keyword
MENU ▼
Read by QxMD icon Read
search

Nucleotide performance

keyword
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/28225862/association-between-c1q-gene-polymorphisms-and-autoimmune-thyroid-diseases
#2
Qiuming Yao, Jie Li, Xiaofei An, Wenjuan Jiang, Qiu Qin, Ronghua Song, Ni Yan, Danfeng Li, Yanfei Jiang, Wen Wang, Liangfeng Shi, Jin-An Zhang
Objective: In the present study, we aimed to assess the associations of C1q gene polymorphisms with autoimmune thyroid diseases (AITD) susceptibility. Subjects and methods: A set of 1,003 AITD patients (661 with Graves' disease and 342 with Hashimoto's thyroiditis) and 880 ethnically- and geographically-matched controls from Chinese Han population were included. Five common single nucleotide polymorphisms (SNPs) (rs294185, rs292001, rs682658, rs665691 and rs294179) in C1q gene locus were genotyped...
February 16, 2017: Archives of Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28225814/e-npp3-controls-plasmacytoid-dendritic-cell-numbers-in-the-small-intestine
#3
Yoki Furuta, Shih-Han Tsai, Makoto Kinoshita, Kosuke Fujimoto, Ryu Okumura, Eiji Umemoto, Yosuke Kurashima, Hiroshi Kiyono, Hisako Kayama, Kiyoshi Takeda
Extracellular adenosine 5'-triphosphate (ATP) performs multiple functions including activation and induction of apoptosis of many cell types. The ATP-hydrolyzing ectoenzyme ecto-nucleotide pyrophosphatase/phosphodiesterase 3 (E-NPP3) regulates ATP-dependent chronic allergic responses by mast cells and basophils. However, E-NPP3 is also highly expressed on epithelial cells of the small intestine. In this study, we showed that E-NPP3 controls plasmacytoid dendritic cell (pDC) numbers in the intestine through regulation of intestinal extracellular ATP...
2017: PloS One
https://www.readbyqxmd.com/read/28225792/the-adamts9-gene-is-associated-with-cognitive-aging-in-the-elderly-in-a-taiwanese-population
#4
Eugene Lin, Shih-Jen Tsai, Po-Hsiu Kuo, Yu-Li Liu, Albert C Yang, Chung-Feng Kao, Cheng-Hung Yang
Evidence indicates that the pathophysiologic mechanisms associated with insulin resistance may contribute to cognitive aging and Alzheimer's diseases. In this study, we hypothesize that single nucleotide polymorphisms (SNPs) within insulin resistance-associated genes, such as the ADAM metallopeptidase with thrombospondin type 1 motif 9 (ADAMTS9), glucokinase regulator (GCKR), and peroxisome proliferator activated receptor gamma (PPARG) genes, may be linked with cognitive aging independently and/or through complex interactions in an older Taiwanese population...
2017: PloS One
https://www.readbyqxmd.com/read/28225367/progranulin-gene-variation-affects-serum-progranulin-levels-differently-in-danish-bipolar-individuals-compared-with-healthy-controls
#5
Henriette N Buttenschøn, Marit N Nielsen, Gangadaar Thotakura, Chris W Lee, Anders Nykjær, Ole Mors, Simon Glerup
OBJECTIVES: The identification of peripheral biomarkers for bipolar disorder is of great importance and has the potential to improve diagnosis, treatment and prognosis. Recent studies have reported lower plasma progranulin levels in bipolar individuals compared with controls and association with single nucleotide polymorphisms (SNPs) within the progranulin gene (GRN). In the present study, we investigated the effect of GRN and sortilin (SORT1) gene variation on serum progranulin levels in bipolar individuals and controls...
February 20, 2017: Psychiatric Genetics
https://www.readbyqxmd.com/read/28224923/high-throughput-sequencing-reveals-modulation-of-micrornas-in-vigna-mungo-upon-mungbean-yellow-mosaic-india-virus-inoculation-highlighting-stress-regulation
#6
Anirban Kundu, Sujay Paul, Avishek Dey, Amita Pal
MicroRNAs (miRNAs) are 20-24 nucleotides long non-coding RNAs known to play important regulatory roles during biotic and abiotic stresses by controlling gene expression. Blackgram (Vigna mungo), an economically important grain legume is highly susceptible to pathogenic begomovirus Mungbean Yellow Mosaic India Virus (MYMIV) and resulting in high yield loss. In this study two different leaf-small-RNA libraries were prepared from the pooled RNA at three different time points of resistant V. mungo inbred line VM84 inoculated either with viruliferous or non-viruliferous whiteflies carrying MYMIV and performed high-throughput Illumina sequencing...
