keyword
MENU ▼
Read by QxMD icon Read
search

sequenceing

keyword
https://www.readbyqxmd.com/read/28103613/tissue-based-next-generation-sequencing-application-in-a-universal-healthcare-system
#1
REVIEW
Seán O Hynes, Brendan Pang, Jacqueline A James, Perry Maxwell, Manuel Salto-Tellez
In the context of solid tumours, the evolution of cancer therapies to more targeted and nuanced approaches has led to the impetus for personalised medicine. The targets for these therapies are largely based on the driving genetic mutations of the tumours. To track these multiple driving mutations the use of next generation sequencing (NGS) coupled with a morphomolecular approach to tumours, has the potential to deliver on the promises of personalised medicine. A review of NGS and its application in a universal healthcare (UHC) setting is undertaken as the technology has a wide appeal and utility in diagnostic, clinical trial and research paradigms...
January 19, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28103546/quantifying-net-synergy-redundancy-of-spontaneous-variability-regulation-via-predictability-and-transfer-entropy-decomposition-frameworks
#2
Alberto Porta, Vlasta Bari, Beatrice De Maria, Anielle C M Takahashi, Stefano Guzzetti, Riccardo Colombo, Aparecida M Catai, Ferdinando Raimondi, Luca Faes
OBJECTIVE: Indexes assessing the balance between redundancy and synergy were hypothesized to be helpful in characterizing cardiovascular control from spontaneous beat-to-beat variations of heart period (HP), systolic arterial pressure (SAP) and respiration (R). METHODS: Net redundancy/synergy indexes were derived according to predictability and transfer entropy decomposition strategies via a multivariate linear regression approach. Indexes were tested in two protocols inducing modifications of the cardiovascular regulation via baroreflex loading/unloading (i...
January 17, 2017: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/28103531/characterization-of-transcriptome-and-identification-of-biomineralization-genes-in-winged-pearl-oyster-pteria-penguin-mantle-tissue
#3
Haimei Li, Baosuo Liu, Guiju Huang, Sigang Fan, Bo Zhang, Jiaqi Su, Dahui Yu
The winged pearl oyster Pteria penguin is a commercially important marine pearl oyster species, with pearls that are quite different from those of other pearl oysters. Among such species, mantle tissue is the main organ responsible for shell and pearl formation, a biomineralization process that is regulated by a series of genes, most of which remain unknown. In this study, we sequenced and characterized the transcriptome of P. penguin mantle tissue using the HiSeq 2000 sequencing platform. A total of 93,204 unique transcripts were assembled from 51,580,076 quality reads, with a mean length of 608bp, and 40,974 unigenes were annotated...
January 8, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28103527/distinct-cortico-striatal-connections-with-subthalamic-nucleus-underlie-facets-of-compulsivity
#4
Laurel S Morris, Kwangyeol Baek, Valerie Voon
The capacity to flexibly respond to contextual changes is crucial to adapting to a dynamic environment. Compulsivity, or behavioural inflexibility, consists of heterogeneous subtypes with overlapping yet discrete neural substrates. The subthalamic nucleus (STN) mediates the switch from automatic to controlled processing to slow, break or stop behaviour when necessary. Rodent STN lesions or inactivation are linked with perseveration or repetitive, compulsive responding. However, there are few studies examining the role of latent STN-centric neural networks and compulsive behaviour in healthy individuals...
December 29, 2016: Cortex; a Journal Devoted to the Study of the Nervous System and Behavior
https://www.readbyqxmd.com/read/28103526/cognitive-representation-of-musical-fractals-processing-hierarchy-and-recursion-in-the-auditory-domain
#5
Mauricio Dias Martins, Bruno Gingras, Estela Puig-Waldmueller, W Tecumseh Fitch
The human ability to process hierarchical structures has been a longstanding research topic. However, the nature of the cognitive machinery underlying this faculty remains controversial. Recursion, the ability to embed structures within structures of the same kind, has been proposed as a key component of our ability to parse and generate complex hierarchies. Here, we investigated the cognitive representation of both recursive and iterative processes in the auditory domain. The experiment used a two-alternative forced-choice paradigm: participants were exposed to three-step processes in which pure-tone sequences were built either through recursive or iterative processes, and had to choose the correct completion...
