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https://www.readbyqxmd.com/read/28333622/constrained-inversion-and-spectral-unmixing-in-multispectral-optoacoustic-tomography
#1
Lu Ding, Xose Luis Dean Ben, Neal C Burton, Robert W Sobol, Vasilis Ntziachristos, Daniel Razansky
Accurate extraction of physical and biochemical parameters from optoacoustic images is often impeded due to the use of unrigorous inversion schemes, incomplete tomographic detection coverage or other experimental factors that cannot be readily accounted for during the image acquisition and reconstruction process. For instance, inaccurate assumptions in the physical forward model may lead to negative optical absorption values in the reconstructed images. Any artifacts present in the single wavelength optoacoustic images can be significantly aggravated when performing a two-step reconstruction consisting in acoustic inversion and spectral unmixing aimed at rendering the distributions of spectrally-distinct absorbers...
March 22, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28333355/wgs-to-predict-antibiotic-mics-for-neisseria-gonorrhoeae
#2
David W Eyre, Dilrini De Silva, Kevin Cole, Joanna Peters, Michelle J Cole, Yonatan H Grad, Walter Demczuk, Irene Martin, Michael R Mulvey, Derrick W Crook, A Sarah Walker, Tim E A Peto, John Paul
Background: Tracking the spread of antimicrobial-resistant Neisseria gonorrhoeae is a major priority for national surveillance programmes. Objectives: We investigate whether WGS and simultaneous analysis of multiple resistance determinants can be used to predict antimicrobial susceptibilities to the level of MICs in N. gonorrhoeae. Methods: WGS was used to identify previously reported potential resistance determinants in 681 N. gonorrhoeae isolates, from England, the USA and Canada, with phenotypes for cefixime, penicillin, azithromycin, ciprofloxacin and tetracycline determined as part of national surveillance programmes...
March 10, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28330125/detection-of-genetic-variation-in-sandalwood-using-various-dna-markers
#3
Dimple M Patel, Ranbir S Fougat, Amar A Sakure, Sushil Kumar, Mukesh Kumar, Jigar G Mistry
In the present study, 20 sandalwood (Santalum album L.) genotypes were characterized using RAPD, ISSR and SSR markers. Twenty-five RAPD and twenty-one ISSR primers that generated clear and reproducible banding patterns amplified 225 and 208 bands, respectively, among 20 sandalwood genotypes. Out of 225, 181 (83.13 %) RAPD bands were polymorphic while out of 208, 156 (75.77 %) ISSR bands were polymorphic. The average polymorphism information content (PIC) for RAPD and ISSR was 0.84 and 0.86, respectively...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28315925/fine-mapping-of-the-restorer-gene-rfp3-from-an-iranian-primitive-rye-secale-cereale-l
#4
Bernd Hackauf, Eva Bauer, Viktor Korzun, Thomas Miedaner
A comparative genetics approach allowed to precisely determine the map position of the restorer gene Rfp3 in rye and revealed that Rfp3 and the restorer gene Rfm1 in barley reside at different positions in a syntenic 4RL/6HS segment. Cytoplasmic male sterility (CMS) is a reliable and striking genetic mechanism for hybrid seed production. Breeding of CMS-based hybrids in cereals requires the use of effective restorer genes as an indispensable pre-requisite. We report on the fine mapping of a restorer gene for the Pampa cytoplasm in winter rye that has been tapped from the Iranian primitive rye population Altevogt 14160...
March 18, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28302415/a-prospective-study-to-assess-the-association-between-genotype-phenotype-and-prakriti-in-individuals-on-phenytoin-monotherapy
#5
Saket J Thaker, Prajakta P Gandhe, Charuta J Godbole, Shital R Bendkhale, Nitin B Mali, Urmila M Thatte, Nithya J Gogtay
BACKGROUND: Genetic polymorphisms in drug metabolizing enzymes (DMEs) impart distinct drug metabolizing capacity and a unique phenotype to an individual. Phenytoin has large inter-individual variability in metabolism due to polymorphisms in CYP2C9 and CYP2C19. As per Ayurveda, Prakriti imparts a unique phenotype to an individual. OBJECTIVE: To assess whether Prakriti can substitute phenotyping [therapeutic drug monitoring (TDM)] and genotyping in individualizing therapy with phenytoin in epilepsy patients...
