Search results for: normal anatomical variants

Authors: Manik Sharma

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Understanding the anatomy and normal anatomical variations of the lower limb arterial system is undeniably important not only to understand the pathology involving the vessels of the lower limb but also as a part of endovascular intervention and surgical planning in cases that demand them as a part of treatment. There have been very few cases of duplication of SFA cited in the literature, close to six worldwide and this being the seventh case in the world and first to be reported in the Indian population. We incidentally came across this normal variant during US lower limb (US-LL) duplex scan in a patient with claudicating pain in bilateral lower limbs hence suspected of having peripheral vascular disease. It was confirmed on CT-Peripheral Angiography (CT-PA), which was done successively.

Keywords: peripheral vascular disease, claudicating pain, normal anatomical variants, endovascular intervention, duplication, CT-peripheral angiography, duplex scan, Iohexol

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Authors: Angelis P. Barlampas

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Theoretical background Disorders of fixation and rotation of the large intestine, result in the existence of its parts in ectopic anatomical positions. In case of symptomatology, the clinical picture is complicated by the possible symptomatology of the neighboring anatomical structures and a differential diagnostic problem arises. Target The purpose of this work is to demonstrate the difficulty of revealing the real cause of abdominal pain, in cases of anatomical variants and the decisive contribution of imaging and especially that of computed tomography. Methods A patient came to the emergency room, because of acute pain in the right hypochondrium. Clinical examination revealed tenderness in the gallbladder area and a positive Murphy's sign. An ultrasound exam depicted a normal gallbladder and the patient was referred for a CT scan. Results Flexible, unfixed ascending colon and cecum, located in the anatomical region of the right mesentery. Opacities of the surrounding peritoneal fat and a small linear concentration of fluid can be seen. There was an appendix of normal anteroposterior diameter with the presence of air in its lumen and without clear signs of inflammation. There was an impression of possible inflammatory swelling at the base of the appendix, (DD phenomenon of partial volume; e.t.c.). Linear opacities of the peritoneal fat in the region of the second loop of the duodenum. Multiple diverticula throughout the colon. Differential Diagnosis The differential diagnosis includes the following: Inflammation of the base of the appendix, diverticulitis of the cecum-ascending colon, a rare case of second duodenal loop ulcer, tuberculosis, terminal ileitis, pancreatitis, torsion of unfixed cecum-ascending colon, embolism or thrombosis of a vascular intestinal branch. Final Diagnosis There is an unfixed cecum-ascending colon, which is exhibiting diverticulitis.

Keywords: unfixed cecum-ascending colon, abdominal pain, malrotation, abdominal CT, congenital anomalies

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Authors: Gbenga F. Akomolafe, Joseph Omojola, Ezekiel S. Joshua, Seyi C. Adediwura, Elijah T. Adesuji, Michael O. Odey, Oyinade A. Dedeke, Ayo H. Labulo

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Microgravity is known to be a major abiotic stress in space which affects plants depending on the duration of exposure. In this work, tomatoes seeds were exposed to long hours of simulated microgravity condition using a one-axis clinostat. The seeds were sown on a 1.5% combination of plant nutrient and agar-agar solidified medium in three Petri dishes. One of the Petri dishes was mounted on the clinostat and allowed to rotate at the speed of 20 rpm for 72 hours, while the others were subjected to the normal gravity vector. The anatomical sections of both clinorotated and normal gravity plants were made after 72 hours and observed using a Phase-contrast digital microscope. The percentage germination, as well as the growth rate of the normal gravity seeds, was higher than the clinorotated ones. The germinated clinorotated roots followed different directions unlike the normal gravity ones which grew towards the direction of gravity vector. The clinostat was able to switch off gravistimulation. Distinct cellular arrangement was observed for tomatoes under normal gravity condition, unlike those of clinorotated ones. The root epidermis and cortex of normal gravity are thicker than the clinorotated ones. This implied that under long-term microgravity influence, plants do alter their anatomical features as a way of adapting to the stress condition.

Keywords: anatomy, clinostat, germination, lycopersicon esculentum, microgravity

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Authors: Susmiati, Ingrid S. Surono, Jamsari, Nur Indrawati Lipoeto

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There are two contradicting opinions on the relationship between fat mass obesity associated (FTO) rs 9939609 variants and obesity on various ethnics and races. The first opinion agrees that there is an association between the two variables, yet another one disagree. Minangkabau ethnic had a different dietary pattern with other ethnics in Indonesia. They had higher fat and low fiber intakes compared to the other ethnics groups. There is little research in genetic factors that influence eating behavior (food preference or food selection). The objective of this study was to investigate the association between FTO rs 9939609 variants with obesity and eating behavior in adolescent girls of Minangkabau Ethnic. The research design was case control study. A total of 275 adolescent girls aged 12-15 years old (130 obese and 145 normal) were randomly chosen from four districts at West Sumatera (Padang, Padang Pariaman, Padang Panjang and Tanah Datar). Genetic variants of FTO rs 9939609 were analyzed with Tetra-primer Amplification Refractory Mutation System-Polimerase Chain Reaction (AMRS PCR), eating behavior were gathered using eating habits questionnaire, and Body Mass Index (BMI) was calculated according to BMI Z-score (WHO). The result showed that genetic variants of FTO rs 9939609 (TT, TA and AA genotype) had associated with obesity (p = 0,013), whereas subject with An Allele was significantly associated with obesity (odds ratio 1,62 [95% confidential interval, 1,00-2,60]). Subjects with An Allele carrier reported a higher consumption of fried food (p < 0.05) as compared to TT genotypes carriers. There is no association between genetic variants and meal frequency, fruit and fiber intakes p > 0.05. The genetic variants of FTO rs 9939609 are associated with obesity and eating behavior in adolescent of Minangkabau Ethics.

Keywords: FTO rs9939609, obesity, eating behavior, adolescents

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Authors: Zoltan Horvath, Dora Nagy

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In this research, it was examined whether individual COVID variants cause differences in the lactate curve of cyclists. After all, the virus variants attacked different organs in our body during the infections. During our tests, we used a traditional lactate step test, the results of which were compared with the values before the infection. In the tests, it has been proven that different virus variants show unique lactate curves. In this way, based on the lactate curve, it is possible to identify which variant caused the disease. Thanks to this, it has been shorten the return time, because we can apply the best return protocol after infection to the competitors.