January 16, 2017: Cognition
https://www.readbyqxmd.com/read/28103496/toddlers-action-prediction-statistical-learning-of-continuous-action-sequences
#6
Claire D Monroy, Sarah A Gerson, Sabine Hunnius
The current eye-tracking study investigated whether toddlers use statistical information to make anticipatory eye movements while observing continuous action sequences. In two conditions, 19-month-old participants watched either a person performing an action sequence (Agent condition) or a self-propelled visual event sequence (Ghost condition). Both sequences featured a statistical structure in which certain action pairs occurred with deterministic transitional probabilities. Toddlers learned the transitional probabilities between the action steps of the deterministic action pairs and made predictive fixations to the location of the next action in the Agent condition but not in the Ghost condition...
January 16, 2017: Journal of Experimental Child Psychology
https://www.readbyqxmd.com/read/28103468/poly-a-binding-proteins-are-required-for-translational-regulation-in-vertebrate-oocytes-and-early-embryos
#7
Saffet Ozturk, Fatma Uysal
Poly(A)-binding proteins (PABPs) function in the timely regulation of gene expression during oocyte maturation, fertilisation and early embryo development in vertebrates. To this end, PABPs bind to poly(A) tails or specific sequences of maternally stored mRNAs to protect them from degradation and to promote their translational activities. To date, two structurally different PABP groups have been identified: (1) cytoplasmic PABPs, including poly(A)-binding protein, cytoplasmic 1 (PABPC1), embryonic poly(A)-binding protein (EPAB), induced PABP and poly(A)-binding protein, cytoplasmic 3; and (2) nuclear PABPs, namely embryonic poly(A)-binding protein 2 and nuclear poly(A)-binding protein 1...
January 20, 2017: Reproduction, Fertility, and Development
https://www.readbyqxmd.com/read/28103323/the-complete-genome-sequence-of-a-second-distinct-betabaculovirus-from-the-true-armyworm-mythimna-unipuncta
#8
Robert L Harrison, Daniel L Rowley, Joseph Mowery, Gary R Bauchan, David A Theilmann, George F Rohrmann, Martin A Erlandson
The betabaculovirus originally called Pseudaletia (Mythimna) sp. granulovirus #8 (MyspGV#8) was examined by electron microscopy, host barcoding PCR, and determination of the nucleotide sequence of its genome. Scanning and transmission electron microscopy revealed that the occlusion bodies of MyspGV#8 possessed the characteristic size range and morphology of betabaculovirus granules. Barcoding PCR using cytochrome oxidase I primers with DNA from the MyspGV#8 collection sample confirmed that it had been isolated from the true armyworm, Mythimna unipuncta (Lepidoptera: Noctuidae) and therefore was renamed MyunGV#8...
2017: PloS One
https://www.readbyqxmd.com/read/28103318/static-and-evolving-norovirus-genotypes-implications-for-epidemiology-and-immunity
#9
Gabriel I Parra, R Burke Squires, Consolee K Karangwa, Jordan A Johnson, Cara Lepore, Stanislav V Sosnovtsev, Kim Y Green
Noroviruses are major pathogens associated with acute gastroenteritis worldwide. Their RNA genomes are diverse, with two major genogroups (GI and GII) comprised of at least 28 genotypes associated with human disease. To elucidate mechanisms underlying norovirus diversity and evolution, we used a large-scale genomics approach to analyze human norovirus sequences. Comparison of over 2000 nearly full-length ORF2 sequences representing most of the known GI and GII genotypes infecting humans showed a limited number (≤5) of distinct intra-genotypic variants within each genotype, with the exception of GII...
January 19, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28103310/epidemiological-and-molecular-characterization-of-a-mexican-population-isolate-with-high-prevalence-of-limb-girdle-muscular-dystrophy-type-2a-due-to-a-novel-calpain-3-mutation
#10
Carlos A Pantoja-Melendez, Antonio Miranda-Duarte, Bladimir Roque-Ramirez, Juan C Zenteno
Limb-Girdle Muscular Dystrophy type 2 (LGMD2) is a group of autosomally recessive inherited disorders defined by weakness and wasting of the shoulder and pelvic girdle muscles. In the past, several population isolates with high incidence of LGMD2 arising from founder mutation effects have been identified. The aim of this work is to describe the results of clinical, epidemiologic, and molecular studies performed in a Mexican village segregating numerous cases of LGMD2. A population census was conducted in the village to identify all LGMD affected patients...
