Search results for: genetic diagnosis

Authors: Ibrahim M Hassan, Lorna Que, Michael Rutland

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Type I SOD is usually diagnosed by anatomical imaging such as ultrasound, CT and MRCP. However, the types II and III SOD yield negative results despite the presence of significant symptoms. In particular, the type III is difficult to diagnose due to the absence of significant biochemical or anatomical abnormalities. Nuclear Medicine can aid in this diagnostic dilemma by demonstrating functional changes in the bile flow. Low dose Morphine (0.04mg/Kg) stimulates the tone of the sphincter of Oddi (SO) and its usefulness has been shown in diagnosing SOD by causing a delay in bile flow when compared to a non morphine provoked - baseline scan. This work expands on that process by using sublingual GTN at 60 minutes post tracer and morphine injection to relax the SO and induce an improvement in bile outflow, and in some cases show immediate relief of morphine induced abdominal pain. The criteria for positive SOD are as follows: if during the first hour of the morphine provocation showed (1) delayed intrahepatic biliary ducts tracer accumulation; plus (2) delayed appearance but persistent retention of activity in the common bile duct, and (3) delayed bile flow into the duodenum. In addition, patients who required GTN within the first hour to relieve abdominal pain were regarded as highly supportive of the diagnosis. Retrospective analysis of 85 patients (pts) (78F and 6M) referred for suspected SOD (type III) who had been intensively investigated because of recurrent right upper quadrant or abdominal pain post cholecystectomy. 99mTc-HIDA scan with morphine-provocation is performed followed by GTN at 60 minutes post tracer injection and a further thirty minutes of dynamic imaging are acquired. 30 pts were negative. 55 pts were regarded as positive for SOD and 38/55 (60%) of these patients with an abnormal result were further evaluated with a baseline 99mTc-HIDA. As expected, all 38 pts showed better bile flow characteristics than during the morphine provocation. 20/55 (36%) patients were treated by ERCP sphincterotomy and the rest were managed conservatively by medical therapy. In all cases regarded as positive for SOD, the sublingual GTN at 60 minutes showed immediate improvement in bile flow. 11/55(20%) who developed severe post-morphine abdominal pain were relieved by GTN almost instantaneously. We propose that GTN is a useful agent in the diagnosis of SOD when performing 99mTc-HIDA scan and that the satisfactory response to the sublingual GTN could offer additional information in patients who have severe pain at the time the procedure or when presenting to the emergency unit because of biliary pain. And also in determining whether a trial of medical therapy may be used before considering surgery.

Keywords: GTN, HIDA, MORPHINE, SOD

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Authors: Fatima Mokeddem

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The phonocardiogram signal (PCG) is a physiological signal that reflects heart mechanical activity, is a promising tool for curious researchers in this field because it is full of indications and useful information for medical diagnosis. PCG segmentation is a basic step to benefit from this signal. Therefore, this paper presents an algorithm that serves the separation of heart sounds and heart murmurs in case they exist in order to use them in several applications and heart sounds analysis. The separation process presents here is founded on three essential steps filtering, envelope detection, and heart sounds segmentation. The algorithm separates the PCG signal into S1 and S2 and extract cardiac murmurs.

Keywords: phonocardiogram signal, filtering, Envelope, Detection, murmurs, heart sounds

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Authors: Mohammad A. Obeidat, Ayman M. Mansour

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Capturing the dynamic behavior of the heart to improve control performance, enhance robustness, and support diagnosis is very important in establishing real time models for the heart. Control Techniques and strategies have been utilized to improve system costs, reliability, and estimation accuracy for different types of systems such as biomedical, industrial, and other systems that required tuning input/output relation and/or monitoring. Simulations are performed to illustrate potential applications of the technology. In this research, a new control technology scheme is used to enhance the performance of the Af system and meet the design specifications.

Keywords: atrial fibrillation, dynamic behavior, closed loop, signal, filter

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Authors: Manisha, Manisha Mathur, Jay K. Desai, Shesh Asopa, Manisha Mehra

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The present study was carried out for the comprehensive analysis of lumpy skin disease (LSD) in cattle and to elucidate the histopathology of vital organs in natural outbreaks. Lumpy skin disease (LSD) is a viral infection that primarily affects cattle. It is caused by a Capri pox virus and is characterized by the formation of skin nodules or lesions. For this study, a postmortem of 20 cows who died of Lumpy skin disease in different regions of Rajasthan was conducted. This study aimed to examine a cow's external and internal organs to confirm if lumpy skin disease was the cause of death. Accurate diagnosis is essential for improving disease surveillance, understanding the disease's progression, and informing control measures. Pathological examinations reveal virus-induced changes across organs, while histopathological analyses provide crucial insights into the disease's pathogenesis, aiding in the development of advanced diagnostics and effective prevention strategies. Histopathological examination of nodular skin lesions revealed edema, hyperemia, acanthosis, severe hydropic degeneration/ballooning degeneration, and hyperkeratosis in the epidermis. In the lungs, congestion, oedema, emphysema, and atelectasis were observed grossly. Microscopically changes were suggestive of interstitial pneumonia, suppurative pneumonia, bronchopneumonia post pneumonic fibrosis, and stage of resolution. Grossely liver showed congestion and necrotic foci microscopically in most of the cases, and the liver showed acute viral hepatitis. Microscopically in kidneys, multifocal interstitial nephritis was observed. There was marked interstitial inflammation and zonal fibrosis with cystically dilated tubules and bowman's capsules. Microscopically, most of the heart tissue section showed normal histology with few sarcocysts in between cardiac muscles. In some cases, loss of cross striation, sarcoplasmic vacuolation, fregmentation, and disintegration of cardiac fibres were observed. The present study revealed the characteristic gross and histopathological changes in different organs in natural cases of lumpy skin disease. Further, the disease was confirmed based on the molecular diagnosis and transmission electron microscopy of capripox infection in the affected cattle in the study area.