Keywords: COVID-Sars19, lactate, virus mutation, lactate profile

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Authors: Atsuko Okazaki, Jurg Ott

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Some genetic diseases (‘digenic traits’) are due to the interaction between two DNA variants. For example, certain forms of Retinitis Pigmentosa (a genetic form of blindness) occur in the presence of two mutant variants, one in the ROM1 gene and one in the RDS gene, while the occurrence of only one of these mutant variants leads to a completely normal phenotype. Detecting such digenic traits by genetic methods is difficult. A common approach to finding disease-causing variants is to compare 100,000s of variants between individuals with a trait (cases) and those without the trait (controls). Such genome-wide association studies (GWASs) have been very successful but hinge on genetic effects of single variants, that is, there should be a difference in allele or genotype frequencies between cases and controls at a disease-causing variant. Frequent pattern mining (FPM) methods offer an avenue at detecting digenic traits even in the absence of single-variant effects. The idea is to enumerate pairs of genotypes (genotype patterns) with each of the two genotypes originating from different variants that may be located at very different genomic positions. What is needed is for genotype patterns to be significantly more common in cases than in controls. Let Y = 2 refer to cases and Y = 1 to controls, with X denoting a specific genotype pattern. We are seeking association rules, ‘X → Y’, with high confidence, P(Y = 2|X), significantly higher than the proportion of cases, P(Y = 2) in the study. Clearly, generally available FPM methods are very suitable for detecting disease-associated genotype patterns. We use fpgrowth as the basic FPM algorithm and built a framework around it to enumerate high-frequency digenic genotype patterns and to evaluate their statistical significance by permutation analysis. Application to a published dataset on opioid dependence furnished results that could not be found with classical GWAS methodology. There were 143 cases and 153 healthy controls, each genotyped for 82 variants in eight genes of the opioid system. The aim was to find out whether any of these variants were disease-associated. The single-variant analysis did not lead to significant results. Application of our FPM implementation resulted in one significant (p < 0.01) genotype pattern with both genotypes in the pattern being heterozygous and originating from two variants on different chromosomes. This pattern occurred in 14 cases and none of the controls. Thus, the pattern seems quite specific to this form of substance abuse and is also rather predictive of disease. An algorithm called Multifactor Dimension Reduction (MDR) was developed some 20 years ago and has been in use in human genetics ever since. This and our algorithms share some similar properties, but they are also very different in other respects. The main difference seems to be that our algorithm focuses on patterns of genotypes while the main object of inference in MDR is the 3 × 3 table of genotypes at two variants.

Keywords: digenic traits, DNA variants, epistasis, statistical genetics

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Authors: Karissa Graham, Andrew Campbell-Lloyd

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The deep inferior epigastric artery perforator flap (DIEP) is used to reconstruct large volumes of tissue. The DIEP flap is based on the deep inferior epigastric artery (DIEA) and vein. Accurate knowledge of the anatomy of these vessels allows for efficient dissection of the flap, minimal damage to surrounding tissue, and a well vascularized flap. A 54 year old lady was assessed for bilateral delayed autologous reconstruction with DIEP free flaps. The right DIEA was consistent with the described anatomy. The left DIEA had a vessel branching shortly after leaving the external iliac artery and before entering the muscle. This independent branch entered the muscle and had a long intramuscular course to the largest perforator. The main DIEA vessel demonstrated a type II branching pattern but had perforators that were too small to have a viable DIEP flap. There were no communicating arterial branches between the independent vessel and DIEA, however, there was one venous communication between them. A muscle sparing transverse rectus abdominis muscle flap was raised using the main periumbilical perforator from the independent vessel. Our case report demonstrated an unreported anatomical variant of the DIEA. A few anatomical variants have been described in the literature, including a unilateral absent DIEA and peritoneal-cutaneous perforators that had no connection to the DIEA. Doing a pre-operative CTA helps to identify these rare anatomical variations, which leads to safer, more efficient, and effective operating.

Keywords: aberrant anatomy, CT angiography, DIEP anatomy, free flap

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Authors: Madeleine Gadd, Rose How, Edward Mathews, John Buchanan, Vicky Cottrell, Andre Coetzee, Karuna Katti

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Introduction: Triphallia, a congenital anomaly describing the presence of three distinct penile shafts, has been reported only once in the literature. This case report describes the serendipitous discovery of the first reported human case of partial orthotopic triphallia during cadaveric dissection. Case Summary: Despite the normal appearance of external genitalia on examination, the dissection of a 78-year-old male revealed a remarkable anatomical variation: two small supernumerary penises situated in a transverse orientation postero inferiorly to the primary penis. The main and the larger supernumerary penile shafts displayed their own corpora cavernosa and glans penis, sharing a single urethra, which coursed through the secondary penis prior to its passage through the primary penis. The smallest of the supernumerary penises was similar in dimension to the secondary penis, at 3.7cm long and 1.2cm wide (compared to the secondary penis at 3.8cm long and 1.3cm wide). However, it lacked a urethra and a typical arrangement of the corpora cavernosa and spongiosum, making this a case of partial triphallia rather than true triphallia. Conclusion: This case report provides a comprehensive anatomical description of partial triphallia in a cadaver, shedding light on the morphology, embryology, and clinical implications of this anomaly. This case report underscores the importance of meticulous anatomical dissections, particularly since, without dissection, this anatomical variation would have remained undiscovered. Although we can only speculate the functional implications of this condition, understanding such anatomical variations contributes to both knowledge of human anatomy and clinical management, should the condition be encountered in living individuals.