2017: PloS One
https://www.readbyqxmd.com/read/28103291/the-gut-brain-axis-in-healthy-females-lack-of-significant-association-between-microbial-composition-and-diversity-with-psychiatric-measures
#11
Susan C Kleiman, Emily C Bulik-Sullivan, Elaine M Glenny, Stephanie C Zerwas, Eun Young Huh, Matthew C B Tsilimigras, Anthony A Fodor, Cynthia M Bulik, Ian M Carroll
OBJECTIVE: This study examined associations between the composition and diversity of the intestinal microbiota and measures of depression, anxiety, eating disorder psychopathology, stress, and personality in a group of healthy adult females. METHODS: Female participants (n = 91) ages 19-50 years with BMI 18.5-25 kg/m2 were recruited from central North Carolina between July 2014 and March 2015. Participants provided a single fecal sample and completed an online psychiatric questionnaire that included five measures: (i) Beck Anxiety Inventory; (ii) Beck Depression Inventory-II; (iii) Eating Disorder Examination-Questionnaire; (iv) Perceived Stress Scale; and (v) Mini International Personality Item Pool...
2017: PloS One
https://www.readbyqxmd.com/read/28103286/mirnas-do-not-regulate-circadian-protein-synthesis-in-the-dinoflagellate-lingulodinium-polyedrum
#12
Steve Dagenais-Bellefeuille, Mathieu Beauchemin, David Morse
Dinoflagellates have been shown to express miRNA by bioinformatics and RNA blot (Northern) analyses. However, it is not yet known if miRNAs are able to alter gene expression in this class of organisms. We have assessed the possibility that miRNA may mediate circadian regulation of gene expression in the dinoflagellate Lingulodinium polyedrum using the Luciferin Binding Protein (LBP) as a specific example. LBP is a good candidate for regulation by miRNA since mRNA levels are constant over the daily cycle while protein synthesis is restricted by the circadian clock to a period of several hours at the start of the night phase...
2017: PloS One
https://www.readbyqxmd.com/read/28103259/characterization-and-genetic-variation-of-vibrio-cholerae-isolated-from-clinical-and-environmental-sources-in-thailand
#13
Achiraya Siriphap, Pimlapas Leekitcharoenphon, Rolf S Kaas, Chonchanok Theethakaew, Frank M Aarestrup, Orasa Sutheinkul, Rene S Hendriksen
Cholera is still an important public health problem in several countries, including Thailand. In this study, a collection of clinical and environmental V. cholerae serogroup O1, O139, and non-O1/non-O139 strains originating from Thailand (1983 to 2013) was characterized to determine phenotypic and genotypic traits and to investigate the genetic relatedness. Using a combination of conventional methods and whole genome sequencing (WGS), 78 V. cholerae strains were identified. WGS was used to determine the serogroup, biotype, virulence, mobile genetic elements, and antimicrobial resistance genes using online bioinformatics tools...
2017: PloS One
https://www.readbyqxmd.com/read/28103252/comparative-and-evolutionary-analysis-of-grass-pollen-allergens-using-brachypodium-distachyon-as-a-model-system
#14
Akanksha Sharma, Niharika Sharma, Prem Bhalla, Mohan Singh
Comparative genomics have facilitated the mining of biological information from a genome sequence, through the detection of similarities and differences with genomes of closely or more distantly related species. By using such comparative approaches, knowledge can be transferred from the model to non-model organisms and insights can be gained in the structural and evolutionary patterns of specific genes. In the absence of sequenced genomes for allergenic grasses, this study was aimed at understanding the structure, organisation and expression profiles of grass pollen allergens using the genomic data from Brachypodium distachyon as it is phylogenetically related to the allergenic grasses...
2017: PloS One
https://www.readbyqxmd.com/read/28103245/anaerobically-grown-escherichia-coli-has-an-enhanced-mutation-rate-and-distinct-mutational-spectra
#15
Sonal Shewaramani, Thomas J Finn, Sinead C Leahy, Rees Kassen, Paul B Rainey, Christina D Moon
Oxidative stress is a major cause of mutation but little is known about how growth in the absence of oxygen impacts the rate and spectrum of mutations. We employed long-term mutation accumulation experiments to directly measure the rates and spectra of spontaneous mutation events in Escherichia coli populations propagated under aerobic and anaerobic conditions. To detect mutations, whole genome sequencing was coupled with methods of analysis sufficient to identify a broad range of mutational classes, including structural variants (SVs) generated by movement of repetitive elements...