Keywords: Capripoxvirus, lumpy skin disease, polymerage chain reaction, transmission electron microscopy

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Authors: Getachew Weldemichael, Sentayehu Alamerew, Leta Tulu, Gezahegn Berecha

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Coffee quality improvement program is becoming the focus of coffee research, as the world coffee consumption pattern shifted to high-quality coffee. However, there is limited information on the genetic variation of C. Arabica for quality improvement in potential specialty coffee growing areas of Ethiopia. Therefore, this experiment was conducted with the objectives of determining the magnitude of variation among 105 coffee accessions collected from east Wollega coffee growing areas and assessing correlations between the different coffee qualities attributes. It was conducted in RCRD with three replications. Data on green bean physical characters (shape and make, bean color and odor) and organoleptic cup quality traits (aromatic intensity, aromatic quality, acidity, astringency, bitterness, body, flavor, and overall standard of the liquor) were recorded. Analysis of variance, clustering, genetic divergence, principal component and correlation analysis was performed using SAS software. The result revealed that there were highly significant differences (P<0.01) among the accessions for all quality attributes except for odor and bitterness. Among the tested accessions, EW104 /09, EW101 /09, EW58/09, EW77/09, EW35/09, EW71/09, EW68/09, EW96 /09, EW83/09 and EW72/09 had the highest total coffee quality values (the sum of bean physical and cup quality attributes). These genotypes could serve as a source of genes for green bean physical characters and cup quality improvement in Arabica coffee. Furthermore, cluster analysis grouped the coffee accessions into five clusters with significant inter-cluster distances implying that there is moderate diversity among the accessions and crossing accessions from these divergent inter-clusters would result in hetrosis and recombinants in segregating generations. The principal component analysis revealed that the first three principal components with eigenvalues greater than unity accounted for 83.1% of the total variability due to the variation of nine quality attributes considered for PC analysis, indicating that all quality attributes equally contribute to a grouping of the accessions in different clusters. Organoleptic cup quality attributes showed positive and significant correlations both at the genotypic and phenotypic levels, demonstrating the possibility of simultaneous improvement of the traits. Path coefficient analysis revealed that acidity, flavor, and body had a high positive direct effect on overall cup quality, implying that these traits can be used as indirect criteria to improve overall coffee quality. Therefore, it was concluded that there is considerable variation among the accessions, which need to be properly conserved for future improvement of the coffee quality. However, the variability observed for quality attributes must be further verified using biochemical and molecular analysis.

Keywords: accessions, Coffea arabica, cluster analysis, correlation, principal component

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Authors: Ron Dick, P. S. D. V. Prasadarao, Glenn Coltman

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Agenesis of the corpus callosum (ACC) is a failure to develop corpus callosum - the large bundle of fibers of the brain that connects the two cerebral hemispheres. It can occur as a partial or complete absence of the corpus callosum. In the general population, its estimated prevalence rate is 1 in 4000 and a wide range of genetic, infectious, vascular, and toxic causes have been attributed to this heterogeneous condition. The diagnosis of ACC is often achieved by neuroimaging procedures. Though persons with ACC can perform normally on intelligence tests they generally present with a range of neuropsychological and social deficits. The deficit profile is characterized by poor coordination of motor movements, slow reaction time, processing speed and, poor memory. Socially, they present with deficits in communication, language processing, the theory of mind, and interpersonal relationships. The present paper illustrates the role of neuropsychological assessment with implications to psychosocial management in a case of agenesis of the corpus callosum. Method: A 27-year old left handed Caucasian male with a history of ACC was self-referred for a neuropsychological assessment to assist him in his employment options. Parents noted significant difficulties with coordination and balance at an early age of 2-3 years and he was diagnosed with dyspraxia at the age of 14 years. History also indicated visual impairment, hypotonia, poor muscle coordination, and delayed development of motor milestones. MRI scan indicated agenesis of the corpus callosum with ventricular morphology, widely spaced parallel lateral ventricles and mild dilatation of the posterior horns; it also showed colpocephaly—a disproportionate enlargement of the occipital horns of the lateral ventricles which might be affecting his motor abilities and visual defects. The MRI scan ruled out other structural abnormalities or neonatal brain injury. At the time of assessment, the subject presented with such problems as poor coordination, slowed processing speed, poor organizational skills and time management, and difficulty with social cues and facial expressions. A comprehensive neuropsychological assessment was planned and conducted to assist in identifying the current neuropsychological profile to facilitate the formulation of a psychosocial and occupational rehabilitation programme. Results: General intellectual functioning was within the average range and his performance on memory-related tasks was adequate. Significant visuospatial and visuoconstructional deficits were evident across tests; constructional difficulties were seen in tasks such as copying a complex figure, building a tower and manipulating blocks. Poor visual scanning ability and visual motor speed were evident. Socially, the subject reported heightened social anxiety, difficulty in responding to cues in the social environment, and difficulty in developing intimate relationships. Conclusion: Persons with ACC are known to present with specific cognitive deficits and problems in social situations. Findings from the current neuropsychological assessment indicated significant visuospatial difficulties, poor visual scanning and problems in social interactions. His general intellectual functioning was within the average range. Based on the findings from the comprehensive neuropsychological assessment, a structured psychosocial rehabilitation programme was developed and recommended.

Keywords: agenesis, callosum, corpus, neuropsychology, psychosocial, rehabilitation

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Authors: Abdulrahman Algaeed

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The Ophthalmic Ultrasound is the easiest method of early diagnosing Retinoblastoma after clinical examination. It can be done with ease without sedation. King Khaled Eye Specialist Hospital is a tertiary care center where Retinoblastoma patients are often seen and treated there. The first modality to rule out the disease is Ophthalmic Ultrasound. Classic Retinoblastoma is easily diagnosed by using the conventional 10MHz Ophthalmic Ultrasound probe in the regular clinic setup. Retinal lesion with multiple, very highly reflective surfaces within lesion typical of Calcium deposits. The use of Standardized A-scan is very useful where internal reflectivity is classified as very highly reflective. Color Doppler is extremely useful as well to show the blood flow within lesion/s. In conclusion: Ophthalmic Ultrasound should be the first tool to be used to diagnose Retinoblastoma after clinical examination. The accuracy of the Exam is very high.

Keywords: doppler, retinoblastoma, reflectivity, ultrasound

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Authors: Retno Supriyanti, Teguh Budiono, Yogi Ramadhani, Haris B. Widodo, Arwita Mulyawati

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Cervical cancer is the leading cause of mortality in cancer-related diseases. In this diagnosis doctors usually perform several tests to determine the presence of cervical cancer in a patient. However, these checks require support equipment to get the results in more detail. One is by using ultrasonography. However, for the developing countries most of the existing ultrasonography has a low resolution. The goal of this research is to obtain abnormalities on low-resolution ultrasound images especially for cervical cancer case. In this paper, we emphasize our work to use Image Enhancement for pre-processing image quality improvement. The result shows that pre-processing stage is promising to support further analysis.

Keywords: cervical cancer, mortality, low-resolution, image enhancement.