Keywords: triphallia, diphallia, congenital abnormalities, genitourinary abnormalities, urology

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Authors: Jake Hindmarch, Edward Farley, Norman Eizenberg, Mark Midwinter

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There is a need to bring the anatomical knowledge of medical students up to the standards required by surgical specialties. Contention exists amongst anatomists, clinicians, and surgeons about the standard of anatomical knowledge medical students need. The aim of this study was to explore the standards which the Royal Australasian College of Surgeons are applying knowledge of anatomy. Furthermore, to align medical school teaching to what the surgical profession requires from graduates.: The 2018 volume of the ANZ Journal of Surgery was narrowed down to 254 articles by applying the search term “Anatomy”. The main topic was then extracted from each paper. The content of the paper was assessed for ‘novel description’ or ‘application’ of anatomical knowledge’ and classified accordingly. The majority of papers with an anatomical focus was from the general surgery specialty, which focused on surgical techniques, outcomes and management. Vascular surgery had the highest percentage of papers with a novel description and application of anatomy. Cardiothoracic and paediatric surgery had no papers with a novel description of anatomy. Finally, a novel application of anatomy was the main focus of each speciality. Firstly, a high proportion of novel applications and descriptions of anatomy are in general surgery. Secondly, vascular surgery had the largest proportion of novel application and description of anatomy, namely due to the rise of therapeutic imaging and endovascular techniques. Finally, all disciplines demonstrated a trend towards having a higher proportion of novel application of anatomical knowledge

Keywords: anatomical knowledge, anatomy, surgery, novel anatomy

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Authors: Tunjo Perić, Franjo Bratić

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In this paper the goal programming methodology for solving multiple objective problem of the technological variants and production plan optimization has been applied. The optimization criteria are determined and the multiple objective linear programming model for solving a problem of the technological variants and production plan optimization is formed and solved. Then the obtained results are analysed. The obtained results point out to the possibility of efficient application of the goal programming methodology in solving the problem of the technological variants and production plan optimization. The paper points out on the advantages of the application of the goal programming methodolohy compare to the Surrogat Worth Trade-off method in solving this problem.

Keywords: goal programming, multi objective programming, production plan, SWT method, technological variants

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Authors: P. B. Sob, T. B. Tengen, A. A. Alugongo

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Mechanical behavior of 6082T6 aluminum is investigated at different temperatures. The strain rate sensitivity is investigated at different temperatures on the grain size variants. The sensitivity of the measured grain size variants on 3-D grain is discussed. It is shown that the strain rate sensitivities are negative for the grain size variants during the deformation of nanostructured materials. It is also observed that the strain rate sensitivities vary in different ways with the equivalent radius, semi minor axis radius, semi major axis radius and major axis radius. From the obtained results, it is shown that the variation of strain rate sensitivity with temperature suggests that the strain rate sensitivity at the low and the high temperature ends of the 6082T6 aluminum range is different. The obtained results revealed transition at different temperature from negative strain rate sensitivity as temperature increased on the grain size variants.

Keywords: nanostructured materials, grain size variants, temperature, yield stress, strain rate sensitivity

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Authors: Kulsum Maula, Md Kamrul Alam, Md Ibrahim Khalil, Md Nazmul Hasan, Mohammad Omar Faruq

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Background: Percutaneous Tube Thoracostomy (PTT) is an invasive procedure that can save a life now and then in different traumatic and non-traumatic conditions. But still, it is an enigma; how our trainee surgeons are at home in this procedure. Objectives: To evaluate the outcome of the percutaneous tube thoracostomy performed by trainees in both trauma and non-trauma patients. Study design: Prospective, Observational Study. The duration of the study was September 2018 to February 2019. Methods: All patients who need PTT in traumatic and non-traumatic conditions were selected by purposive sampling. Thereafter, they were scrutinized according to eligibility criteria and 96 patients were finalized. A pre-tested, observation-based, peer-reviewed data collection sheet was prepared before the study. Data regarding clinical and surgical outcome profiles were recorded. Data were compiled, edited, and analyzed. Results: Among 96 patients, the highest 32.29% belonged to age group 31-40 years and the lowest 9.37% belonged to the age group ≤20. The mean age of the respondents was 29.19±9.81. We found out of 96 patients, 70(72.91%) were indicated PTT for traumatic conditions and the rest 26(27.08%) were indicated PTT for non-traumatic chest conditions, where 36(37.5%) had simple penumothorax, 21(21.87%) haemothorax, 14(14.58%) massive pleural effusion, 13(13.54%) tension pneumothorax, 10(10.41%) haemopneumothorax, and 2(2.08%) had pyothorax respectively. In 53.12% of patients had right-sided intercostal chest tube (ICT) insertion, whereas 46.87% had left-sided ICT insertion. In our study, 89.55 % of the tube was placed at the normal anatomical position. Besides, 10.41% of tube thoracostomy were performed deviated from anatomical site. Among 96 patients 62.5% patients had length of incision 2-3cm, 35.41% had >3cm and 2.08% had <2cm respectively. Out of 96 patients, 75(78.13%) showed uneventful outcomes, whereas 21(21.87%) had complications, including 11.15%(11) each had wound infection, 4.46%(4) subcutaneous emphysema, 4.28%(3) drain auto expulsion, 2.85%(2) hemorrhage, 1.45%(1) had a non-functioning drain and empyema with ascending infection respectively (p=<0.05). Conclusion: PTT is a life-saving procedure that is most frequently implemented in chest trauma patients in our country. In the majority of cases, the outcome of PTT was uneventful (78.13). Besides this, more than one-third of patients had a length of incision more than 3 cm that needed extra stitches and 10.41% of cases of PTT were placed other than the normal anatomical site. Trainees of Dhaka Medical College Hospitals are doing well in their performance of PTT insertion, but still, some anatomical orientations are necessary to avoid operative and post-operative complications.

