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https://www.readbyqxmd.com/read/28227814/embedded-cmos-basecalling-for-nanopore-dna-sequencing
#1
Chengjie Wang, Junli Zheng, Sebastian Magierowski, Ebrahim Ghafar-Zadeh, Chengjie Wang, Junli Zheng, Sebastian Magierowski, Ebrahim Ghafar-Zadeh, Junli Zheng, Chengjie Wang, Ebrahim Ghafar-Zadeh, Sebastian Magierowski
DNA sequencing based on nanopore sensors is now entering the marketplace. The ability to interface this technology to established CMOS microelectronics promises significant improvements in functionality and miniaturization. Among the key functions to benefit from this interface will be basecalling, the conversion of raw electronic molecular signatures to nucleotide sequence predictions. This paper presents the design and performance potential of custom CMOS base-callers embedded alongside nanopore sensors. A basecalliing architecture implemented in 32-nm technology is discussed with the ability to process the equivalent of 20 human genomes per day in real-time at a power density of 5 W/cm(2) assuming a 3-mer nanopore sensor...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227475/label-free-detection-of-sex-determining-region-y-sry-via-capacitive-biosensor
#2
Shilpa Sivashankar, Christos Sapsanis, Sumeyra Agambayev, Ulrich Buttner, Khaled Nabil Salama, Shilpa Sivashankar, Christos Sapsanis, Sumeyra Agambayev, Ulrich Buttner, Khaled Nabil Salama, Khaled Nabil Salama, Shilpa Sivashankar, Sumeyra Agambayev, Christos Sapsanis, Ulrich Buttner
In this work, we present for the first time, the use of a simple fractal capacitive biosensor for the quantification and detection of sex-determining region Y (SRY) genes. This section of genetic code, which is found on the Y chromosome, finds importance for study as it causes fetuses to develop characteristics of male sex-like gonads when a mutation occurs. It is also an important genetic code in men, and disorders involving the SRY gene can cause infertility and sexual malfunction that lead to a variety of gene mutational disorders...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227431/bio-active-polymer-implants-to-adipose-tissue-as-in-situ-source-of-reprogramming-cells
#3
Andrey Mikhailov, Fumihiro Sugiyama, Saori Mizuno, Yoshiyuki Sankai, Andrey Mikhailov, Fumihiro Sugiyama, Saori Mizuno, Yoshiyuki Sankai, Saori Mizuno, Andrey Mikhailov, Fumihiro Sugiyama, Yoshiyuki Sankai
The implants from natural polymer chitosan was developed by sorption of non-viral DNA vector. These assemblies were shown to be biocompatible and able to transfect the surrounding cells with reprogramming factors. Transgenic rats from the strain allowing visualization of Nanog-positive stem cells received these implants into their adipose deposits. After 8 days we were able to detect in situ-transfected cells. Transfected cells were positive for YFP fluorescence and transiently expressed the markers correlating with stemness...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227267/constrained-variant-detection-with-sparc-sparsity-parental-relatedness-and-coverage
#4
Mario Banuelos, Rubi Almanza, Lasith Adhikari, Roummel F Marcia, Suzanne Sindi, Mario Banuelos, Rubi Almanza, Lasith Adhikari, Roummel F Marcia, Suzanne Sindi, Mario Banuelos, Roummel F Marcia, Lasith Adhikari, Rubi Almanza, Suzanne Sindi
Structural variants (SVs) are rearrangements of DNA sequences such as inversions, deletions, insertions and translocations. The common method for detecting SVs has been to sequence data from a test genome and map it to a reference genome. More recently, DNA sequencing studies may consist of hundreds, or even thousands of individuals, some of which may be related. In order to improve our ability to identify SVs, we boost the true SV signals by simultaneously analyzing parent and child genomes. Our algorithmic formulation - SPaRC - employs realistic criteria such as sparsity of SVs, relatedness between individuals and variable sequencing coverage throughout the genome...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227168/a-novel-method-for-splice-sites-prediction-using-sequence-component-and-hidden-markov-model
#5
Elham Pashaei, Alper Yilmaz, Mustafa Ozen, Nizamettin Aydin, Elham Pashaei, Alper Yilmaz, Mustafa Ozen, Nizamettin Aydin, Nizamettin Aydin, Alper Yilmaz, Elham Pashaei, Mustafa Ozen
With increasing growth of DNA sequence data, it has become an urgent demand to develop new methods to accurately predict the genes. The performance of gene detection methods mainly depend on the efficiency of splice site prediction methods. In this paper, a novel method for detecting splice sites is proposed by using a new effective DNA encoding method and AdaBoost.M1 classifier. Our proposed DNA encoding method is based on multi-scale component (MSC) and first order Markov model (MM1). It has been applied to the HS3D dataset with repeated 10 fold cross validation...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226779/biologically-inspired-design-of-feedback-control-systems-implemented-using-dna-strand-displacement-reactions