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Authors: Noelene Rose

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The DSM has been plagued with conceptual issues since its inception, not least discriminant validity and comorbidity issues. An attempt to remain a-theoretical in the divide between the psycho-dynamicists and the behaviourists contributed to much of this, in particular relating to the Personality Disorders. With the DSM-5, although the criterion have remained unchanged, major conceptual and structural directions have been flagged and proposed in section III. The biggest changes concern the Personality Disorders. While Narcissistic Personality Disorder (NPD) was initially tagged for removal, instead the addition of section III proposes a move away from a categorical approach to a more dimensional approach, with a measure of Global Function of Personality. This global measure is an assessment of impairment of self-other relations; a measure of trait narcissism. In the same way mainstream psychology has struggled in its diagnosis of narcissism, so too in its treatment. Kohut’s self psychology represents the most significant inroad in theory and treatment for the narcissistic disorders. Kohut had moved away from a categorical system, towards disorders of the self. According to this theory, disorders of the self are the result of childhood trauma (impaired attunement) resulting in a developmental arrest. Self-psychological, Psychodynamic treatment of narcissism, however, is expensive, in time and money and outside the awareness or access of most people. There is more than a suggestion that narcissism is on the increase, created in trauma and worsened by a fearful world climate. A dimensional model of narcissism, from mild to severe, requires cut off points for diagnosis. But where do we draw the line? Mainstream psychology is inclined to set it high when there is some degree of impairment in functioning in daily life. Transpersonal Psychology is inclined to set it low, with the concept that we all have some degree of narcissism and that it is the point and the path of our life journey to transcend our focus on our selves. Mainstream psychology stops its focus on trait narcissism with a healthy level of self esteem, but it is at this point that Transpersonal Psychology can complement the discussion. From a Transpersonal point of view, failure to begin the process of self-transcendence will also create emotional symptoms of meaning or purpose, often later in our lives, and is also conceived of as a developmental arrest. The maps for this transcendence are hidden in plain sight; in the chakras of kundalini yoga, in the sacraments of the Catholic Church, in the Kabbalah tree of life of Judaism, in Maslow’s hierarchy of needs, to name a few. This paper outlines some proposed research exploring the use of daily practices that can be incorporated into the therapy room; practices that utilise meditation, visualisation and imagination: that are informed by spiritual technology and guided by the psychodynamic theory of Self Psychology.

Keywords: narcissism, self-psychology, self-practice, self-transcendence

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Authors: Efrain Rodriguez, Cristhian Riano, Alberto Alvares

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In recent years, robots manipulators with parallel architectures are used in additive manufacturing processes – 3D printing. These robots have advantages such as speed and lightness that make them suitable to help with the efficiency and productivity of these processes. Consequently, the interest for the development of parallel robots for additive manufacturing applications has increased. This article deals with the conceptual design and dimensional synthesis of the linear delta robot for additive manufacturing. Firstly, a methodology based on structured processes for the development of products through the phases of informational design, conceptual design and detailed design is adopted: a) In the informational design phase the Mudge diagram and the QFD matrix are used to aid a set of technical requirements, to define the form, functions and features of the robot. b) In the conceptual design phase, the functional modeling of the system through of an IDEF0 diagram is performed, and the solution principles for the requirements are formulated using a morphological matrix. This phase includes the description of the mechanical, electro-electronic and computational subsystems that constitute the general architecture of the robot. c) In the detailed design phase, a digital model of the robot is drawn on CAD software. A list of commercial and manufactured parts is detailed. Tolerances and adjustments are defined for some parts of the robot structure. The necessary manufacturing processes and tools are also listed, including: milling, turning and 3D printing. Secondly, a dimensional synthesis method applied on design of the linear delta robot is presented. One of the most important key factors in the design of a parallel robot is the useful workspace, which strongly depends on the joint space, the dimensions of the mechanism bodies and the possible interferences between these bodies. The objective function is based on the verification of the kinematic model for a prescribed cylindrical workspace, considering geometric constraints that possibly lead to singularities of the mechanism. The aim is to determine the minimum dimensional parameters of the mechanism bodies for the proposed workspace. A method based on genetic algorithms was used to solve this problem. The method uses a cloud of points with the cylindrical shape of the workspace and checks the kinematic model for each of the points within the cloud. The evolution of the population (point cloud) provides the optimal parameters for the design of the delta robot. The development process of the linear delta robot with optimal dimensions for additive manufacture is presented. The dimensional synthesis enabled to design the mechanism of the delta robot in function of the prescribed workspace. Finally, the implementation of the robotic platform developed based on a linear delta robot in an additive manufacturing application using the Fused Deposition Modeling (FDM) technique is presented.

Keywords: additive manufacturing, delta parallel robot, dimensional synthesis, genetic algorithms

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Authors: Bouchaïb Gazzaz, Hamid El Amri, Hind Dehbi, Abderraouf Hilali

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Medical cannabis has been cultivated and used in many countries around the world. The story of the use of cannabis as a therapeutic agent is difficult to trace, in particular, because the laws regulating its production, distribution, possession, and consumption are relatively recent. Nowadays, in countries where it is authorized, medical cannabis is used in a very wide variety of illnesses and pathologies, particularly in cancer cures. Presently, cannabinoid receptor agonists (like nabilone and dronabinol) are used for reducing chemotherapy induced vomiting. This review aims to discuss a recent finding on the use of therapeutic cannabis in patients with cancer. First, this work addresses the progress made in the use of cannabinoids as therapeutic agent and their application in the treatment of different types of cancer. Secondly, a detailed analysis of the pharmacogenetic aspect of cannabis will be discussed.

Keywords: cannabinoids, endocannabinoids system, cancer treatment, cannabinoid receptors, genetic polymorphism, pharmacogenomics

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Authors: Dost Muhammad Halepoto, Laila AL-Ayadhi

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Neurodevelopmental disorders such as autism can cause lifelong disability. Genetic and environmental factors are believed to contribute to the development of autism spectrum disorder (ASD), but relatively few studies have considered potential environmental risks. Several industrial chemicals and other environmental exposures are recognized causes of neurodevelopmental disorders and subclinical brain dysfunction. The toxic effects of such chemicals in the developing human brain are not known. This review highlights the role of environmental risk factors including drugs, toxic chemicals, heavy metals, pesticides, vaccines, and other suspected neurotoxicants including persistent organic pollutants for ASD. It also provides information about the environmental toxins to yield new insights into factors that affect autism risk as well as an opportunity to investigate the relation between autism and environmental exposure.