Keywords: PTT, trainee, trauma, non-chest trauma patients

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Authors: L. Lamola, E. Manolas, A. Krause

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Background: The incidence of childhood cancer incidence is increasing gradually in low-middle income countries, such as South Africa. Globally, there is an extensive range of familial- and hereditary-cancer syndromes, where underlying germline variants increase the likelihood of developing cancer in childhood. Next-Generation Sequencing (NGS) technologies have been key in determining the occurrence and genetic contribution of germline variants to paediatric cancer development. We aimed to design and evaluate a candidate gene panel specific to inherited cancer-predisposing genes to provide a comprehensive insight into the contribution of germline variants to childhood cancer. Methods: 32 paediatric patients (aged 0-18 years) diagnosed with a malignant tumour were recruited, and biological samples were obtained. After quality control, DNA was sequenced using an ion Ampliseq 50 candidate gene panel design and Ion Torrent S5 technologies. Sequencing variants were called using Ion Torrent Suite software and were subsequently annotated using Ion Reporter and Ensembl's VEP. High priority variants were manually analysed using tools such as MutationTaster, SIFT-INDEL and VarSome. Putative identified candidates were validated via Sanger Sequencing. Results: The patients studied had a variety of cancers, the most common being nephroblastoma (13), followed by osteosarcoma (4) and astrocytoma (3). We identified 10 pathogenic / likely pathogenic variants in 10 patients, most of which were novel. Conclusions: According to the literature, we expected ~10% of our patient population to harbour pathogenic or likely pathogenic germline variants, however, we reported about 3 times (~30%) more than we expected. Majority of the identified variants are novel; this may be because this is the first study of its kind in an understudied South African population.

Keywords: Africa, genetics, germline-variants, paediatric-cancer

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Authors: Agnieszka H. Ludwig-Slomczynska, Michal T. Seweryn, Przemyslaw Kapusta, Ewelina Pitera, Katarzyna Cyganek, Urszula Mantaj, Lucja Dobrucka, Ewa Wender-Ozegowska, Maciej T. Malecki, Pawel Wolkow

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Obesity results from an imbalance between energy intake and its expenditure. Genome-Wide Association Study (GWAS) analyses have led to discovery of only about 100 variants influencing body mass index (BMI), which explain only a small portion of genetic variability. Analysis of gene epistasis gives a chance to discover another part. Since it was shown that interaction and communication between nuclear and mitochondrial genome are indispensable for normal cell function, we have looked for epistatic interactions between the two genomes to find their correlation with BMI. Methods: The analysis was performed on 366 T1DM patients using Illumina Infinium OmniExpressExome-8 chip and followed by imputation on Michigan Imputation Server. Only genes which influence mitochondrial functioning (listed in Human MitoCarta 2.0) were included in the analysis – variants of nuclear origin (MAF > 5%) in 1140 genes and 42 mitochondrial variants (MAF > 1%). Gene expression analysis was performed on GTex data. Association analysis between genetic variants and BMI was performed with the use of Linear Mixed Models as implemented in the package 'GENESIS' in R. Analysis of association between mRNA expression and BMI was performed with the use of linear models and standard significance tests in R. Results: Among variants involved in epistasis between mitochondria and nucleus we have identified one in mitochondrial transcription factor, TFB2M (rs6701836). It interacted with mitochondrial variants localized to MT-RNR1 (p=0.0004, MAF=15%), MT-ND2 (p=0.07, MAF=5%) and MT-ND4 (p=0.01, MAF=1.1%). Analysis of the interaction between nuclear variant rs6701836 (nuc) and rs3021088 localized to MT-ND2 mitochondrial gene (mito) has shown that the combination of the two led to BMI decrease (p=0.024). Each of the variants on its own does not correlate with higher BMI [p(nuc)=0.856, p(mito)=0.116)]. Although rs6701836 is intronic, it influences gene expression in the thyroid (p=0.000037). rs3021088 is a missense variant that leads to alanine to threonine substitution in the MT-ND2 gene which belongs to complex I of the electron transport chain. The analysis of the influence of genetic variants on gene expression has confirmed the trend explained above – the interaction of the two genes leads to BMI decrease (p=0.0308). Each of the mRNAs on its own is associated with higher BMI (p(mito)=0.0244 and p(nuc)=0.0269). Conclusıons: Our results show that nuclear-mitochondrial epistasis can influence BMI in T1DM patients. The correlation between transcription factor expression and mitochondrial genetic variants will be subject to further analysis.

Keywords: body mass index, epistasis, mitochondria, type 1 diabetes

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Authors: Dumith Kulasekara

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This paper examines the representation of the body that particularly stresses the anatomical organs and the psychic conditions in contemporary art. The paper looks closely at the works that address personal and social meanings implying psychic conditions by bringing the internal hidden anatomical organs of the body to the surface of the visual language. The paper argues that contemporary artists conceptualize the idea of the body as a site of generating psychic conditions by excavating the body as material, subject, and object in art practice. The paper conceptualizes this excavating process of the body acts similarly to the idea of dissecting the corporeal body to understand its internal organism that again shapes the materiality of the surface of the body. In doing so, the paper brings together this argument, knowledge produced in the historical and contemporary anatomical education in art and science, and psychoanalytical approaches to the theme to develop new interpretations of representing psyche in the anatomical-bodied. The present paper defines this new form of body conceptually and materially addresses the issues related to psychic conditions: sexual desires, gender, traumas, and memories. The paper suggests that representation of the anatomical-bodied brings a new direction of the multidisciplinary approach introduced by artists to visualize the body and psyche in the contemporary context. The paper also presents an in-depth- discussion on technological, scientific, and philosophical knowledge employed in representing the idea of the body in addressing different psychic conditions to challenge the experiencing the body in contemporary art. Therefore, the paper focuses on examining the theme in the different forms of visual language and contexts in contemporary art. Finally, this research aims to offer a theoretical and conceptual background to curate an exhibition on the title of the anatomical-bodied and psyche in contemporary art with the body of work discussed in this paper.

