Genetics Applications最新文献

{"title":"New insertions-induced Hb H disease","authors":"M. Alipour, S. Afzali, Khalil Khashei","doi":"10.31383/ga.vol5iss1pp64-67","DOIUrl":"https://doi.org/10.31383/ga.vol5iss1pp64-67","url":null,"abstract":"In spite of high incidence of α-thalassemia as the most common inherited disorder of hemoglobin (Hb) production in Southeast Asia, the role of point mutations in this aspect not still well known. This fact can lead to missing rare variants of α-thalassemia mutations by the routine screening, which they may need to be screened for possibility of causing Hb H disease. In this study we found two insertions in alpha1 gene which cause to Hb H disease. One of the insertions, 108/109, is a new findings and another one, codon 44, is the mutation which has been followed for the first time. These new molecular findings about changes in α-globin production which results in decreased of hemoglobin (Hb) value, have high-impact clinical importance.","PeriodicalId":32642,"journal":{"name":"Genetics Applications","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49613212","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Contemporary population genetics data for 23 Y-STR loci in the general Bosnian-Herzegovinian population","authors":"Naida Babić Jordamović, Tamara Kojović, S. Dogan, L. Bešić, Lana Salihefendić, R. Konjhodžić, Sabahudin Ćordić, V. Škaro, Petar Projić, Vesna Hadžiavdić, Adna Ašić, D. Marjanovic","doi":"10.31383/ga.vol5iss1pp51-63","DOIUrl":"https://doi.org/10.31383/ga.vol5iss1pp51-63","url":null,"abstract":"Bosnia and Herzegovina is located in the South-Eastern Europe, characterized by numerous historical influences, massive migration processes and complex population structure. For that reason, the aim of this study is to provide an accurate and precise update of the population genetics data of allele frequencies on 23 Y-STR loci in Bosnia and Herzegovina using larger sample size. For this purpose, 480 adult male individuals from the general population have been genotyped over 23 Y-STR loci contained in the PowerPlex Y23 system. Population genetics parameters have been calculated, namely allele and haplotype frequencies, gene and haplotype diversity, as well as Rst and P values for the assessment of interpopulation differences. The obtained results are in close agreement with previously published data for Bosnian-Herzegovinian population, as well as for local subpopulations. This study offers significantly increased resolution and information content, with 454 unique haplotypes. Population comparison reveals no statistically significant differences between the study population and 12 European populations used for comparison, as visualized through an MDS plot and neighbour-joining phylogenetic tree. This study offers representative data for local Y chromosomes that can be used for forensic applications, paternity and kinship testing, as well as for genealogical studies.","PeriodicalId":32642,"journal":{"name":"Genetics Applications","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48094483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In Memoriam: Mirsad Kurtović (1962– 2021)","authors":"Editorial Team","doi":"10.31383/ga.vol5iss1pp1-1","DOIUrl":"https://doi.org/10.31383/ga.vol5iss1pp1-1","url":null,"abstract":"","PeriodicalId":32642,"journal":{"name":"Genetics Applications","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44758175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparison of SARS-CoV-2 Virus Variant Genomes Detected in China and the USA","authors":"M. C. Sahingil, Y. Ozkazanc","doi":"10.31383/ga.vol4iss2pp10-26","DOIUrl":"https://doi.org/10.31383/ga.vol4iss2pp10-26","url":null,"abstract":"In the spreading period of the SARS-CoV-2 virus which is the cause of COVID-19 in the world, it is seen that the genome of the virus mutates and this mutation processes create new SARS-CoV-2 variants. In this study, we examined two variant genome groups. The first group includes the genomes of variants detected in China, while the second includes those detected in the USA. We applied the multiple sequence alignment process on these publicly available SARS-CoV-2 virus genomes and reported the obtained results. There are 87 genomes for China variants and 200 for USA variants in the used data. The analyses were made for each domain of the genomes. The results of the analysis show that the variant genomes in the two SARS-CoV-2 groups examined have some similar mutation features as well as different characteristics. It is also one of the results obtained in this study that the domains where the most mutations are detected on the genome are regions that have properties that affect the interaction of the virus with the host.","PeriodicalId":32642,"journal":{"name":"Genetics Applications","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46085015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Laboratory testing and screening for SARS-CoV-2: A review of current methods","authors":"D. Marjanovic, D. Primorac, V. Matišić, Vitorio Perić, Vilim Molnar, R. Zadro","doi":"10.31383/ga.vol4iss2pp1-9","DOIUrl":"https://doi.org/10.31383/ga.vol4iss2pp1-9","url":null,"abstract":"In a relatively short period of time new