Keywords: Autism Spectrum Disorder, ASD, environmental factors, neurodevelopmental disorder

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Authors: O. Adjoul, A. Feugier, K. Benfriha, A. Aoussat

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In general, issues related to design and maintenance are considered in an independent manner. However, the decisions made in these two sets influence each other. The design for maintenance is considered an opportunity to optimize the life cycle cost of a product, particularly in the nuclear or aeronautical field, where maintenance expenses represent more than 60% of life cycle costs. The design of large-scale systems starts with product architecture, a choice of components in terms of cost, reliability, weight and other attributes, corresponding to the specifications. On the other hand, the design must take into account maintenance by improving, in particular, real-time monitoring of equipment through the integration of new technologies such as connected sensors and intelligent actuators. We noticed that different approaches used in the Design For Maintenance (DFM) methods are limited to the simultaneous characterization of the reliability and maintainability of a multi-component system. This article proposes a method of DFM that assists designers to propose dynamic maintenance for multi-component industrial systems. The term "dynamic" refers to the ability to integrate available monitoring data to adapt the maintenance decision in real time. The goal is to maximize the availability of the system at a given life cycle cost. This paper presents an approach for simultaneous optimization of the design and maintenance of multi-component systems. Here the design is characterized by four decision variables for each component (reliability level, maintainability level, redundancy level, and level of monitoring data). The maintenance is characterized by two decision variables (the dates of the maintenance stops and the maintenance operations to be performed on the system during these stops). The DFM model helps the designers choose technical solutions for the large-scale industrial products. Large-scale refers to the complex multi-component industrial systems and long life-cycle, such as trains, aircraft, etc. The method is based on a two-level hybrid algorithm for simultaneous optimization of design and maintenance, using genetic algorithms. The first level is to select a design solution for a given system that considers the life cycle cost and the reliability. The second level consists of determining a dynamic and optimal maintenance plan to be deployed for a design solution. This level is based on the Maintenance Free Operating Period (MFOP) concept, which takes into account the decision criteria such as, total reliability, maintenance cost and maintenance time. Depending on the life cycle duration, the desired availability, and the desired business model (sales or rental), this tool provides visibility of overall costs and optimal product architecture.

Keywords: availability, design for maintenance (DFM), dynamic maintenance, life cycle cost (LCC), maintenance free operating period (MFOP), simultaneous optimization

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Authors: Alexander Heckman, Rohan Goswami, Zachi Attia, Paul Friedman, Peter Noseworthy, Demilade Adedinsewo, Pablo Moreno-Franco, Rickey Carter, Tathagat Narula

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Background: Postoperative atrial fibrillation (POAF) is associated with adverse health consequences, higher costs, and longer hospital stays. Utilizing existing predictive models that rely on clinical variables and circulating biomarkers, multiple societies have published recommendations on the treatment and prevention of POAF. Although reasonably practical, there is room for improvement and automation to help individualize treatment strategies and reduce associated complications. Methods and Results: In this retrospective cohort study of solid organ transplant recipients, we evaluated the diagnostic utility of a previously developed AI-based ECG prediction for silent AF on the development of POAF within 30 days of transplant. A total of 2261 non-cardiac transplant patients without a preexisting diagnosis of AF were found to have a 5.8% (133/2261) incidence of POAF. While there were no apparent sex differences in POAF incidence (5.8% males vs. 6.0% females, p=.80), there were differences by race and ethnicity (p<0.001 and 0.035, respectively). The incidence in white transplanted patients was 7.2% (117/1628), whereas the incidence in black patients was 1.4% (6/430). Lung transplant recipients had the highest incidence of postoperative AF (17.4%, 37/213), followed by liver (5.6%, 56/1002) and kidney (3.6%, 32/895) recipients. The AUROC in the sample was 0.62 (95% CI: 0.58-0.67). The relatively low discrimination may result from undiagnosed AF in the sample. In particular, 1,177 patients had at least 1 AI-ECG screen for AF pre-transplant above .10, a value slightly higher than the published threshold of 0.08. The incidence of POAF in the 1104 patients without an elevated prediction pre-transplant was lower (3.7% vs. 8.0%; p<0.001). While this supported the hypothesis that potentially undiagnosed AF may have contributed to the diagnosis of POAF, the utility of the existing AI-ECG screening algorithm remained modest. When the prediction for POAF was made using the first postoperative ECG in the sample without an elevated screen pre-transplant (n=1084 on account of n=20 missing postoperative ECG), the AUROC was 0.66 (95% CI: 0.57-0.75). While this discrimination is relatively low, at a threshold of 0.08, the AI-ECG algorithm had a 98% (95% CI: 97 – 99%) negative predictive value at a sensitivity of 66% (95% CI: 49-80%). Conclusions: This study's principal finding is that the incidence of POAF is rare, and a considerable fraction of the POAF cases may be latent and undiagnosed. The high negative predictive value of AI-ECG screening suggests utility for prioritizing monitoring and evaluation on transplant patients with a positive AI-ECG screening. Further development and refinement of a post-transplant-specific algorithm may be warranted further to enhance the diagnostic yield of the ECG-based screening.

Keywords: artificial intelligence, atrial fibrillation, cardiology, transplant, medicine, ECG, machine learning

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Authors: Steven Robinson, Adriana Dager, Param Patel

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Wandering spleen is a rare variant where there is abnormal development of the ligamentous peritoneal attachments of the spleen which normally anchor it in the left upper quadrant of the abdomen. Ligamentous abnormalities can be congenital, or acquired through pregnancy, injury, or iatrogenic causes. Absence or laxity of these ligaments allows migration of the spleen into ectopic portions of the abdomen, which is also associated with an elongated vascular pedicle. Incidence of wandering spleen is reported at less than 0.25% with a female to male ratio of approximately 6:1. The most common complication of a wandering spleen is torsion around its vascular pedicle which can lead to thrombosis and infarction. Torsion of a wandering spleen is a rare but important cause of an acute abdomen. Imaging, and specifically CT or ultrasound, is crucial in the diagnosis. We present a case of a torsed wandering spleen which was treated with splenectomy.

Keywords: Wandering Spleen, Torsion, Splenic Torsion, Spleen

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Authors: Adel Bessadok

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The theory of values postulates that each human has a set of values, or attractive and trans-situational goals, that drive their actions. The Basic Human Values as an incentive construct that apprehends human's values have been shown to govern a wide range of human behaviors. Individuals within and within societies have very different value preferences that reflect their enculturation, their personal experiences, their social places and their genetic heritage. Using a focus group composed by Islamic religious Preachers and a sample of 800 young students; this ongoing study will establish Moderate Islamic Values parameters. We analyze later, for the same students sample the difference between Moderate Islamic Values and Schwartz’s Basic Human Values. Keywords—Moderate Islamic Values, Basic Human Values, Exploratory Factor Analysis and Confirmatory Factor Analysis.