#6
Mathias Foo, Rucha Sawlekar, Vishwesh V Kulkarni, Declan G Bates, Mathias Foo, Rucha Sawlekar, Vishwesh V Kulkarni, Declan G Bates, Vishwesh V Kulkarni, Rucha Sawlekar, Declan G Bates, Mathias Foo
The use of abstract chemical reaction networks (CRNs) as a modelling and design framework for the implementation of computing and control circuits using enzyme-free, entropy driven DNA strand displacement (DSD) reactions is starting to garner widespread attention in the area of synthetic biology. Previous work in this area has demonstrated the theoretical plausibility of using this approach to design biomolecular feedback control systems based on classical proportional-integral (PI) controllers, which may be constructed from CRNs implementing gain, summation and integrator operators...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226777/predicting-schizophrenia-by-fusing-networks-from-snps-dna-methylation-and-fmri-data
#7
Su-Ping Deng, Dongdong Lin, Vince D Calhoun, Yu-Ping Wang, Su-Ping Deng, Dongdong Lin, Vince D Calhoun, Yu-Ping Wang, Vince D Calhoun, Su-Ping Deng, Yu-Ping Wang, Dongdong Lin
In order to comprehensively utilize complementary information from multiple types of data for better disease diagnosis, in this study, we applied a network fusion based approach to integrating three types of data including genetic, epigenetic and neuroimaging data from a study of schizophrenia patients (SCZ). A network is a map of interactions, which contributes to investigating the connectivity of components or links between sub-units. We exploited the potential of using networks as features for discriminating SCZ from healthy controls...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226775/evaluation-of-multidrug-cancer-chronotherapy-based-on-cell-cycle-model-under-influences-of-circadian-clock
#8
Hiroshi Inokawa, Norihiro Katayama, Mitsuyuki Nakao, Hiroshi Inokawa, Norihiro Katayama, Mitsuyuki Nakao, Mitsuyuki Nakao, Hiroshi Inokawa, Norihiro Katayama
The intracellular circadian clock mechanisms are known to affect various substantial cellular machinery such as cell cycle progression, inflammatory response, apoptosis, and DNA repair. Cancer growth in various tissues is still under circadian control, which may be at least partly underlain by the survived connections between the intracellular machinery and the clock. Considering such findings, chronotherapy has been applied to cancer treatments, in which anti-cancer drugs are administered in scheduled circadian times so as to resolve the trade-off between damages against the normal and cancer cells...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226773/biclustering-strategies-for-genetic-marker-selection-in-gynecologic-tumor-cell-lines
#9
A Alevyzaki, S Sfakianakis, E S Bei, E Obermayr, R Zeillinger, D Fotiadis, M Zervakis, A Alevyzaki, S Sfakianakis, E S Bei, E Obermayr, R Zeillinger, D Fotiadis, M Zervakis, R Zeillinger, D Fotiadis, E S Bei, S Sfakianakis, M Zervakis, A Alevyzaki, E Obermayr
Over the past few decades great interest has been focused on cell lines derived from tumors, because of their usability as models to understand the biology of cancer. At the same time, advanced technologies such as DNA-microarrays have been broadly used to study the expression level of thousands of genes in primary tumors or cancer cell lines in a single experiment. Results from microarray analysis approaches have provided valuable insights into the underlying biology and proven useful for tumor classification, prognostication and prediction...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226512/hyperthermia-by-electromagnetic-fields-to-enhanced-clinical-results-in-oncology
#10
Gerard C van Rhoon, Maarten M Paulides, Jeannette M L van Holthe, Martine Franckena, Gerard C van Rhoon, Maarten M Paulides, Jeannette M L van Holthe, Martine Franckena, Maarten M Paulides, Martine Franckena, Gerard C van Rhoon, Jeannette M L van Holthe
Confining treatment to the tumor to improve therapeutic outcome and reduce toxicity, is a hot issue in cancer research. Hyperthermia is recognized as a strong sensitizer for radiotherapy and chemotherapy enhancing tumor control without increasing toxicity. Today's electromagnetic hyperthermia systems heat large tissue volumes with limited ability to selectively heat the tumor. Fortunately, tremendous improvements in 3-dimensional electromagnetic & temperature modelling provide an exciting opportunity to design advanced multi-element electromagnetic applicator systems...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226421/opening-plenary-speaker-human-genomics-precision-medicine-and-advancing-human-health
#11
Eric D Green