January 19, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28103242/genome-wide-binding-of-posterior-hoxa-d-transcription-factors-reveals-subgrouping-and-association-with-ctcf
#16
Ivana Jerković, Daniel M Ibrahim, Guillaume Andrey, Stefan Haas, Peter Hansen, Catrin Janetzki, Irene González Navarrete, Peter N Robinson, Jochen Hecht, Stefan Mundlos
Homeotic genes code for key transcription factors (HOX-TFs) that pattern the animal body plan. During embryonic development, Hox genes are expressed in overlapping patterns and function in a partially redundant manner. In vitro biochemical screens probing the HOX-TF sequence specificity revealed largely overlapping sequence preferences, indicating that co-factors might modulate the biological function of HOX-TFs. However, due to their overlapping expression pattern, high protein homology, and insufficiently specific antibodies, little is known about their genome-wide binding preferences...
January 19, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28103239/identifying-t-cell-receptors-from-high-throughput-sequencing-dealing-with-promiscuity-in-tcr%C3%AE-and-tcr%C3%AE-pairing
#17
Edward S Lee, Paul G Thomas, Jeff E Mold, Andrew J Yates
Characterisation of the T cell receptors (TCR) involved in immune responses is important for the design of vaccines and immunotherapies for cancer and autoimmune disease. The specificity of the interaction between the TCR heterodimer and its peptide-MHC ligand derives largely from the juxtaposed hypervariable CDR3 regions on the TCRα and TCRβ chains, and obtaining the paired sequences of these regions is a standard for functionally defining the TCR. A brute force approach to identifying the TCRs in a population of T cells is to use high-throughput single-cell sequencing, but currently this process remains costly and risks missing small clones...
January 19, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28103193/comprehensive-use-of-curvature-for-robust-and-accurate-online-surface-reconstruction
#18
Damien Lefloch, Markus Kluge, Hamed Sarbolandi, Tim Weyrich, Andreas Kolb
Interactive real-time scene acquisition from hand-held depth cameras has recently developed much momentum, enabling applications in ad-hoc object acquisition, augmented reality and other fields. A key challenge to online reconstruction remains error accumulation in the reconstructed camera trajectory, due to drift-inducing instabilities in the range scan alignments of the underlying iterative-closest-point (ICP) algorithm. Various strategies have been proposed to mitigate that drift, including SIFT-based pre-alignment, color-based weighting of ICP pairs, stronger weighting of edge features, and so on...
January 5, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28103180/fluoroquinolone-macrolide-and-ketolide-resistance-in-haemophilus-parainfluenzae-from-south-africa
#19
Regina Esinam Abotsi, Usha Govinden, Krishnee Moodley, Sabiha Essack
Fluoroquinolones and ketolides are among the drugs of choice for the treatment of Haemophilus parainfluenzae infections. There has been a report of an emerging fluoroquinolone and telithromycin resistance in H. parainfluenzae isolates from the private sector of KwaZulu-Natal Province of South Africa that necessitates molecular investigation. The aim of this study is to characterize these resistance delineating mutations in genes commonly associated with reduced susceptibility. Ten H. parainfluenzae isolates retrieved from the sputum of 10 patients with H...
January 19, 2017: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
https://www.readbyqxmd.com/read/28103138/discovery-of-a-novel-splice-variant-of-fcar-cd89-unravels-sequence-segments-necessary-for-efficient-secretion-a-story-of-bad-signal-peptides-and-good-ones-that-nevertheless-do-not-make-it
#20
Wai-Heng Lua, Wei-Li Ling, Chinh Tran-To Su, Joshua Yi Yeo, Chandra Shekhar Verma, Birgit Eisenhaber, Frank Eisenhaber, Samuel Ken-En Gan
The IgA receptor, Fcar (CD89) consists of five sequence segments: two segments (S1, S2) forming the potential signal peptide, two extracellular EC domains that include the IgA binding site, and the transmembrane and cytoplasmic tail (TM/C) region. Numerous Fcar splice variants have been reported with various combinations of the sequence segments mentioned above. Here, we report a novel splice variant termed variant APD isolated from a healthy volunteer that lacks only the IgA-binding EC1 domain. Despite possessing the complete signal peptide S1+S2, the variant APD is only found in the intracellular space whereas the wild-type variant 1 is efficiently secreted and variant 4 leaks to the extracellular space...
January 19, 2017: Cell Cycle
keyword
keyword
102242
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"