March 14, 2017: Journal of Ayurveda and Integrative Medicine
https://www.readbyqxmd.com/read/28302018/harmony-search-as-a-powerful-tool-for-feature-selection-in-qspr-study-of-the-drugs-lipophilicity
#6
Behnoosh Bahadori, Morteza Atabati
Lipophilicity represents one of the most studied and most frequently used fundamental physicochemical properties. In the present work harmony search (HS) algorithm is suggested to feature selection in quantitative structure-property relationship (QSPR) modeling to predict lipophilicity of neutral, acidic, basic and amphotheric drugs that were determined by UHPLC. Harmony search is a music-based metaheuristic optimization algorithm. It was affected by the observation that the aim of music is to search for a perfect state of harmony...
March 15, 2017: Combinatorial Chemistry & High Throughput Screening
https://www.readbyqxmd.com/read/28289927/nmr-assignments-of-sparsely-labeled-proteins-using-a-genetic-algorithm
#7
Qi Gao, Gordon R Chalmers, Kelley W Moremen, James H Prestegard
Sparse isotopic labeling of proteins for NMR studies using single types of amino acid ((15)N or (13)C enriched) has several advantages. Resolution is enhanced by reducing numbers of resonances for large proteins, and isotopic labeling becomes economically feasible for glycoproteins that must be expressed in mammalian cells. However, without access to the traditional triple resonance strategies that require uniform isotopic labeling, NMR assignment of crosspeaks in heteronuclear single quantum coherence (HSQC) spectra is challenging...
March 13, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28278209/assessment-of-the-genomic-prediction-accuracy-for-feed-efficiency-traits-in-meat-type-chickens
#8
Tianfei Liu, Chenglong Luo, Jie Wang, Jie Ma, Dingming Shu, Mogens Sandø Lund, Guosheng Su, Hao Qu
Feed represents the major cost of chicken production. Selection for improving feed utilization is a feasible way to reduce feed cost and greenhouse gas emissions. The objectives of this study were to investigate the efficiency of genomic prediction for feed conversion ratio (FCR), residual feed intake (RFI), average daily gain (ADG) and average daily feed intake (ADFI) and to assess the impact of selection for feed efficiency traits FCR and RFI on eviscerating percentage (EP), breast muscle percentage (BMP) and leg muscle percentage (LMP) in meat-type chickens...
2017: PloS One
https://www.readbyqxmd.com/read/28277080/shuffling-cross-validation-bee-algorithm-as-a-new-descriptor-selection-method-for-retention-studies-of-pesticides-in-biopartitioning-micellar-chromatography
#9
Kobra Zarei, Morteza Atabati, Monire Ahmadi
Bee algorithm (BA) is an optimization algorithm inspired by the natural foraging behaviour of honey bees to find the optimal solution which can be proposed to feature selection. In this paper, shuffling cross-validation-BA (CV-BA) was applied to select the best descriptors that could describe the retention factor (log k) in the biopartitioning micellar chromatography (BMC) of 79 heterogeneous pesticides. Six descriptors were obtained using BA and then the selected descriptors were applied for model development using multiple linear regression (MLR)...
February 22, 2017: Journal of Environmental Science and Health. Part. B, Pesticides, Food Contaminants, and Agricultural Wastes
https://www.readbyqxmd.com/read/28275816/genetic-mapping-and-haplotype-analysis-of-a-locus-for-quantitative-resistance-to-fusarium-graminearum-in-soybean-accession-pi-567516c
#10
Peng Cheng, Cassidy R Gedling, Gunvant Patil, Tri D Vuong, J Grover Shannon, Anne E Dorrance, Henry T Nguyen
A major novel quantitative disease resistance locus, qRfg_Gm06, for Fusarium graminearum was genetically mapped to chromosome 6. Genomic-assisted haplotype analysis within this region identified three putative candidate genes. Fusarium graminearum causes seed, root rot, and seedling damping-off in soybean which contributes to reduced stands and yield. A cultivar Magellan and PI 567516C were identified with low and high levels of partial resistance to F. graminearum, respectively. Quantitative disease resistance loci (QDRL) were mapped with 241 F7:8 recombinant inbred lines (RILs) derived from a cross of Magellan × PI 567516C...
