Search results for: Babak Qasemi-Panahi

Authors: Babak Nemat

Abstract:

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: 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: 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: 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: Nozar Kishi, Babak Kamrani, Filmon Habte

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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

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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

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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

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