Keywords: moderate Islamic values, basic human values, exploratory factor analysis, confirmatory factor analysis

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Authors: Murray David Schane

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Though years of clinical encounters with patients with autism spectrum disorders and those with a schizoid personality the many defining diagnostic features shared between these conditions have been explored and current neurobiological differences have been reviewed; and, critical and different treatment strategies for each have been devised. The paper compares and contrasts the apparent similarities between autism spectrum disorders and the schizoid personality are found in these DSM descriptive categories: restricted range of social-emotional reciprocity; poor non-verbal communicative behavior in social interactions; difficulty developing and maintaining relationships; detachment from social relationships; lack of the desire for or enjoyment of close relationships; and preference for solitary activities. In this paper autism, fundamentally a communicative disorder, is revealed to present clinically as a pervasive aversive response to efforts to engage with or be engaged by others. Autists with the Asperger presentation typically have language but have difficulty understanding humor, irony, sarcasm, metaphoric speech, and even narratives about social relationships. They also tend to seek sameness, possibly to avoid problems of social interpretation. Repetitive behaviors engage many autists as a screen against ambient noise, social activity, and challenging interactions. Also in this paper, the schizoid personality is revealed as a pattern of social avoidance, self-sufficiency and apparent indifference to others as a complex psychological defense against a deep, long-abiding fear of appropriation and perverse manipulation. Neither genetic nor MRI studies have yet located the explanatory data that identifies the cause or the neurobiology of autism. Similarly, studies of the schizoid have yet to group that condition with those found in schizophrenia. Through presentations of clinical examples, the treatment of autists of the Asperger type is revealed to address the autist’s extreme social aversion which also precludes the experience of empathy. Autists will be revealed as forming social attachments but without the capacity to interact with mutual concern. Empathy will be shown be teachable and, as social avoidance relents, understanding of the meaning and signs of empathic needs that autists can recognize and acknowledge. Treatment of schizoids will be shown to revolve around joining empathically with the schizoid’s apprehensions about interpersonal, interactive proximity. Models of both autism and schizoid personality traits have yet to be replicated in animals, thereby eliminating the role of translational research in providing the kind of clues to behavioral patterns that can be related to genetic, epigenetic and neurobiological measures. But as these clinical examples will attest, treatment strategies have significant impact.

Keywords: autism spectrum, schizoid personality traits, neurobiological implications, critical diagnostic distinctions

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Authors: Santi Maneewatchararangsri, Wanpen Chaicumpa, Patcharin Saengjaruk, Urai Chaisri

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Leptospirosis is a globally neglected disease that continues to be a significant public health and veterinary burden, with millions of cases reported each year. Early and accurate differential diagnosis of leptospirosis from other febrile illnesses and the development of a broad spectrum of leptospirosis vaccines are needed. The LipL32 outer membrane lipoprotein is a member of Leptospira adhesive matrices and has been found to exert hemolytic activity to erythrocytes in vitro. Therefore, LipL32 is regarded as a potential target for diagnosis, broad-spectrum leptospirosis vaccines, and for passive immunotherapy. In this study, we established LipL32-specific mouse monoclonal antibodies, mAbLPF1 and mAbLPF2, and their respective mouse- and humanized-engineered single chain variable fragment (ScFv). Their antibodies’ neutralizing activities against Leptospira-mediated hemolysis in vitro, and the therapeutic efficacy of mAbs against heterologous Leptospira infected hamsters were demonstrated. The epitope peptide of mAb LPF1 was mapped to a non-contiguous carboxy-terminal β-turn and amphipathic α-helix of LipL32 structure contributing to phospholipid/host cell adhesion and membrane insertion. We found that the mAbLPF2 epitope was located on the interacting loop of peptide binding groove of the LipL32 molecule responsible for interactions with host constituents. Epitope sequences are highly conserved among Leptospira spp. and are absent from the LipL32 superfamily of other microorganisms. Both epitopes are surface-exposed, readily accessible by mAbs, and immunogenic. However, they are less dominant when revealed by LipL32-specific immunoglobulins from leptospirosis-patient sera and rabbit hyperimmune serum raised by whole Leptospira. Our study also demonstrated an adhesion inhibitory activity of LipL32 protein to host membrane components and cells mediated by mAbs as well as an anti-hemolytic activity of the respective antibodies. The therapeutic antibodies, particularly the humanized-ScFv, have a potential for further development as non-drug therapeutic agent for human leptospirosis, especially in subjects allergic to antibiotics. The epitope peptides recognized by two therapeutic mAbs have potential use as tools for structure-function studies. Finally, protective peptides may be used as a target for epitope-based vaccines for control of leptospirosis.

Keywords: leptospira lipl32-specific antibodies, therapeutic epitopes, epitopes characterization, immunotherapy

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Authors: Aleksandra Chałupnik, Zuzanna Chilimoniuk, Joanna Borowik, Aleksandra Borkowska, Anna Torres

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Background: Precocious puberty is the occurrence of secondary sexual characteristics in girls before the age of 8. The diverse etiology of premature puberty is crucial to determine whether it is true precocious puberty, depending on the activation of the hypothalamic-pituitary-gonadal axis, or pseudo-precocious, which is independent of the activation of this axis. Whatever the cause, premature action of the sex hormones leads to the common symptoms of various forms of puberty. These include the development of sexual characteristics, acne, acceleration of growth rate and acceleration of skeletal maturation. Due to the possible genetic basis of the disorders, an interdisciplinary search for the cause is needed. Case report: The case report concerns a patient of a pediatric gynecology clinic who, at the age of two years, developed advanced thelarhe (M3) and started recurrent vaginal bleeding. In August 2019, gonadotropin suppression initially and after LHRH stimulation and high estradiol levels were reported at the Endocrinology Department. Imaging examinations showed a cyst in the right ovary projection. The bone age was six years. The entire clinical picture indicated pseudo- (peripheral) precocious in the course of ovarian autonomic cyst. In the follow-up ultrasound performed in September, the image of the cyst was stationary and normalization of estradiol levels and clinical symptoms was noted. In December 2019, cyst regression and normal gonadotropin and estradiol concentrations were found. In June 2020, white mucus tinged with blood on the underwear, without any other disturbing symptoms, was observed for several days. Two consecutive USG examinations carried out in the same month confirmed the change in the right ovary, the diameter of which was 25 mm with a very high level of estradiol. Germinal tumor markers were normal. On the Tanner scale, the patient scored M2P1. The labia and hymen had puberty features. The correct vaginal entrance was visible. Another active vaginal bleeding occurred in the first week of July 2020. The considered laparoscopic treatment was abandoned due to the lack of oncological indications. Treatment with Tamoxifen was recommended in July 2020. In the initiating period of treatment, no maturation progression, and even reduction of symptoms, no acceleration of growth and a marked reduction in the size of the cysts were noted. There was no bleeding. After the size of the cyst and hormonal activity increased again, the treatment was changed to Anastrozole, the effect of which led to a reduction in the size of the cyst. Conclusions: The entire clinical picture indicates alleged (peripheral) puberty. Premature puberty in girls, which is manifested as enlarged mammary glands with high levels of estrogens secreted by autonomic ovarian cysts and prepubertal levels of gonadotropins, may indicate McCune-Albright syndrome. Vaginal bleeding may also occur in this syndrome. Cancellation of surgical treatment of the cyst made it impossible to perform a molecular test that would allow to confirm the diagnosis. Taking into account the fact that cysts are often one of the first symptoms of McCune-Albrigt syndrome, it is important to remember about multidisciplinary care for the patient and careful search for skin and bone changes or other hormonal disorders.