March 8, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28270566/orbitofrontal-neuroadaptations-and-cross-species-synaptic-biomarkers-in-heavy-drinking-macaques
#11
Sudarat Nimitvilai, Joachim D Uys, John J Woodward, Patrick K Randall, Lauren E Ball, Robert W Williams, Byron C Jones, Lu Lu, Kathleen A Grant, Patrick J Mulholland
Cognitive impairments, uncontrolled drinking, and neuropathological cortical changes characterize alcohol use disorder. Dysfunction of the orbitofrontal cortex (OFC), a critical cortical sub-region that controls learning, decision-making, and prediction of reward outcomes, contributes to executive cognitive function deficits in alcoholics. Electrophysiological and quantitative synaptomics techniques were used to test the hypothesis that heavy drinking produces neuroadaptations in the macaque OFC. Integrative bioinformatics and reverse genetic approaches were used to identify and validate synaptic proteins with novel links to heavy drinking in BXD mice...
March 7, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28270201/exploration-of-haplotype-research-consortium-imputation-for-genome-wide-association-studies-in-20-032-generation-scotland-participants
#12
Reka Nagy, Thibaud S Boutin, Jonathan Marten, Jennifer E Huffman, Shona M Kerr, Archie Campbell, Louise Evenden, Jude Gibson, Carmen Amador, David M Howard, Pau Navarro, Andrew Morris, Ian J Deary, Lynne J Hocking, Sandosh Padmanabhan, Blair H Smith, Peter Joshi, James F Wilson, Nicholas D Hastie, Alan F Wright, Andrew M McIntosh, David J Porteous, Chris S Haley, Veronique Vitart, Caroline Hayward
BACKGROUND: The Generation Scotland: Scottish Family Health Study (GS:SFHS) is a family-based population cohort with DNA, biological samples, socio-demographic, psychological and clinical data from approximately 24,000 adult volunteers across Scotland. Although data collection was cross-sectional, GS:SFHS became a prospective cohort due to of the ability to link to routine Electronic Health Record (EHR) data. Over 20,000 participants were selected for genotyping using a large genome-wide array...
March 7, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28268598/predicting-schizophrenia-by-fusing-networks-from-snps-dna-methylation-and-fmri-data
#13
Su-Ping Deng, Dongdong Lin, Vince D Calhoun, Yu-Ping Wang
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/28267574/applying-evolutionary-genetics-to-developmental-toxicology-and-risk-assessment
#14
REVIEW
Maxwell C K Leung, Andrew C Procter, Jared V Goldstone, Jonathan Foox, Robert DeSalle, Carolyn J Mattingly, Mark E Siddall, Alicia R Timme-Laragy
Evolutionary thinking continues to challenge our views on health and disease. Yet, there is a communication gap between evolutionary biologists and toxicologists in recognizing the connections among developmental pathways, high-throughput screening, and birth defects in humans. To increase our capability in identifying potential developmental toxicants in humans, we propose to apply evolutionary genetics to improve the experimental design and data interpretation with various in vitro and whole-organism models...
March 4, 2017: Reproductive Toxicology
https://www.readbyqxmd.com/read/28260614/classification-of-alzheimer-s-disease-and-prediction-of-mild-cognitive-impairment-to-alzheimer-s-conversion-from-structural-magnetic-resource-imaging-using-feature-ranking-and-a-genetic-algorithm
#15
Iman Beheshti, Hasan Demirel, Hiroshi Matsuda
We developed a novel computer-aided diagnosis (CAD) system that uses feature-ranking and a genetic algorithm to analyze structural magnetic resonance imaging data; using this system, we can predict conversion of mild cognitive impairment (MCI)-to-Alzheimer's disease (AD) at between one and three years before clinical diagnosis. The CAD system was developed in four stages. First, we used a voxel-based morphometry technique to investigate global and local gray matter (GM) atrophy in an AD group compared with healthy controls (HCs)...