Keywords: anatomy, body, contemporary art, psyche, psychoanalysis, representation, trauma

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Authors: Jakub Elbl, Lukáš Plošek, Antonín Kintl, Jaroslav Hynšt, Soňa Javoreková, Jaroslav Záhora, Libor Kalhotka, Olga Urbánková, Ivana Charousová

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This work presents the first results from the long-term laboratory experiment dealing with impact of drought on soil properties. Three groups of the treatment (A, B and C) with different regime of irrigation were prepared. The soil water content was maintained at 70 % of soil water holding capacity in group A, at 40 % in group B. In group C, soil water regime was maintained in the range of wilting point. Each group of the experiment was divided into three variants (A1 = B1, C1; A2 = B2, C2 etc.) with three repetitions: Variants A1 (B1, C1) were controls without addition of another fertilizer. Variants A2 (B2, C2) were fertilized with mineral nitrogen fertilizer DAM 390 (0.140 Mg of N per ha) and variants A3 (B3, C3) contained 45 g of Cp per a pot. The significant differences (ANOVA, P<0.05) in the leaching of mineral nitrogen and values of saturated hydraulic conductivity (Ksat) were found. The highest values of Ksat were found in variants (within each group) with addition of compost (A3, B3, C3). Conversely, the lowest values of Ksat were found in variants with addition of mineral nitrogen. Low values of Ksat indicate an increased level of hydrophobicity in individual groups of the experiment. Moreover, all variants with compost addition showed lower amount of mineral nitrogen leaching and high level of microbial activity than variants without. This decrease of mineral nitrogen leaching was about 200 % in comparison with the control variant and about 300 % with variant, where mineral nitrogen was added. Based on these results, we can conclude that changes of soil water content directly have impact on microbial activity, soil hydrophobicity and loss of mineral nitrogen from the soil.

Keywords: drought, microbial activity, mineral nitrogen, soil hydrophobicity

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Authors: Sila Akhan, Muge Toygar, Murat Sayan, Simge Fidan

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Chronic viral hepatitis B, C, and D can cause hepatocellular carcinoma (HCC), cirrhosis and death. The proper treatment reduce the risk of development of HCC importantly, but not to zero point. Materials and Methods: We analysed retrospectively our chronic viral hepatitis B, C and D patients who attended to our Infectious Diseases policlinic between 2004-2018. From 589 biopsy-proven chronic hepatitis patients 3 have hepatocellular carcinoma on our follow up. First case is 74 years old patient. His HCV infection diagnosis was made 8 years ago. First treatment was pegylated interferon plus ribavirin only 28 weeks, because of HCV RNA breakthrough under treatment. In 2013 he was retreated with telaprevir, pegylated interferon plus ribavirin 24 weeks. But at the end of the therapy HCV RNA was found 1.290.000 IU/mL. He has abdominal ultrasonography (US) controls and alpha-fetoprotein (AFP) at 6 months intervals. All seemed normal until 2015 then he has an abdominal magnetic resonance imaging (MRI) and found HCC by chance. His treatment began in Oncology Clinic after verified with biopsy of HCC. And then sofosbuvir/ledipasvir was given to him for HCV 24 weeks. Sustained virologic response (SVR) was obtained. He is on cure for HCV infection and under control of Oncology for HCC. Second patient is 36 years old man. He knows his HBV infection since 2008. HBsAg and HBeAg positive; HDV RNA negative. Liver biopsy revealed grade:4, stage 3-4 according modified Knodell scoring system. In 2010 tenofovir treatment was began. His abdominal US and AFP were normal. His controls took place at 6 months intervals and HBV DNA negative, US, and AFP were normal until 2016 continuously. AFP found 37 above the normal range and then HCC was found in MRI. Third patient is 57 years old man. As hepatitis B infection was first diagnosed; he has cirrhosis and was began tenofovir as treatment. In short time he has HCC despite normal AFP values. Conclusion: In Mediterranian countries including Turkey naturally occurring pre-S/S variants are more than 75% of all chronic hepatitis B patients. This variants may contribute to the development of progressive liver damage and hepatocarcinogenesis. HCV-induced development of HCC is a gradual process and is affected by the duration of disease and viral genotype. All the chronic viral hepatitis patients should be followed up in 6 months intervals not only with US and AFP for HCC. Despite they have proper treatment there is always the risk development of HCC. Chronic hepatitis patients cannot be dropped from follow up even treated well.

Keywords: HCC, HCV, HBV, DAA

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Authors: Abdelmagid Basyouny Sakr

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Terminological variation is a reality and it is now recognized by terminologists. This paper investigates the terminological variation in the context of specialized economic texts in Italian. It aims to find whether certain patterns or tendencies can be derived from the analysis of these texts. Term variants pose two different kinds of difficulties. The first one is being able to recognize linguistic expressions that denote the same concept in running text. Another one lies in knowing which variant should be considered and for what purpose. This would help to differentiate between variants that could be candidates for inclusion in terminological resources and the ones which are synonyms or contextual variants. New insights about terminological variation in specialized texts could contribute to improve specialized dictionaries which will better account for the different ways in which a given thought is expressed.

Keywords: corpus linguistics, specialized communication, terms and concepts, terminological variation

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Authors: S. Fahiminiya, J. Nadaf, F. Rauch, L. Jerome-Majewska, J. Majewski

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Background: Sequencing of protein coding regions of human genome (Whole Exome Sequencing; WES), has demonstrated a great success in the identification of causal mutations for several rare genetic disorders in human. Generally, most of WES studies have focused on rare variants in coding exons and splicing-sites where missense substitutions lead to the alternation of protein product. Although focusing on this category of variants has revealed the mystery behind many inherited genetic diseases in recent years, a subset of them remained still inconclusive. Here, we present the result of our WES studies where analyzing only rare variants in coding regions was not conclusive but further investigation revealed the involvement of non-coding variants and copy number variations (CNV) in etiology of the diseases. Methods: Whole exome sequencing was performed using our standard protocols at Genome Quebec Innovation Center, Montreal, Canada. All bioinformatics analyses were done using in-house WES pipeline. Results: To date, we successfully identified several disease causing mutations within gene coding regions (e.g. SCARF2: Van den Ende-Gupta syndrome and SNAP29: 22q11.2 deletion syndrome) by using WES. In addition, we showed that variants in non-coding regions and CNV have also important value and should not be ignored and/or filtered out along the way of bioinformatics analysis on WES data. For instance, in patients with osteogenesis imperfecta type V and in patients with glucocorticoid deficiency, we identified variants in 5'UTR, resulting in the production of longer or truncating non-functional proteins. Furthermore, CNVs were identified as the main cause of the diseases in patients with metaphyseal dysplasia with maxillary hypoplasia and brachydactyly and in patients with osteogenesis imperfecta type VII. Conclusions: Our study highlights the importance of considering non-coding variants and CNVs during interpretation of WES data, as they can be the only cause of disease under investigation.