April 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28224759/genomic-variants-at-20p11-associated-with-body-fat-mass-in-the-european-population
#7
Yu-Fang Pei, Hai-Gang Ren, Lu Liu, Xiao Li, Chen Fang, Yun Huang, Wen-Zhu Hu, Wei-Wen Kong, An-Ping Feng, Xin-Yi You, Wen Zhao, Hui Shen, Qing Tian, Yong-Hong Zhang, Hong-Wen Deng, Lei Zhang
OBJECTIVE: Body fat mass (BFM) is more homogeneous and accurate than body total mass in measuring obesity but has rarely been studied. Aiming to uncover the genetic basis of fat-induced obesity, a genome-wide association meta-analysis of BFM, after adjustment by body lean mass, was performed in the European population. METHODS: Three samples of European ancestry were included in the meta-analysis: the Framingham Heart Study (N = 6,004), the Kansas City osteoporosis study (N = 2,207), and the Omaha osteoporosis study (N = 968)...
February 22, 2017: Obesity
https://www.readbyqxmd.com/read/28224052/compacting-and-correcting-trinity-and-oases-rna-seq-de-novo-assemblies
#8
Cédric Cabau, Frédéric Escudié, Anis Djari, Yann Guiguen, Julien Bobe, Christophe Klopp
BACKGROUND: De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is still possible to improve them in several ways including redundancy reduction or error correction. Trinity and Oases are two commonly used de novo transcriptome assemblers. The contig sets they produce are of good quality. Still, their compaction (number of contigs needed to represent the transcriptome) and their quality (chimera and nucleotide error rates) can be improved...
2017: PeerJ
https://www.readbyqxmd.com/read/28223827/common-variations-within-hace1-gene-and-neuroblastoma-susceptibility-in-a-southern-chinese-population
#9
Zhuorong Zhang, Ruizhong Zhang, Jinhong Zhu, Fenghua Wang, Tianyou Yang, Yan Zou, Jing He, Huimin Xia
Neuroblastoma is a common fatal pediatric cancer of the developing sympathetic nervous system, which accounts for ~10% of all pediatric cancer deaths. To investigate genetic risk factors related to neuroblastoma, many genome-wide association studies have been performed, and single nucleotide polymorphisms (SNPs) within HACE1 gene have been identified to associate with neuroblastoma risk. However, the association of the HACE1 SNPs with neuroblastoma needs to be validated in Southern Chinese children. We genotyped five SNPs located in the HACE1 gene (rs4336470 C>T, rs9404576 T>G, rs4079063 A>G, rs2499663 T>C, and rs2499667 A>G) in 256 Southern Chinese patients in comparison with 531 ethnically matched healthy controls...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28222201/linkage-and-mapping-of-quantitative-trait-loci-associated-with-angular-leaf-spot-and-powdery-mildew-resistance-in-common-beans
#10
Denis Bassi, Boris Briñez, Juliana Santa Rosa, Paula Rodrigues Oblessuc, Caléo Panhoca de Almeida, Stella Maris Nucci, Larissa Chariel Domingos da Silva, Alisson Fernando Chiorato, Rosana Pereira Vianello, Luis Eduardo Aranha Camargo, Matthew Wohlgemuth Blair, Luciana Lasry Benchimol-Reis
Angular leaf spot (ALS) and powdery mildew (PWM) are two important fungi diseases causing significant yield losses in common beans. In this study, a new genetic linkage map was constructed using single sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs), in a segregating population derived from the AND 277 x SEA 5 cross, with 105 recombinant inbred lines. Phenotypic evaluations were performed in the greenhouse to identify quantitative trait loci (QTLs) associated with resistance by means of the composite interval mapping analysis...
February 20, 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28222164/comt-and-drd2-ankk-1-gene-gene-interaction-account-for-resetting-of-gamma-neural-oscillations-to-auditory-stimulus-driven-attention
#11
Manuel Garcia-Garcia, Marc Via, Katarzyna Zarnowiec, Iria SanMiguel, Carles Escera, Immaculada C Clemente
Attention capture by potentially relevant environmental stimuli is critical for human survival, yet it varies considerably among individuals. A large series of studies has suggested that attention capture may depend on the cognitive balance between maintenance and manipulation of mental representations and the flexible switch between goal-directed representations and potentially relevant stimuli outside the focus of attention; a balance that seems modulated by a prefrontostriatal dopamine pathway. Here, we examined inter-individual differences in the cognitive control of attention through studying the effects of two single nucleotide polymorphisms regulating dopamine at the prefrontal cortex and the striatum (i...