Keywords: McCune Albrigth's syndrome, ovarian cyst, pediatric gynaecology, precocious puberty

Procedia PDF Downloads 185

Authors: Adamu Usman, Grace Stanley Balami

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Pearl millet (Pennisetum glaucum L. R. Br.) is a cereal cultivated in arid and semi-arid areas of the world. It supports more than 100 million people around the world. Parasitic weed (Striga hermonthica Del. Benth) is a major constraint to its production. Estimated yield losses are put at 10 - 95% depending on variety, ecology and cultural practices. Potentials in selection of traits in pearl millets for grain yield have been reported and it depends on genotypic variability and heritability among landraces. Variability and heritability among cultivars could offer opportunities for improvement. The study was conducted to determine the genetic variability among cultivars and estimate broad sense heritability among grain yield and related traits. F1 breeding populations were generated with 9 parental cultivars, viz; Ex-Gubio, Ex-Monguno, Ex-Baga as males and PEO 5984, Super-SOSAT, SOSAT-C88, Ex-Borno and LCIC9702 as females through Line × Tester mating during 2017 dry season at Lushi Irrigation Station, Bauchi Metropolitan in Bauchi State, Nigeria. The F1 population and the parents were evaluated during cropping season of 2018 at Bauchi and Maiduguri. Data collected were subjected to analysis of variance. Results showed significant difference among cultivars and among traits indicating variability. Number of plants at emergence, days to 50% flowering, days to 100% flowering, plant height, panicle length, number of plants at harvest, Striga count at 90 days after sowing, panicle weight and grain yield were significantly different. Significant variability offer opportunity for improvement as superior individuals can be isolated. Genotypic variance estimates of traits were largely greater than environmental variances except in plant height and 1000 seed weight. Environmental variances were low and in some cases negligible. The phenotypic variances of all traits were higher than genotypic variances. Similarly phenotypic coefficient of variation (PCV) was higher than genotypic coefficient of variation (GCV). High heritability was found in days to 50% flowering (90.27%), Striga count at 90 days after sowing (90.07%), number of plants at harvest (87.97%), days to 100% flowering (83.89%), number of plants at emergence (82.19%) and plant height (73.18%). Greater heritability estimates could be due to presence of additive gene. The result revealed wider variability among genotypes and traits. Traits having high heritability could easily respond to selection. High value of GCV, PCV and heritability estimates indicate that selection for these traits are possible and could be effective.

Keywords: variability, heritability, phenotypic, genotypic, striga

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Authors: R. Korchiyne, A. Sbihi, S. M. Farssi, R. Touahni, M. Tahiri Alaoui

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Trabecular bone structure is important texture in the study of osteoporosis. Legendre multifractal spectrum can reflect the complex and self-similarity characteristic of structures. The main objective of this paper is to develop a new technique of medical image classification based on Legendre multifractal spectrum. Novel features have been developed from basic geometrical properties of this spectrum in a supervised image classification. The proposed method has been successfully used to classify medical images of bone trabeculations, and could be a useful supplement to the clinical observations for osteoporosis diagnosis. A comparative study with existing data reveals that the results of this approach are concordant.

Keywords: multifractal analysis, medical image, osteoporosis, fractal dimension, Legendre spectrum, supervised classification

Procedia PDF Downloads 510

Authors: Zhenyu Zhang, Hsi-Hsien Wei

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Highway networks play a vital role in post-disaster recovery for disaster-damaged areas. Damaged bridges in such networks can disrupt the recovery activities by impeding the transportation of people, cargo, and reconstruction resources. Therefore, rapid restoration of damaged bridges is of paramount importance to long-term disaster recovery. In the post-disaster recovery phase, the key to restoration scheduling for a highway network is prioritization of bridge-repair tasks. Resilience is widely used as a measure of the ability to recover with which a network can return to its pre-disaster level of functionality. In practice, highways will be temporarily blocked during the downtime of bridge restoration, leading to the decrease of highway-network functionality. The failure to take downtime effects into account can lead to overestimation of network resilience. Additionally, post-disaster recovery of highway networks is generally divided into emergency bridge repair (EBR) in the response phase and long-term bridge repair (LBR) in the recovery phase, and both of EBR and LBR are different in terms of restoration objectives, restoration duration, budget, etc. Distinguish these two phases are important to precisely quantify highway network resilience and generate suitable restoration schedules for highway networks in the recovery phase. To address the above issues, this study proposes a novel resilience quantification method for the optimization of long-term bridge repair schedules (LBRS) taking into account the impact of EBR activities and restoration downtime on a highway network’s functionality. A time-dependent integer program with recursive functions is formulated for optimally scheduling LBR activities. Moreover, since uncertainty always exists in the LBRS problem, this paper extends the optimization model from the deterministic case to the stochastic case. A hybrid genetic algorithm that integrates a heuristic approach into a traditional genetic algorithm to accelerate the evolution process is developed. The proposed methods are tested using data from the 2008 Wenchuan earthquake, based on a regional highway network in Sichuan, China, consisting of 168 highway bridges on 36 highways connecting 25 cities/towns. The results show that, in this case, neglecting the bridge restoration downtime can lead to approximately 15% overestimation of highway network resilience. Moreover, accounting for the impact of EBR on network functionality can help to generate a more specific and reasonable LBRS. The theoretical and practical values are as follows. First, the proposed network recovery curve contributes to comprehensive quantification of highway network resilience by accounting for the impact of both restoration downtime and EBR activities on the recovery curves. Moreover, this study can improve the highway network resilience from the organizational dimension by providing bridge managers with optimal LBR strategies.