Starting with the launch of the Human Genome Project in 1990, the past quarter-century has brought spectacular achievements in genomics that dramatically empower the study of human biology and disease. The human genomics enterprise is now in the midst of an important transition, as the growing foundation of genomic knowledge is being used by researchers and clinicians to tackle increasingly complex problems in biomedicine. Of particular prominence is the use of revolutionary new DNA sequencing technologies for generating prodigious amounts of DNA sequence data to elucidate the complexities of genome structure, function, and evolution, as well as to unravel the genomic bases of rare and common diseases...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226412/rage-polymorphisms-and-oxidative-stress-levels-in-hashimoto-s-thyroiditis
#12
Maria Giannakou, Katerina Saltiki, Emily Mantzou, Eleni Loukari, Georgios Philippou, Konstantinos Terzidis, Kiriaki Lili, Charalampos Stavrianos, Miltiades Kyprianou, Maria Alevizaki
BACKGROUND: Polymorphisms of the receptor for advanced glycation end products (RAGE) gene have been studied in various autoimmune disorders, but not in Hashimoto's thyroiditis. Also, increased oxidative stress has been described in patients with Hashimoto's thyroiditis. The aim of the present study was to investigate the possible role of two common RAGE polymorphisms (-429T>C, -374T>A) in Hashimoto's thyroiditis; in parallel we studied oxidative stress levels. MATERIALS AND METHODS: 300 consecutive euthyroid women were examined and classified into three groups: Hashimoto's thyroiditis with treatment (n=96), Hashimoto's thyroiditis without treatment (n=109) and controls (n=95)...
February 22, 2017: European Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28226269/the-causes-and-consequences-of-dna-methylome-variation-in-plants
#13
REVIEW
Danelle K Seymour, Claude Becker
Epigenetic variation - polymorphisms at the level of DNA methylation or histone modifications - modulates chromatin accessibility, which can perturb transcriptional activity and spur phenotypic variation. Determining the origin, frequency spectrum, and consequences of epigenetic variants is key to understanding the role of this variation in generating stable phenotypic variation in plants. Here we review recent literature on DNA methylation variation in both model and crop plant species with a focus on the link between genotype, epigenotype, and transcription...
February 19, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28226256/endocrine-and-cellular-stress-effects-of-zinc-oxide-nanoparticles-and-nifedipine-in-marsh-frogs-pelophylax-ridibundus
#14
Halina Falfushynska, Lesya Gnatyshyna, Oksana Horyn, Inna Sokolova, Oksana Stoliar
Freshwater organisms including amphibians experience increasing exposures to emerging pollutants such as nanoparticles and pharmaceuticals, which can affect their fitness and performance. We studied the effects of two common pollutants extensively used in industry, pharmaceutical and personal care products, nano-zinc oxide (nZnO) and a Ca-channel blocker nifedipine (Nfd), on endocrine status and cellular stress markers of the marsh frog Pelophylax ridibundus. Males were exposed for 14days to nZnO (3.1μM), Zn(2+) (3...
February 8, 2017: Aquatic Toxicology
https://www.readbyqxmd.com/read/28226235/plant-mitochondrial-genomes-dynamics-and-mechanisms-of-mutation
#15
José M Gualberto, Kathleen J Newton
The large mitochondrial genomes of angiosperms are unusually dynamic because of recombination activities involving repeated sequences. These activities generate subgenomic forms and extensive genomic variation even within the same species. Such changes in genome structure are responsible for the rapid evolution of plant mitochondrial DNA and for the variants associated with cytoplasmic male sterility and abnormal growth phenotypes. Nuclear genes modulate these processes, and over the past decade, several of these genes have been identified...
February 9, 2017: Annual Review of Plant Biology
https://www.readbyqxmd.com/read/28226213/an-oscillatory-reaction-induced-periodic-c-quadruplex-dna-gating-of-artificial-ion-channels
#16
Jian Wang, Ruochen Fang, Jue Hou, Huacheng Zhang, Ye Tian, Huanting Wang, Lei Jiang
Many biological ion channels controlled by biochemical reactions have autonomous and periodic gating functions, which play important roles in continuous mass transport and signal transmission of living systems. Inspired by these functional biological ion channel systems, here we report an artificial self-oscillating nanochannel system that can autonomously and periodically control its gating process under constant conditions. The system is constructed by integrating a chemical oscillator, consisting of BrO3-, Fe(CN)64-, H+, and SO32-, into a synthetic proton-sensitive nanochannel modified with C-quadruplex (C4) DNA motors...