2017: PloS One
https://www.readbyqxmd.com/read/28222155/glm-based-optimization-of-ngs-data-analysis-a-case-study-of-roche-454-ion-torrent-pgm-and-illumina-nextseq-sequencing-data
#12
Sarah Sandmann, Aniek O de Graaf, Bert A van der Reijden, Joop H Jansen, Martin Dugas
BACKGROUND: There are various next-generation sequencing techniques, all of them striving to replace Sanger sequencing as the gold standard. However, false positive calls of single nucleotide variants and especially indels are a widely known problem of basically all sequencing platforms. METHODS: We considered three common next-generation sequencers-Roche 454, Ion Torrent PGM and Illumina NextSeq-and applied standard as well as optimized variant calling pipelines...
2017: PloS One
https://www.readbyqxmd.com/read/28220580/molecular-diagnosis-of-von-willebrand-disease
#13
REVIEW
L Baronciani, A Goodeve, F Peyvandi
The role of molecular characterization in the diagnosis of von Willebrand disease (VWD) is not essential if the patients have been extensively investigated using phenotypic analysis. On the other hand, if some of these phenotype assays are not available, the identification of the mutation causing the disease could be crucial for an accurate diagnosis. Nevertheless, there are several reasons for performing molecular analysis in patients phenotypically well characterized, e.g. to identify the mutation causing VWD can be useful for patients and their family members when prenatal diagnosis is required (type 3 or severe type 2)...
February 20, 2017: Haemophilia: the Official Journal of the World Federation of Hemophilia
https://www.readbyqxmd.com/read/28220155/specificity-of-snp-detection-with-molecular-beacons-is-improved-by-stem-and-loop-separation-with-spacers
#14
Valentina M Farzan, Mikhail L Markelov, Alexander Yu Skoblov, German A Shipulin, Timofei S Zatsepin
Molecular beacons (MBs) are valuable tools in molecular biology, clinical diagnostics and analytical chemistry. Here we describe a novel approach for the design of MBs with nucleotide or non-nucleotide linkers between the stem and loop regions. Such modified MBs have significantly improved specificity and performance for single nucleotide polymorphism (SNP) detection. These advantages are especially distinct, when compared to the classic MBs, in the case of possible interactions between the stem and loop regions...
February 21, 2017: Analyst
https://www.readbyqxmd.com/read/28219476/genetic-parameters-and-genome-wide-associations-of-twinning-rate-in-a-local-breed-the-maremmana-cattle
#15
B Moioli, R Steri, C Marchitelli, G Catillo, L Buttazzoni
This study seeks to verify the feasibility of increasing twinning in a herd of the Italian autochtonous Maremmana breed. The data set included 1260 individuals born from 1963 to 2014, 527 males and 733 females, 402 of them calving at least once from 1983 through 2015. Breeding values for twinning were estimated by a single-trait linear animal model. However, since twinning is a dichotomous trait and the frequency of twins is far smaller than the frequency of single births, breeding values were also estimated by a single-trait animal threshold model...
February 21, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/28219347/aquaculture-genomics-genetics-and-breeding-in-the-united-states-current-status-challenges-and-priorities-for-future-research
#16
EDITORIAL
Hisham Abdelrahman, Mohamed ElHady, Acacia Alcivar-Warren, Standish Allen, Rafet Al-Tobasei, Lisui Bao, Ben Beck, Harvey Blackburn, Brian Bosworth, John Buchanan, Jesse Chappell, William Daniels, Sheng Dong, Rex Dunham, Evan Durland, Ahmed Elaswad, Marta Gomez-Chiarri, Kamal Gosh, Ximing Guo, Perry Hackett, Terry Hanson, Dennis Hedgecock, Tiffany Howard, Leigh Holland, Molly Jackson, Yulin Jin, Karim Kahlil, Thomas Kocher, Tim Leeds, Ning Li, Lauren Lindsey, Shikai Liu, Zhanjiang Liu, Kyle Martin, Romi Novriadi, Ramjie Odin, Yniv Palti, Eric Peatman, Dina Proestou, Guyu Qin, Benjamin Reading, Caird Rexroad, Steven Roberts, Mohamed Salem, Andrew Severin, Huitong Shi, Craig Shoemaker, Sheila Stiles, Suxu Tan, Kathy F J Tang, Wilawan Thongda, Terrence Tiersch, Joseph Tomasso, Wendy Tri Prabowo, Roger Vallejo, Hein van der Steen, Khoi Vo, Geoff Waldbieser, Hanping Wang, Xiaozhu Wang, Jianhai Xiang, Yujia Yang, Roger Yant, Zihao Yuan, Qifan Zeng, Tao Zhou
Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships...