Keywords: disaster management, highway network, long-term bridge repair schedule, resilience, restoration downtime

Procedia PDF Downloads 146

Authors: Dali Gaganidze, Ekaterine Abashidze

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Potato is one of the main agricultural crops in Georgia. Georgia produces early and late potato varieties in almost all regions. In traditional potato growing regions (Svaneti, Samckhet javaheti and Tsalka), the yield is higher than 30-35 t/ha. Among the plant pests that limit potato production and quality, the potato cyst nematodes (PCN) are harmful around the world. Yield losses caused by PCN are estimated up to 30%. Rout surveys conducted in two geographically distinct regions of Georgia producing potatoes - Samtskhe - Javakheti and Svaneti revealed potato cyst nematode Globodera rostochiensi. The aim of the study was the Phylogenetic analyses of Globodera rostochiensi revealed in Georgia by the amplification and sequencing of 28S gen in the D3 region and intergenic ITS1-15.8S-ITS2 region. Identification of all the samples from the two Globodera populations (Samtskhe - Javakheti and Svaneti), i.e., G. rostochiensis (20 isolates) were confirmed by conventional multiplex PCR with ITS 5 universal and PITSp4, PITSr3 specific primers of the cyst nematodes’ (G. pallida, G. rostochiensis). The size of PCR fragment 434 bp confirms that PCN samples from two populations, Samtskhe- Javakheti and Svaneti, belong to G. rostochiensi . The ITS1–5.8S-ITS2 regions were amplified using prime pairs: rDNA1 ( 5’ -TTGATTACGTCCCTGCCCTTT-3’ and rDNA2( 5’ TTTCACTCGCCGTTACTAAGG-3’), D3 expansion regions were amplified using primer pairs: D3A (5’ GACCCCTCTTGAAACACGGA-3’) and D3B (5’-TCGGAAGGAACCAGCTACTA-3’. PCR products of each region were cleaned up and sequenced using an ABI 3500xL Genetic Analyzer. Obtained sequencing results were analyzed by computer program BLASTN (https://blast.ncbi.nlm.nih.gov/Blast.cg). Phylogenetic analyses to resolve the relationships between the isolates were conducted in MEGA7 using both distance- and character-based methods. Based on analysis of G.rostochiensis isolate`s D3 expansion regions are grouped in three major clades (A, B and C) on the phylogenetic tree. Clade A is divided into three subclades; clade C is divided into two subclades. Isolates from the Samtckhet-javakheti population are in subclade 1 of clade A and isolates in subclade 1 of clade C. Isolates) from Svaneti populations are in subclade 2 of clade A and in clad B. In Clade C, subclade two is presented by three isolates from Svaneti and by one isolate (GL17) from Samckhet-Javakheti. . Based on analysis of G.rostochiensis isolate`s ITS1–5.8S-ITS2 regions are grouped in two main clades, the first contained 20 Georgian isolates of Globodera rostochiensis from Svaneti . The second clade contained 15 isolates of Globodera rostochiensis from Samckhet javakheti. Our investigation showed of high genetic variation of D3 and ITS1–5.8S-ITS2 region of rDNA of the isolates of G. rostochiensis from different geographic origins (Svameti, Samckhet-Javakheti) of Georgia. Acknowledgement: The research has been supported by the Shota Rustaveli National Scientific Foundation of Georgia : Project # FR17_235

Keywords: globodera rostochiensi, PCR, phylogenetic tree, sequencing

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Authors: Jessica A. Hellings, Piyushkumar Jani

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Background: Systemic autoimmune disorders are increasingly implicated in neuropsychiatric illness, especially in the setting of treatment resistance in individuals of all ages. Gluten allergy in fullest extent results in celiac disease, affecting multiple organs including central nervous system (CNS). Clinicians often lack awareness of the association between neuropsychiatric illness and gluten allergy, partly since many such research studies are published in immunology and gastroenterology journals. Methods: Following a Pubmed literature search and online searches on celiac disease websites, 40 articles are critically reviewed in detail. This work reviews celiac disease, gluten intolerance and current evidence of their relationship to neuropsychiatric and systemic illnesses. The review also covers current work-up and diagnosis, as well as dietary interventions, gluten restriction outcomes, and future research directions. Results: Gluten allergy in susceptible individuals damages the small intestine, producing a leaky gut and malabsorption state, as well as allowing antibodies into the bloodstream, which attack major organs. Lack of amino acid precursors for neurotransmitter synthesis together with antibody-associated brain changes and hypoperfusion may result in neuropsychiatric illness. This is well documented; however, studies in neuropsychiatry are often small. In the large CATIE trial, subjects with schizophrenia had significantly increased antibodies to tissue transglutaminase (TTG), and antigliadin antibodies, both significantly greater gluten antibodies than in control subjects. On later follow up, TTG-6 antibodies were identified in these subjects’ brains but not in their intestines. Significant evidence mostly from small studies also exists for gluten allergy and celiac-related depression, anxiety disorders, attention-deficit/hyperactivity disorder, autism spectrum disorders, ataxia, and epilepsy. Dietary restriction of gluten resulted in remission in several published cases, including for treatment-resistant schizophrenia. Conclusions: Ongoing and larger studies are needed of the diagnosis and treatment efficacy of the gluten-free diet in neuropsychiatric illness. Clinicians should ask about the patient history of anemia, hypothyroidism, irritable bowel syndrome and family history of benefit from the gluten-free diet, not limited to but especially in cases of treatment resistance. Obtaining gluten antibodies by a simple blood test, and referral for gastrointestinal work-up in positive cases should be considered.

Keywords: celiac, gluten, neuropsychiatric, translational

Procedia PDF Downloads 160

Authors: Baye Berihun Getahun, Mulugeta Atnaf Tiruneh, Richard G. F. Visser

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Resource-poor farmers practice low-input farming systems, and yet, most breeding programs give less attention to this huge farming system, which serves as a source of food and income for several people in developing countries. The high-input conventional breeding system appears to have failed to adequately meet the needs and requirements of 'difficult' environments operating under this system. Moreover, the unavailability of resources for crop production is getting for their peaks, the environment is maltreated by excessive use of agrochemicals, crop productivity reaches its plateau stage, particularly in the developed nations, the world population is increasing, and food shortage sustained to persist for poor societies. In various parts of the world, genetic gain at the farmers' level remains low which could be associated with low adoption of crop varieties, which have been developed under high input systems. Farmers usually use their local varieties and apply minimum inputs as a risk-avoiding and cost-minimizing strategy. This evidence indicates that the conventional high-input plant breeding system has failed to feed the world population, and the world is moving further away from the United Nations' goals of ending hunger, food insecurity, and malnutrition. In this review, we discussed the rationality of focused breeding programs for low-input farming systems and, the technical aspect of crop breeding that accommodates future food needs and its significance for developing countries in the decreasing scenario of resources required for crop production. To this end, the application of exotic introgression techniques like polyploidization, pan-genomics, comparative genomics, and De novo domestication as a pre-breeding technique has been discussed in the review to exploit the untapped genetic diversity of the crop wild relatives (CWRs). Desired recombinants developed at the pre-breeding stage are exploited through appropriate breeding approaches such as evolutionary plant breeding (EPB), rhizosphere-related traits breeding, and participatory plant breeding approaches. Populations advanced through evolutionary breeding like composite cross populations (CCPs) and rhizosphere-associated traits breeding approach that provides opportunities for improving abiotic and biotic soil stress, nutrient acquisition capacity, and crop microbe interaction in improved varieties have been reviewed. Overall, we conclude that low input farming system is a huge farming system that requires distinctive breeding approaches, and the exotic pre-breeding introgression techniques and the appropriate breeding approaches which deploy the skills and knowledge of both breeders and farmers are vital to develop heterogeneous landrace populations, which are effective for farmers practicing low input farming across the world.