coronavirus disease (COVID-19) has become a global threat, both to human health and to the functioning of human society in general. This pandemic is certainly neither the first nor is it likely to be the last disease episode in human history. At the moment, it is still too early to make a reliable assessment of its total effect on human civilization, but it can already be stated that this disease, and its causative agent SARS-CoV-2 virus, have caused a strong scientific response all around the World. For the first time in this magnitude, it has united the resources of large scientific institutions and companies with the aim of finding solutions for fast and accurate virus detection procedures, effective and safe vaccine, reliable medical treatments, etc. It is astonishing that only a month has passed from the first officially detected case to the complete sequencing of the SARS-CoV-2 virus genome and the creation of the first detection systems based on RT-PCR method. After that, numerous scientific teams and companies worked together, or independently, to improve the detection methods. Their work included further optimization of PCR and other genetic approaches, as well as the development of detection methods based on the analysis of specific antibodies and viral antigens. The aim of this paper is to review the results that were achieved in this area so far, analyze the strategies currently used in the world and the region, and to predict future steps in the process of optimizing and improving methods for SARS CoV-2 detection in individual patients and the global human population.","PeriodicalId":32642,"journal":{"name":"Genetics Applications","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44971117","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of Nucleotide Patterns in Meconium Microbiota to Improve the Management of Meconium Aspiration Syndrome in Clinical Practice","authors":"F. Akçeşme, Şeyma İş","doi":"10.31383/ga.vol4iss2pp27-36","DOIUrl":"https://doi.org/10.31383/ga.vol4iss2pp27-36","url":null,"abstract":"For many years, airways, lungs and meconium, which is a thick green substance and accumulates in the baby’s intestines during pregnancy, have been assumed to be sterile. However, this assumption has been revised by the development of microbiota analysis, which is used for the identification of microorganisms as a new promising technique; it has been found that various microorganisms exist in the lungs and in the meconium fluid. Meconium Aspiration Syndrome (MAS) as a common neonatal problem can give rise to the development of lung infections in newborns and even cases leading to death are encountered. Various strategies regarding antibiotic therapy have been developed against the risk of infection, but positive outcome could not be obtained for each case. In this study, 16S rRNA gene sequences of bacteria existing in meconium microbiota and infected lung microbiota were subjected to comparative sequence analysis. Our aim was to identify positions of nucleotide patterns between the hypervariable regions of the bacterial 16S rRNA gene sequences that could provide similar functions among bacterial groups. Furthermore, similarity analysis was conducted to identify molecular signatures via phylogenetic framework to understand the etiology of the infections after MAS. Interestingly, Bifidobacteria which are used as probiotics were found to be similar to Actynomyces which are known as opportunistic pathogens. Furthermore, Clostridium leptum was associated with pulmonary inflammation for the first time. This study proposes the usage of microbiota analysis to improve the MAS management in clinical practice.","PeriodicalId":32642,"journal":{"name":"Genetics Applications","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41722958","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"1 Model reduction in chemical process optimization","authors":"John P. Eason, L. Biegler","doi":"10.1515/9783110499001-001","DOIUrl":"https://doi.org/10.1515/9783110499001-001","url":null,"abstract":": Chemical processes are often described by heterogeneous models that range from algebraic equations for lumped parameter systems to black-box models for PDE systems. The integration, solution, and optimization of this ensemble of process models is often difficult and computationally expensive. As a result, reduction in the form of reduced-order models and data-driven surrogate models is widely applied in chemical processes. This chapter reviews the development and application of reduced models (RMs) in this area, as well as their integration to process optimization. Special at-tention is given to the construction of reduced models that provide suitable represen-tations of their detailed counterparts, and a novel trust region filter algorithm with reduced models is described that ensures convergence to the optimum with truth models. Two case studies on CO 2 capture are described and optimized with this trust region filter method. These results demonstrate the effectiveness and wide applicability of the trust region approach with reduced models.","PeriodicalId":32642,"journal":{"name":"Genetics Applications","volume":"72 