February 27, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28260510/prediction-of-activities-of-braf-v600e-inhibitors-by-sw-mlr-and-ga-mlr-methods
#16
Parinaz Pargolghasemi, Mir Saleh Hoseininezhad-Namin, Aiyoub Parchehbaf Jadid
BACKGROUND: quantitative structure-activity relationship(QSAR) models couldprovide both statistical significanceand useful chemical insights for drug design. The QSARmethod has found applications for predicting diverse properties of organic compounds, including antiviral activities, toxicities and biological activities. In this work, a quantitative structure-activity relationship was utilized for prediction of allosteric BRAF (V600E) inhibitory activities. METHODS: A data set which contains 54 molecules was classified to training and test sets...
March 3, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28251966/-scanning-for-kras-nras-braf-and-pik3ca-mutations-by-dna-melting-analysis-with-taqman-probes
#17
I V Botezatu, I O Panchuk, A M Stroganova, A I Senderovich, V N Kondratova, V P Shelepov, A V Lichtenstein
Scanning for mutations by DNA melting analysis (DMA) is based on asymmetric PCR followed by the melting of duplexes formed by single-stranded amplicons with TaqMan probes. The method is optimally suited for clinical genetic testing; it is easy to perform, high-throughput, and sensitive. The detection limit of mutant alleles by the DMA method is about 3%, which is much higher than the sensitivity of Sanger sequencing. In addition, the DMA method is realized in a closed-tube format, while 2-h assay is carried out in a single tube without any intermediate or additional procedures thereby minimizing the risk of cross contamination of the samples...
January 2017: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28251931/sleep-characteristics-modify-the-association-of-genetic-predisposition-with-obesity-and-anthropometric-measurements-in-119-679-uk-biobank-participants
#18
Carlos Celis-Morales, Donald M Lyall, Yibing Guo, Lewis Steell, Daniel Llanas, Joey Ward, Daniel F Mackay, Stephany M Biello, Mark Es Bailey, Jill P Pell, Jason Mr Gill
Background: Obesity is a multifactorial condition influenced by genetics, lifestyle, and environment.Objective: We investigated whether the association of a validated genetic profile risk score for obesity (GPRS-obesity) with body mass index (BMI) and waist circumference (WC) was modified by sleep characteristics.Design: This study included cross-sectional data from 119,859 white European adults, aged 37-73 y, participating in the UK Biobank. Interactions of GPRS-obesity and sleep characteristics (sleep duration, chronotype, day napping, and shift work) with their effects on BMI and WC were investigated...
March 1, 2017: American Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/28249583/molecular-surveillance-of-artemisinin-resistance-falciparum-malaria-among-migrant-goldmine-workers-in-myanmar
#19
Myat Htut Nyunt, Bo Wang, Khin Myo Aye, Kyin Hla Aye, Jin-Hee Han, Seong-Kyun Lee, Kay Thwe Han, Ye Htut, Eun-Taek Han
BACKGROUND: Artemisinin resistance has been reported in Greater Mekong Sub-region countries, including Myanmar. After discovery of artemisinin resistance marker (K13), molecular surveillance on artemisinin resistance in endemic regions have been conducted. As the migrant population represents a high percentage of malaria cases, molecular surveillance of artemisinin resistance among migrant workers is of great concern. METHODS: A cross-sectional survey was conducted in Shwegyin Township, where migrants work in the goldmines...
March 1, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28242603/optimization-and-validation-of-analysis-method-based-on-27-plex-snp-panel-for-ancestry-inference
#20
Jiang Li, Sun Qifan, Ma Quan, Zhao Wenting, Liu Jing, Zhao Lei, Ji Anquan, Li Caixia
Anthropology generally divides the individuals into the East Asian Mongolia race, European Caucasian race and African Nigro race. The 27-plex single nucleotide polymorphism (SNP) panel for ancestry information has been established to differentiate samples from East Asian, European, African and admixture populations of East Asian and European origin by genotyping and ancestry inference. To infer ancestry for unknown individuals, we established an optimized analysis pipeline based on the likelihood ratio, ancestry component and individual ancestry assignment...
February 20, 2017: Yi Chuan, Hereditas
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