Keywords: low input farming, evolutionary plant breeding, composite cross population, participatory plant breeding

Procedia PDF Downloads 40

Authors: Liang Zhao, Jili Zhang, Chongquan Zhong

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Energy consumption data, in particular those involving public buildings, are impacted by many factors: the building structure, climate/environmental parameters, construction, system operating condition, and user behavior patterns. Traditional methods for data analysis are insufficient. This paper delves into the data mining technology to determine its application in the analysis of building energy consumption data including energy consumption prediction, fault diagnosis, and optimal operation. Recent literature are reviewed and summarized, the problems faced by data mining technology in the area of energy consumption data analysis are enumerated, and research points for future studies are given.

Keywords: data mining, data analysis, prediction, optimization, building operational performance

Procedia PDF Downloads 848

Authors: Huang Xiaoling, Liu Lufeng

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In this paper, we seek to determine one reasonable local hub port and optimal routes for a containership fleet, performing pick-ups and deliveries, between the hub and spoke ports in a same region. The relationship between a hub port, and traffic in feeder lines is analyzed. A new network planning method is proposed, an integrated hub port location and route design, a capacitated vehicle routing problem with pick-ups, deliveries and time deadlines are formulated and solved using an improved genetic algorithm for positioning the hub port and establishing routes for a containership fleet. Results on the performance of the algorithm and the feasibility of the approach show that a relatively small fleet of containerships could provide efficient services within deadlines.

Keywords: route planning, hub port location, container feeder service, regional transportation network

Procedia PDF Downloads 445

Authors: Ayse Ozge Demir, Nihat Mert

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In this research, Kilis and Honamli goats are used, which are specific local genetic resources of Turkey. The herds were independent, but they had similar care and nutrition circumstances. From each breed 30 samples were taken, in all 120 samples were collected. Erytrocyte, all blood and serum samples were used for hemoglobine (Hb), glutathione (GSH) and Tf with Cp analysis, respectively. In the analysis of this samples, Hb and Tf bands were determined by electrophoresis. However, Cp and GSH levels were analyzed by the spectrophotometer. Three Hb phenotypes (AA, BB, AB) and Six Tf phenotypes (AA, AB, AC, BB, BC, CC) were determined in this study. In addition, both the observed and the expected values of polymorphic characteristic for 2 characters were presented according to the Hardy-Weinberg Equilibrium (HWE). Cp levels were detected as 0.822 ± 0.055 mg/dl and 1.793 ± 0.109 mg/dl in Kilis and Honamli herds, respectively. GSH levels were detected as, 42,486 ± 1,034 mg/dl and 33.515 ± 0.345 mg/dl in these breeds, respectively,. On the other hand, the high and low GSH levels (GSHH and GSHh) of herds were presented.

Keywords: electrophoresis, gene resource, goat, spectrophotometer

Procedia PDF Downloads 344

Authors: Omar Dib, Alexandre Caminada, Marie-Ange Manier

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The purpose of this study is to introduce a novel approach to solve the one-to-one shortest path problem. A directed connected graph is assumed in which all edges’ weights are positive. Our method is based on a memetic algorithm in which we combine a genetic algorithm (GA) and a variable neighborhood search method (VNS). We compare our approximate method with two exact algorithms Dijkstra and Integer Programming (IP). We made experimentations using random generated, complete and real graph instances. In most case studies, numerical results show that our method outperforms exact methods with 5% average gap to the optimality. Our algorithm’s average speed is 20-times faster than Dijkstra and more than 1000-times compared to IP. The details of the experimental results are also discussed and presented in the paper.

Keywords: shortest path problem, Dijkstra’s algorithm, integer programming, memetic algorithm

Procedia PDF Downloads 463

Authors: Leonard Lipovich, Pattaraporn Thepsuwan, Anton-Scott Goustin, Juan Cai, Donghong Ju, James B. Brown

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Two-thirds of human genes do not encode any known proteins. Aside from long non-coding RNA (lncRNA) genes with recently-discovered functions, the ~40,000 non-protein-coding human genes remain poorly understood, and a role for their transcripts as de-facto unconventional messenger RNAs has not been formally excluded. Ribosome profiling (Riboseq) predicts translational potential, but without independent evidence of proteins from lncRNA open reading frames (ORFs), ribosome binding of lncRNAs does not prove translation. Previously, we mass-spectrometrically documented translation of specific lncRNAs in human K562 and GM12878 cells. We now examined lncRNA translation in human MCF7 cells, integrating strand-specific Illumina RNAseq, Riboseq, and deep mass spectrometry in biological quadruplicates performed at two core facilities (BGI, China; City of Hope, USA). We excluded known-protein matches. UCSC Genome Browser-assisted manual annotation of imperfect (tryptic-digest-peptides)-to-(lncRNA-three-frame-translations) alignments revealed three peptides hypothetically explicable by 'stop-to-nonstop' in-frame replacement of stop codons by amino acids in two ORFs of the lncRNA MMP24-AS1. To search for this phenomenon genomewide, we designed and implemented a novel pipeline, matching tryptic-digest spectra to wildcard-instead-of-stop versions of repeat-masked, six-frame, whole-genome translations. Along with singleton putative stop-to-nonstop events affecting four other lncRNAs, we identified 24 additional peptides with stop-to-nonstop in-frame substitutions from multiple positive-strand MMP24-AS1 ORFs. Only UAG and UGA, never UAA, stop codons were impacted. All MMP24-AS1-matching spectra met the same significance thresholds as high-confidence known-protein signatures. Targeted resequencing of MMP24-AS1 genomic DNA and cDNA from the same samples did not reveal any mutations, polymorphisms, or sequencing-detectable RNA editing. This unprecedented apparent gene-specific violation of the genetic code highlights the importance of matching peptides to whole-genome, not known-genes-only, ORFs in mass-spectrometry workflows, and suggests a new mechanism enhancing the combinatorial complexity of the proteome. Funding: NIH Director’s New Innovator Award 1DP2-CA196375 to LL.

Keywords: genetic code, lncRNA, long non-coding RNA, mass spectrometry, proteogenomics, ribo-seq, ribosome, RNAseq

Procedia PDF Downloads 228