other polyesters. These characteristics make it ideal for EP protection applications. The current research topic focuses on the preparation and rapid evaluation of the biological activity of nanotechnology-based antimicrobial agents to treat textile surfaces used for PE. This work will be carried out to provide antibacterial solutions that can be transferred to a workplace application in the fight against short-term biological risks. Three main objectives are proposed during this research topic: 1) the development of suitable methods for the deposition of antibacterial agents on the surface of textiles; 2) the development of a method for measuring the antibacterial activity of the prepared textiles and 3) the study of the biodegradability of the prepared textiles. The studied textile is a non-woven fabric based on a biodegradable polymer manufactured by the electrospinning method. Indeed, nanofibers are increasingly studied due to their unique characteristics, such as high surface-to-volume ratio, improved thermal, mechanical, and electrical properties, and confinement effects. The electrospun film will be surface modified by plasma treatment and then loaded with hybrid antibacterial silver and titanium dioxide nanoparticles by the dip-coating method. This work uses simple methods with emerging technologies to fabricate nanofibers with suitable size and morphology to be used as components for protective equipment. The antibacterial agents generally used are based on silver, zinc, copper, etc. However, to our knowledge, few researchers have used hybrid nanoparticles to ensure antibacterial activity with biodegradable polymers. Also, we will exploit visible light to improve the antibacterial effectiveness of the fabric, which differs from the traditional contact mode of killing bacteria and presents an innovation of active protective equipment. Finally, this work will allow for the innovation of new antibacterial textile materials through a simple and ecological method.

Keywords: protective equipment, antibacterial textile materials, biodegradable polymer, electrospinning, hybrid antibacterial nanoparticles

Procedia PDF Downloads 56

Authors: Babak Forouraghi

Abstract:

A genetic circuit is a collection of interacting genes and proteins that enable individual cells to implement and perform vital biological functions such as cell division, growth, death, and signaling. In cell engineering, synthetic gene circuits are engineered networks of genes specifically designed to implement functionalities that are not evolved by nature. These engineered networks enable scientists to tackle complex problems such as engineering cells to produce therapeutics within the patient's body, altering T cells to target cancer-related antigens for treatment, improving antibody production using engineered cells, tissue engineering, and production of genetically modified plants and livestock. Construction of computational models to realize genetic circuits is an especially challenging task since it requires the discovery of flow of genetic information in complex biological systems. Building synthetic biological models is also a time-consuming process with relatively low prediction accuracy for highly complex genetic circuits. The primary goal of this study was to investigate the utility of a pre-trained bidirectional encoder transformer that can accurately predict gene expressions in genetic circuit designs. The main reason behind using transformers is their innate ability (attention mechanism) to take account of the semantic context present in long DNA chains that are heavily dependent on spatial representation of their constituent genes. Previous approaches to gene circuit design, such as CNN and RNN architectures, are unable to capture semantic dependencies in long contexts as required in most real-world applications of synthetic biology. For instance, RNN models (LSTM, GRU), although able to learn long-term dependencies, greatly suffer from vanishing gradient and low-efficiency problem when they sequentially process past states and compresses contextual information into a bottleneck with long input sequences. In other words, these architectures are not equipped with the necessary attention mechanisms to follow a long chain of genes with thousands of tokens. To address the above-mentioned limitations of previous approaches, a transformer model was built in this work as a variation to the existing DNA Bidirectional Encoder Representations from Transformers (DNABERT) model. It is shown that the proposed transformer is capable of capturing contextual information from long input sequences with attention mechanism. In a previous work on genetic circuit design, the traditional approaches to classification and regression, such as Random Forrest, Support Vector Machine, and Artificial Neural Networks, were able to achieve reasonably high R2 accuracy levels of 0.95 to 0.97. However, the transformer model utilized in this work with its attention-based mechanism, was able to achieve a perfect accuracy level of 100%. Further, it is demonstrated that the efficiency of the transformer-based gene expression classifier is not dependent on presence of large amounts of training examples, which may be difficult to compile in many real-world gene circuit designs.

Keywords: transformers, generative ai, gene expression design, classification

Procedia PDF Downloads 39

Authors: Babak Forouraghi

Abstract:

A genetic circuit is a collection of interacting genes and proteins that enable individual cells to implement and perform vital biological functions such as cell division, growth, death, and signaling. In cell engineering, synthetic gene circuits are engineered networks of genes specifically designed to implement functionalities that are not evolved by nature. These engineered networks enable scientists to tackle complex problems such as engineering cells to produce therapeutics within the patient's body, altering T cells to target cancer-related antigens for treatment, improving antibody production using engineered cells, tissue engineering, and production of genetically modified plants and livestock. Construction of computational models to realize genetic circuits is an especially challenging task since it requires the discovery of the flow of genetic information in complex biological systems. Building synthetic biological models is also a time-consuming process with relatively low prediction accuracy for highly complex genetic circuits. The primary goal of this study was to investigate the utility of a pre-trained bidirectional encoder transformer that can accurately predict gene expressions in genetic circuit designs. The main reason behind using transformers is their innate ability (attention mechanism) to take account of the semantic context present in long DNA chains that are heavily dependent on the spatial representation of their constituent genes. Previous approaches to gene circuit design, such as CNN and RNN architectures, are unable to capture semantic dependencies in long contexts, as required in most real-world applications of synthetic biology. For instance, RNN models (LSTM, GRU), although able to learn long-term dependencies, greatly suffer from vanishing gradient and low-efficiency problem when they sequentially process past states and compresses contextual information into a bottleneck with long input sequences. In other words, these architectures are not equipped with the necessary attention mechanisms to follow a long chain of genes with thousands of tokens. To address the above-mentioned limitations, a transformer model was built in this work as a variation to the existing DNA Bidirectional Encoder Representations from Transformers (DNABERT) model. It is shown that the proposed transformer is capable of capturing contextual information from long input sequences with an attention mechanism. In previous works on genetic circuit design, the traditional approaches to classification and regression, such as Random Forrest, Support Vector Machine, and Artificial Neural Networks, were able to achieve reasonably high R2 accuracy levels of 0.95 to 0.97. However, the transformer model utilized in this work, with its attention-based mechanism, was able to achieve a perfect accuracy level of 100%. Further, it is demonstrated that the efficiency of the transformer-based gene expression classifier is not dependent on the presence of large amounts of training examples, which may be difficult to compile in many real-world gene circuit designs.

Keywords: machine learning, classification and regression, gene circuit design, bidirectional transformers

Procedia PDF Downloads 39