February 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28218664/determination-of-vegfr-2-kdr-604a-g-polymorphism-in-pancreatic-disorders
#17
Vlad Pădureanu, Mihail Virgil Boldeanu, Ioana Streaţă, Mihai Gabriel Cucu, Isabela Siloşi, Lidia Boldeanu, Maria Bogdan, Anca Ştefania Enescu, Maria Forţofoiu, Aurelia Enescu, Elena Mădălina Dumitrescu, Dragoş Alexandru, Valeriu Marian Şurlin, Mircea Cătălin Forţofoiu, Ileana Octavia Petrescu, Florin Petrescu, Mihai Ioana, Marius Eugen Ciurea, Adrian Săftoiu
Pancreatic disorders have a high prevalence worldwide. Despite the fact that screening methods became more effective and the knowledge we have nowadays about pancreatic diseases has enhanced, their incidence remains high. Our purpose was to determine whether single nucleotide polymorphism (SNP) of VEGFR-2/KDR (vascular endothelial growth factor receptor 2/kinase insert domain receptor) influences susceptibility to develop pancreatic pathology. Genomic DNA was extracted from blood samples collected from patients diagnosed with acute pancreatitis (n = 110), chronic pancreatitis (n = 25), pancreatic cancer (n = 82) and healthy controls (n = 232)...
February 17, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28218639/genetic-variations-as-modifying-factors-to-dietary-zinc-requirements-a-systematic-review
#18
REVIEW
Kaitlin J Day, Melissa M Adamski, Aimee L Dordevic, Chiara Murgia
Due to reduced cost and accessibility, the use of genetic testing has appealed to health professionals for personalising nutrition advice. However, translation of the evidence linking polymorphisms, dietary requirements, and pathology risk proves to be challenging for nutrition and dietetic practitioners. Zinc status and polymorphisms of genes coding for zinc-transporters have been associated with chronic diseases. The present study aimed to systematically review the literature to assess whether recommendations for zinc intake could be made according to genotype...
February 17, 2017: Nutrients
https://www.readbyqxmd.com/read/28217922/characterization-of-e-ntpdase-ec-3-6-1-5-activity-in-hepatic-lymphocytes-a-different-activity-profile-from-peripheral-lymphocytes
#19
Pedro H Doleski, Stephen A Adefegha, Fernanda L Cabral, Daniela B R Leal
: The activity of ectonucleoside triphosphate diphosphohydrolase (E-NTPDase; EC 3.6.1.5) was characterized in hepatic lymphocytes (HL) of rats. For this purpose, a specific method for the isolation of lymphocytes from hepatic tissue was developed. Subsequently, E-NTPDase activity of rat HL was compared with that of rat peripheral lymphocytes. The HL showed high cell count and viability. Also, the characterization test revealed that the optimal E-NTPDase activities were attained at 37°C and pH 8...
February 19, 2017: Cell Biochemistry and Function
https://www.readbyqxmd.com/read/28217366/crizotinib-inhibits-hyperpolarization-activated-cyclic-nucleotide-gated-channel-4-activity
#20
Zhushan Zhang, Tai-Qin Huang, Igor Nepliouev, Hengtao Zhang, Adam S Barnett, Paul B Rosenberg, Sai-Hong I Ou, Jonathan A Stiber
BACKGROUND: Sinus bradycardia is frequently observed in patients treated with crizotinib, a receptor tyrosine kinase inhibitor used for the treatment of anaplastic lymphoma kinase (ALK)-rearranged non-small cell lung cancer (NSCLC). We investigated whether crizotinib could influence heart rate (HR) through direct cardiac effects. METHODS: The direct effect of crizotinib on HR was studied using ECG analysis of Langendorff-perfused mouse hearts. The whole-cell patch clamp technique was used to measure the effects of crizotinib on the hyperpolarization-activated funny current, If, in mouse sinoatrial node cells (SANCs) and hyperpolarization-activated cyclic nucleotide-gated channel 4 (HCN4) activity in HEK-293 cells stably expressing human HCN4...
2017: Cardiooncology
keyword
keyword
77354
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"