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79639312","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Preface to the third volume of Model Order Reduction","authors":"P. Benner, S. Grivet-Talocia, A. Quarteroni, G. Rozza, W. Schilders, L. M. Silveira","doi":"10.1515/9783110499001-201","DOIUrl":"https://doi.org/10.1515/9783110499001-201","url":null,"abstract":"The third volume of the Model Order Reduction handbook project offers several remarkable instances of applications of model order reduction (MOR) approaches to the solution of problems arising from themost diverse areas of application. Through these examples, we would like to provide the reader with an overview of thematurity of this emerging field and its readiness to address challenging problems ofmultifaceted complexity. We start with several chapter contributions to classical fields of engineering. The first one, by J. Eason and L. Biegler, is onmodel reduction in the optimization of a variety of heterogeneous chemical processes. In particular, two case studies are presented on CO2 capture using nonlinear programming and NLP filter models. The second chapter, by B. Lohmann et al., is on MOR in mechanical engineering. Four applications are discussed, concerning the reduction of a thermo-mechanical machining tool of a car body and driver’s seat, of an elastic crankshaft, and a leaf spring model. The third chapter, by E. Deckers et al., presents several case studies of MOR for acoustics and vibrations inmechanical applications. Two different viewpoints are developed: the application of MOR from a purely mathematical perspective and a consideration of expected properties of MOR based on physical arguments from the field of mechanics. Two chapters devoted to microelectronics and electromagnetism, a very classical and successful arena for MOR methods, follow. The first of those, by B. Nouri et al., pursues a twofold goal: to describe the context in which the need for MOR arose in microelectronics, and to present an overview of their applications to address the issues of high-speed interconnects in microelectronics at various levels of the design hierarchy. The next chapter, by D. Ioan et al., proposes a computer-aided consistent and accurate description of the behavior of electromagnetic devices at various speeds or frequencies, and describes procedures to generate compact electrical circuits featuring an approximately equivalent behavior. The chapter by M. Yano is on model reduction in computational aerodynamics. The focus is on techniques that are designed to address nonlinearity, limited stability, limited regularity, and a wide range of scales that have been demonstrated successful for multidimensional large-scale aerodynamic flows. The next two chapters address a somehow less conventional field of applications, that of life sciences. The chapter by B. Karasözen is on MOR in neurosciences, more specifically on the exploitation of models of large-scale neuronal networks to provide an accurate and fast prediction of patterns and their propagation in different areas of the brain. The following chapter, by N. Dal Santo et al., introduces MOR methods to face some of the most challenging processes of the cardiovascular system. Two specific","PeriodicalId":32642,"journal":{"name":"Genetics Applications","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87781675","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"8 Reduced-order modeling for applications to the cardiovascular system","authors":"N. D. Santo, A. Manzoni, S. Pagani, A. Quarteroni","doi":"10.1515/9783110499001-008","DOIUrl":"https://doi.org/10.1515/9783110499001-008","url":null,"abstract":": The capability to provide fast and reliable numerical simulations is of paramount importance when dealing with complex applications arising from medi-cine. More than for other branches of engineering and applied sciences, performing accurate computations in a short amount of time – minutes, rather than hours, or even days – is crucial when dealing with problems arising from life sciences, like, e. g., in the simulation of the cardiovascular system. Moreover, many sources of variability carried by subject-specific features have to be incorporated into the mathematical models, to quantify their impact on the computed results. For these reasons, bringing computational results into clinical practice represents a great challenge. Reduced-order modeling techniques such as the reduced basis method represent a key tool towards the possibility to address these challenges, thus making the numerical modeling of the cardiovascular system a new, fascinating testbed for these methodologies.","PeriodicalId":32642,"journal":{"name":"Genetics Applications","volume":"91 10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89846624","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"12 Model order reduction and digital twins","authors":"","doi":"10.1515/9783110499001-012","DOIUrl":"https://doi.org/10.1515/9783110499001-012","url":null,"abstract":"","PeriodicalId":32642,"journal":{"name":"Genetics Applications","volume":"13 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1515/9783110499001-012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72542732","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}