Keywords: whole exome sequencing data, non-coding variants, copy number variations, rare diseases

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Authors: Farshad Negintaji, Hamid Reza Zeraat Pisheh, Mahshid Ghanea, Zahra Khalifeh, Mohammad Bagher Rahami

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This study has been examined the anatomical components of mosques with the approach of attending to Islamic wisdom and investigated the distinction between the anatomical design of mosques (traditional and modern) by considering the category of perception in Islamic architecture. To this end, this article by reviewing the theoretical and empirical literature of mosques' anatomy and the role of anatomy on the architectural design of Iranian mosques by examining the quantitative and qualitative indicators and in order to understand and identify the anatomy of mosques, indicators such as: entrance, portico, minarets, domes, bedchamber and pool have been used. The aim of this study has been to investigate materials, the functional properties, technology, sizes and fitness of (traditional and modern) mosques. For this purpose, a questionnaire was prepared in which the anatomical and spiritual elements of the mosque shape have been questioned. Research is related to field and is of descriptive, analytical and inferential type and quantitative and qualitative indicators have been examined.

Keywords: Islamic wisdom, Islamic architecture, mosque anatomy, the minaret, dome, bedchamber, entrance, pool, perception

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Authors: P. B. Sob, A. A. Alugongo, T. B. Tengen

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The activation volume of 6082T6 aluminum is investigated at different temperatures on grain size variants. The deformation activation volume was computed on the basis of the relationship between the Boltzmann’s constant k, the testing temperatures, the material strain rate sensitivity and the material yield stress of grain size variants. The material strain rate sensitivity is computed as a function of yield stress and strain rate of grain size variants. The effect of the material strain rate sensitivity and the deformation activation volume of 6082T6 aluminum at different temperatures of 3-D grain are discussed. It is shown that the strain rate sensitivities and activation volume are negative for the grain size variants during the deformation of nanostructured materials. It is also observed that the activation volume vary in different ways with the equivalent radius, semi minor axis radius, semi major axis radius and major axis radius. From the obtained results it is shown that the variation of activation volume increased and decreased with the testing temperature. It was revealed that, increased in strain rate sensitivity led to decrease in activation volume whereas increased in activation volume led to decrease in strain rate sensitivity.

Keywords: nanostructured materials, grain size variants, temperature, yield stress, strain rate sensitivity, activation volume

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Authors: Lamis Naddaf, Yuval Tabach

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In this research, we identified the missense genetic variants that have the potential to enhance resistance against cancer. Such field has not been widely explored, as researchers tend to investigate mutations that cause diseases, in response to the suffering of patients, rather than those mutations that protect from them. In conjunction with the genomic revolution, and the advances in genetic engineering and synthetic biology, identifying the protective variants will increase the power of genotype-phenotype predictions and can have significant implications on improved risk estimation, diagnostics, prognosis and even for personalized therapy and drug discovery. To approach our goal, we systematically investigated the sites of the coding genomes and picked up the alleles that showed a correlation with the species’ cancer resistance. We predicted 250 protecting variants (PVs) with a 0.01 false discovery rate and more than 20 thousand PVs with a 0.25 false discovery rate. Cancer resistance in Mammals and reptiles was significantly predicted by the number of PVs a species has. Moreover, Genes enriched with the protecting variants are enriched in pathways relevant to tumor suppression like pathways of Hedgehog signaling and silencing, which its improper activation is associated with the most common form of cancer malignancy. We also showed that the PVs are more abundant in healthy people compared to cancer patients within different human races.

Keywords: comparative genomics, machine learning, cancer resistance, cancer-protecting alleles

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Authors: Mohammed Althobiti, Patrick Booms, Dorota Fiszer, Philip Hopkins

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Malignant hyperthermia (MH) is a pharmacogenetic disorder of skeletal muscle. MH results from anaesthetics induced breakdown of calcium homeostasis. RYR1 and CACN1AS mutations represent the aetiology in ~70% of the MH population. Previous studies indicate that up to 25% of MH patients carry no variants in these genes. Therefore, the aim of this study is to investigate the relationships between MH susceptibility and genes encoding skeletal muscle Ca2+ channels as well as accessory proteins. The JSRP, encoding JP-45, was previously sequenced and novel genetic variants were identified. The variant p.P108L (c.323C > T) was identified in exon 4 and encodes a change from a proline at amino acid 108 to leucine residue. The variant P108L was detected in two patients out of 50 with 4% frequency in the sample population. The alignment of DNA sequences in different species indicates highly conserved proline sequences involved in the substitution of the P108L variant. In this study, the variant P108L co-segregates with the SNP p.V92A (c.275T > C) at the same exon, both variants being inherited in the same two patients only. This indicates that the two variants may represent a haplotype. Therefore, a set of single nucleotide polymorphisms and statistical analysis will be used to investigate the effects of haplotypes on MH susceptibility. Furthermore, investigating the effect of the P108L variant in combination with RYR1 mutations or other genetic variants in other genes as a combination of two or more genetic variants, haplotypes may then provide stronger genetic evidence indicating that JSRP1 is associated with MH susceptibility. In conclusion, these preliminary results lend a potential modifier role of the variant P108L in JSRP1 in MH susceptibility and further investigations are suggested to confirm these results.