February 22, 2017: ACS Nano
https://www.readbyqxmd.com/read/28226066/chlamydia-trachomatis-infection-in-young-pregnant-women-in-southern-brazil-a-cross-sectional-study
#17
Mariângela Freitas da Silveira, Iândora Krolow Timm Sclowitz, Ludmila Gonçalves Entiauspe, Marilia Arndt Mesenburg, Dulce Stauffert, Guilherme Lucas de Oliveira Bicca, Carine Pieniz, Adriane Brod Manta
This study estimated the prevalence of Chlamydia trachomatis infection during pregnancy in a sample of women up to 29 years of age in the city of Pelotas, Rio Grande do Sul State, Brazil, and investigated socio-demographic risk factors such as maternal age, marital status, maternal schooling, and family income. C. trachomatis infection was diagnosed with PCR using BD ProbeTecTM CT/GC Amplified DNA Assay. Socio-demographic, behavioral, and reproductive data were collected using structured questionnaires. All collections were performed by previously trained medical students...
February 13, 2017: Cadernos de Saúde Pública
https://www.readbyqxmd.com/read/28225902/diagnosis-of-human-herpes-virus-1-and-2-hhv-1-and-hhv-2-use-of-a-synthetic-standard-curve-for-absolute-quantification-by-real-time-polymerase-chain-reaction
#18
Lyana Rodrigues Pinto Lima, Amanda Perse da Silva, Jonas Schmidt-Chanasit, Vanessa Salete de Paula
The use of quantitative real time polymerase chain reaction (qPCR) for herpesvirus detection has improved the sensitivity and specificity of diagnosis, as it is able to detect shedding episodes in the absence of clinical lesions and diagnose clinical specimens that have low viral loads. With an aim to improve the detection and quantification of herpesvirus by qPCR, synthetic standard curves for human herpesvirus 1 and 2 (HHV-1 and HHV-2) targeting regions gD and gG, respectively, were designed and evaluated...
March 2017: Memórias do Instituto Oswaldo Cruz
https://www.readbyqxmd.com/read/28225896/diagnosis-of-human-herpes-virus-1-and-2-hhv-1-and-hhv-2-use-of-a-synthetic-standard-curve-for-absolute-quantification-by-real-time-polymerase-chain-reaction
#19
Lyana Rodrigues Pinto Lima, Amanda Perse da Silva, Jonas Schmidt-Chanasit, Vanessa Salete de Paula
The use of quantitative real time polymerase chain reaction (qPCR) for herpesvirus detection has improved the sensitivity and specificity of diagnosis, as it is able to detect shedding episodes in the absence of clinical lesions and diagnose clinical specimens that have low viral loads. With an aim to improve the detection and quantification of herpesvirus by qPCR, synthetic standard curves for human herpesvirus 1 and 2 (HHV-1 and HHV-2) targeting regions gD and gG, respectively, were designed and evaluated...
February 16, 2017: Memórias do Instituto Oswaldo Cruz
https://www.readbyqxmd.com/read/28225881/zinc-and-metalloproteinases-2-and-9-what-is-their-relation-with-breast-cancer
#20
Aldenora Oliveira do Nascimento Holanda, Ana Raquel Soares de Oliveira, Kyria Jayanne Clímaco Cruz, Juliana Soares Severo, Jennifer Beatriz Silva Morais, Benedito Borges da Silva, Dilina do Nascimento Marreiro
Zinc is the catalytic component of proteins that regulate responses to DNA damage, intracellular signaling enzymes, and matrix metalloproteinases, which are important proteins in carcinogenesis. The objective of this review is to bring current information on the participation of zinc and matrix metalloproteinases types 2 and 9 in mechanisms involved in the pathogenesis of breast cancer. We conducted a literature review, in consultation with the PubMed, Lilacs, and Scielo databases. The zinc and cysteine residues are structural elements shared by all members of the family of matrix metalloproteinases, and these proteins appear to be involved in the propagation of various types of neoplasms, including breast cancer...
January 1, 2017: Revista da Associação Médica Brasileira
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