Keywords: JSRP1, malignant hyperthermia, RyR1, skeletal muscle

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Authors: Maria Lopez-Ibarra, Ana Velazquez-Wong, Lucelli Yañez-Gutierrez, Maria Araujo-Solis, Fabio Salamanca-Gomez, Alfonso Mendez-Tenorio, Haydeé Rosas-Vargas

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Congenital heart diseases (CHD) are the most common congenital abnormalities. These conditions can occur as both an element of distinct chromosomal malformation syndromes or as non-syndromic forms. Their etiology is not fully understood. Genetic variants such copy number variants have been associated with CHD. The aim of our study was to analyze these genomic variants in peripheral blood from Mexican children diagnosed with non-syndromic CHD. We included 16 children with atrial and ventricular septal defects and 5 healthy subjects without heart malformations as controls. To exclude the most common heart disease-associated syndrome alteration, we performed a fluorescence in situ hybridization test to identify the 22q11.2, responsible for congenital heart abnormalities associated with Di-George Syndrome. Then, a microarray based comparative genomic hybridization was used to identify global copy number variants. The identification of copy number variants resulted from the comparison and analysis between our results and data from main genetic variation databases. We identified copy number variants gain in three chromosomes regions from pediatric patients, 4q13.2 (31.25%), 9q34.3 (25%) and 20q13.33 (50%), where several genes associated with cellular, biosynthetic, and metabolic processes are located, UGT2B15, UGT2B17, SNAPC4, SDCCAG3, PMPCA, INPP6E, C9orf163, NOTCH1, C20orf166, and SLCO4A1. In addition, after a hierarchical cluster analysis based on the fluorescence intensity ratios from the comparative genomic hybridization, two congenital heart disease groups were generated corresponding to children with atrial or ventricular septal defects. Further analysis with a larger sample size is needed to corroborate these copy number variants as possible biomarkers to differentiate between heart abnormalities. Interestingly, the 20q13.33 gain was present in 50% of children with these CHD which could suggest that alterations in both coding and non-coding elements within this chromosomal region may play an important role in distinct heart conditions.

Keywords: aCGH, bioinformatics, congenital heart diseases, copy number variants, fluorescence in situ hybridization

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Authors: Elsayed Fath Khalifa, Samer Mohamed Daghash

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The aim of the current work study to increase the anatomical knowledge about the cattle egret which considered economically important for farmers. The study was carried out on ten adult, apparently healthy cattle egrets of both sexes. Each bird was exsanguinated; the caudal vena cava was cannulated and flushed with warm normal saline solution (0.9%) then injected with blue colored neoprine (60%) latex in order to study the tributaries of the hepatic portal vein. The origin, course and tributaries of the right and left hepatic portal veins were studied. The hepatic portal venous system collected venous blood from the abdominal viscera including; glandular and muscular stomachs, liver, pancreas, spleen, small intestine and large intestine. The hepatic portal vein was formed by the left and the right hepatic portal veins. The smaller left one drained blood from the glandular and muscular stomachs through the ventral and the left proventriculus as well as the left gastric veins. The most tributaries of the right hepatic portal vein drained blood from the rest of the gastrointestinal tract and the spleen by the proventriculosplenic, the gastropancreaticoduodenal and the common mesenteric veins.

Keywords: cattle egret, common mesenteric vein, hepatic portal vein, anatomy

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Authors: Sophie Mills, Constantinos Aristotelous, Leila L. Touil, Richard C. W. James

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Objectives: Historical studies of the anatomy of the spinal accessory nerve (SAN) have reported conflicting results regarding its relationship with the internal jugular vein (IJV). A literature review was undertaken to establish the prevalence of anatomical variations of the SAN encountered during routine neck dissection surgery in order to increase awareness and reduce morbidity associated with iatrogenic SAN injury. Materials and Methods: The largest systematic review to date was performed using PRISMA-ScR guidelines, which yielded nine articles following the application of inclusion and exclusion criteria. A case report is also included, which demonstrates the rare anatomical relationship of the SAN traversing a fenestrated IJV, seen for the first time in the senior author’s career. Results: The mean number of dissections per study was 119, of which 55.6% (n=5) studies were performed on cadaver subjects, and 44.4% (n=4) were surgical dissections. Incidences of the SAN lateral to the IJV and medial to the IJV ranged from 38.9%-95.7% and 2.8%-57.4%, respectively. Over half of the studies reported incidences of the SAN traversing the IJV in 0.9%-2.8% of dissections. One study reported an isolated variant of the SAN dividing around the IJV with a prevalence of 0.5%. Conclusion: At the level of the posterior belly of the digastric muscle, the surgeon can anticipate the identification of the SAN lateral to the IJV in approximately three-quarters of cases, whilst around one-quarter are estimated to be medial. A mean of 1.6% of SANs traverses a fenestration of the vein. It is essential for surgeons to be aware of these anatomical variations and their prevalence to prevent injury to vital structures during surgery.

Keywords: anatomical variant, internal jugular vein, neck dissection, spinal accessory nerve

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Authors: Alitajer Saeed, Negintaji Farshad

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This study has been examined the relationship between anatomical components of mosques and place attachment of people to anatomies of mosques with the approach of attending to Islamic wisdom. To this end, this article by reviewing the theoretical and empirical literature of mosques' anatomy and the role of anatomy on the architectural design of Iranian mosques by examining the quantitative and qualitative indicators and in order to understand and identify the anatomy of mosques, components such as: entrance, portico, minarets, domes, bedchamber and pool have been investigated. For this purpose, SPSS software has been used. Research is related to field and is of descriptive, analytical and inferential type and quantitative and qualitative indicators have been examined. Statistical analysis obtained from the questionnaire indicates that there is a significant relationship between the anatomical components of architecture and place attachment of the participants. By understanding and identifying the anatomy of mosques and appropriate planning to use the anatomy in Islamic architecture and considering it as an eminent indicators of designing, it can present great Iranian architecture.

Keywords: Islamic wisdom, Islamic architecture, mosque anatomy place attachment, Islamic art

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Authors: Hamsa T. Tayeb, Mohammad A. Arafah, Dana M. Bakheet, Duaa M. Khalaf, Agnieszka Tarnoska, Nduna Dzimiri

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Background: CYP2D6 is a member of the cytochrome P450 mixed-function oxidase system. The enzyme is responsible for the metabolism and elimination of approximately 25% of clinically used drugs, especially in breast cancer and psychiatric therapy. Different phenotypes have been described displaying alleles that lead to a complete loss of enzyme activity, reduced function (poor metabolizers – PM), hyperfunctionality (ultrarapid metabolizers–UM) and therefore drug intoxication or loss of drug effect. The prevalence of these variants may vary among different ethnic groups. Furthermore, the xTAG system has been developed to categorized all patients into different groups based on their CYP2D6 substrate metabolization. Aim of the study: To determine the prevalence of the different CYP2D6 variants in our population, and to evaluate their clinical relevance in personalized medicine. Methodology: We used the Luminex xMAP genotyping system to sequence 305 Saudi individuals visiting the Blood Bank of our Institution and determine which polymorphisms of CYP2D6 gene are prevalent in our region. Results: xTAG genotyping showed that 36.72% (112 out of 305 individuals) carried the CYP2D6_*2. Out of the 112 individuals with the *2 SNP, 6.23% had multiple copies of *2 SNP (19 individuals out of 305 individuals), resulting in an UM phenotype. About 33.44% carried the CYP2D6_*41, which leads to decreased activity of the CYP2D6 enzyme. 19.67% had the wild-type alleles and thus had normal enzyme function. Furthermore, 15.74% carried the CYP2D6_*4, which is the most common nonfunctional form of the CYP2D6 enzyme worldwide. 6.56% carried the CYP2D6_*17, resulting in decreased enzyme activity. Approximately 5.73% carried the CYP2D6_*10, consequently decreasing the enzyme activity, resulting in a PM phenotype. 2.30% carried the CYP2D6_*29, leading to decreased metabolic activity of the enzyme, and 2.30% carried the CYP2D6_*35, resulting in an UM phenotype, 1.64% had a whole-gene deletion CYP2D6_*5, thus resulting in the loss of CYP2D6 enzyme production, 0.66% carried the CYP2D6_*6 variant. One individual carried the CYP2D6_*3(B), producing an inactive form of the enzyme, which leads to decrease of enzyme activity, resulting in a PM phenotype. Finally, one individual carried the CYP2D6_*9, which decreases the enzyme activity. Conclusions: Our study demonstrates that different CYP2D6 variants are highly prevalent in ethnic Saudi Arabs. This finding sets a basis for informed genotyping for these variants in personalized medicine. The study also suggests that xTAG is an appropriate procedure for genotyping the CYP2D6 variants in personalized medicine.

Keywords: CYP2D6, hormonal breast cancer, pharmacogenetics, polymorphism, psychiatric treatment, Saudi population

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Authors: Kuniyoshi Abe

Abstract:

Bi-conjugate gradient (Bi-CG) is a well-known method for solving linear equations Ax = b, for x, where A is a given n-by-n matrix, and b is a given n-vector. Typically, the dimension of the linear equation is high and the matrix is sparse. A number of hybrid Bi-CG methods such as conjugate gradient squared (CGS), Bi-CG stabilized (Bi-CGSTAB), BiCGStab2, and BiCGstab(l) have been developed to improve the convergence of Bi-CG. Bi-CGSTAB has been most often used for efficiently solving the linear equation, but we have seen the convergence behavior with a long stagnation phase. In such cases, it is important to have Bi-CG coefficients that are as accurate as possible, and the stabilization strategy, which stabilizes the computation of the Bi-CG coefficients, has been proposed. It may avoid stagnation and lead to faster computation. Motivated by a large number of processors in present petascale high-performance computing hardware, the scalability of Krylov subspace methods on parallel computers has recently become increasingly prominent. The main bottleneck for efficient parallelization is the inner products which require a global reduction. The resulting global synchronization phases cause communication overhead on parallel computers. The parallel variants of Krylov subspace methods reducing the number of global communication phases and hiding the communication latency have been proposed. However, the numerical stability, specifically, the convergence speed of the parallel variants of Bi-CGSTAB may become worse than that of the standard Bi-CGSTAB. In this paper, therefore, we compare the convergence speed between the standard Bi-CGSTAB and the parallel variants by numerical experiments and show that the convergence speed of the standard Bi-CGSTAB is faster than the parallel variants. Moreover, we propose the stabilization strategy for the parallel variants.

Keywords: bi-conjugate gradient stabilized method, convergence speed, Krylov subspace methods, linear equations, parallel variant

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Authors: Kinnsley Travis, Camerron M. Crowder

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Mapk8ip3 (Mitogen-Activated Protein Kinase 8 Interacting Protein 3) is a gene that codes for the JIP3 protein, which is a part of the JIP scaffolding protein family. This protein is involved in axonal vesicle transport, elongation and regeneration. Variants in the Mapk8ip3 gene are associated with a rare-genetic condition that results in a neurodevelopmental disorder that can cause a range of phenotypes including global developmental delay and intellectual disability. Currently, there are 18 known individuals diagnosed to have sequenced confirmed Mapk8ip3 genetic disorders. This project focuses on examining the impact of a subset of missense patient variants on the Jip3 protein function by overexpressing the mRNA of these variants in a zebrafish knockout model for Jip3. Plasmids containing cDNA with individual missense variants were reverse transcribed, purified, and injected into single-cell zebrafish embryos (Wild Type, Jip3 -/+, and Jip3 -/-). At 6-days post mRNA microinjection, morphological, behavioral, and microscopic phenotypes were examined in zebrafish larvae. Morphologically, we compared the size and shape of the zebrafish during their development over a 5-day period. Total locomotive activity was assessed using the Microtracker assay and patterns of movement over time were examined using the DanioVision assay. Lastly, we used confocal microscopy to examine sensory axons for swelling and shortened length, which are phenotypes observed in the loss-of-function knockout Jip3 zebrafish model. Using these assays during embryonic development, we determined the impact of various missense variants on Jip3 protein function, compared to knockout and wild-type zebrafish embryo models. Variants in the gene Mapk8ip3 cause rare-neurodevelopmental disorders due to an essential role in axonal vesicle transport, elongation and regeneration. A subset of missense variants was examined by overexpressing the mRNA of these variants in a Jip3 knock-out zebrafish. Morphological, behavioral, and microscopic phenotypes were examined in zebrafish larvae. Using these assays, the spectrum of disorders can be phenotypically determined and the impact of variant location can be compared to knockout and wild-type zebrafish embryo models.

Keywords: rare disease, neurodevelopmental disorders, mrna overexpression, zebrafish research

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