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Gene: a gene-centered information resource at NCBI

Garth R. Brown, Vichet Hem, Kenneth S. Katz, Michael Ovetsky, Craig Wallin, Olga Ermolaeva, Igor Tolstoy, Tatiana Tatusova, Kim D. Pruitt, Donna R. Maglott, Terence D. Murphy
2014 Nucleic Acids Research  
The National Center for Biotechnology Information's (NCBI) Gene database (www.ncbi.nlm.nih.gov/gene) integrates gene-specific information from multiple data sources. NCBI Reference Sequence (RefSeq) genomes for viruses, prokaryotes and eukaryotes are the primary foundation for Gene records in that they form the critical association between sequence and a tracked gene upon which additional functional and descriptive content is anchored. Additional content is integrated based on the genomic
more » ... on and RefSeq transcript and protein sequence data. The content of a Gene record represents the integration of curation and automated processing from Ref-Seq, collaborating model organism databases, consortia such as Gene Ontology, and other databases within NCBI. Records in Gene are assigned unique, tracked integers as identifiers. The content (citations, nomenclature, genomic location, gene products and their attributes, phenotypes, sequences, interactions, variation details, maps, expression, homologs, protein domains and external databases) is available via interactive browsing through NCBI's Entrez system, via NCBI's Entrez programming utilities (E-Utilities and Entrez Direct) and for bulk transfer by FTP.
doi:10.1093/nar/gku1055 pmid:25355515 pmcid:PMC4383897 fatcat:s23gtmpvcnanffuoi4jnnegexa

Molecular dissection of the quantitative inheritance of wood property traits in loblolly pine

David B. Neale, Mitchell M. Sewell, Garth R. Brown
2002 Annals of Forest Science  
Even though both of these traits are associated with microfibrils, there is little phenotypic correlation (-0.13 ≤ r ≤ 0.11) and little congruence, either positive or negative, among the QTL effects for  ...  comparative maps between Pinus taeda × P. radiata [6] , whereas ESTP markers were used to create comparative maps between P. taeda and P. elliottii [3] and between P. taeda and P. pinaster (Chagné and Brown  ... 
doi:10.1051/forest:2002045 fatcat:xysy5mwn7zgebiffvouub5z4n4

A sequence mutation in the cinnamyl alcohol dehydrogenase gene associated with altered lignification in loblolly pine

Geoffrey P. Gill, Garth R. Brown, David B. Neale
2003 Plant Biotechnology Journal  
Homozygous seedlings ( cad-n1/cad-n1 ) obtained by selfing, contain between 0 and 1% of wild-type CAD activity and display a brown-red wood phenotype.  ... 
doi:10.1046/j.1467-7652.2003.00024.x pmid:17163902 fatcat:i2x6ygn27rbhhjmb4hhhgbze74

Enhancement of low-energy electron emission in 2D radioactive films

Alex Pronschinske, Philipp Pedevilla, Colin J. Murphy, Emily A. Lewis, Felicia R. Lucci, Garth Brown, George Pappas, Angelos Michaelides, E. Charles H. Sykes
2015 Nature Materials  
High-energy radiation has been utilized for decades, however, the role of low-energy electrons created during irradiation has only recently begun to be appreciated 1,2 . Low-energy electrons are the most important component of radiation damage in biological environments because they have subcellular ranges, interact destructively with chemical bonds, and are the most abundant product of ionizing particles in tissue. However, methods for generating them locally without external stimulation do
more » ... exist. To address this we synthesized one atom thick films of the radioactive isotope 125 I on gold that are stable under ambient conditions. Scanning tunnelling microscopy, supported by electronic structure simulations, allowed us to directly observe nuclear transmutation of individual 125 I atoms into 125 Te, and explain the surprising stability of the 2-D film as it underwent radioactive decay. The metal interface geometry induces a 600% amplification of low-energy electron emission (<10 eV) 3 compared to atomic 125 I. Therefore, this enhancement of biologically active low energy electrons opens a new direction for highly targeted nanoparticle therapies 4-6 . Nuclear decay is one of the most extreme processes and is central to a range of fields including energy, medicine, imaging, labelling, archaeology and sensing. Radiation in the form of alpha particles, beta particles and gamma rays have fundamentally different interactions with matter and therefore exhibit different mean-free paths (∼1 μm, 1 mm and 1 cm, respectively). These forms of primary radiation deposit their energy over the course of their trajectory by ionizing their surroundings and producing non-thermal secondary electrons. Only very recently has the ability of low-energy secondary electrons to induce chemical reactions and biological damage begun to be appreciated 1 , because they have energies below the typical ionization threshold of organic matter. For example, low-energy electrons (3-20 eV) have been shown to be effective at causing DNA cleavage 2,4,7 . This ability stems from their high cross-section for breaking chemical bonds, and as a consequence they have a very short meanfree path of ∼1-10 nm in solution 8, 9 . Furthermore, hot electrons that are not captured by surrounding molecules become thermalized as solvated electrons which are known to be chemically and biological active 9-12 . To harness these unique properties, the design of radioactive materials that increase and localize the flux of short-range lowenergy electrons to target sites is crucial for their application in targeted cancer therapies that minimize damage to healthy cells. Thus far, it has not been possible to design atomically precise radioactive materials that maximize these effects due to self-destruction arising from nuclear recoil, Coulomb explosion and self-irradiation 13-16 . We report a straightforward method for synthesizing monolayer films of radioactive 125 I atoms on gold-coated mica substrates under ambient conditions, and characterize their composition and their electron emission. Despite being synthesized from radioactive 125 I (> 99.9% purity) they are robust with respect to self-destruction, and provide well-defined, intense planar sources of secondary electrons. 125 I decays by electron capture (EC) of a core shell electron to produce a nuclear excited state of 125 Te (Figure 1a) , the majority of which eject another core
doi:10.1038/nmat4323 pmid:26076306 fatcat:3cyowmsjhbbdjf2krvwivrre34

DNA Sequence Variation and Selection of Tag Single-Nucleotide Polymorphisms at Candidate Genes for Drought-Stress Response in Pinus taeda L

Santiago C. González-Martínez, Elhan Ersoz, Garth R. Brown, Nicholas C. Wheeler, David B. Neale
2005 Genetics  
The level of within-gene LD was low, with an average pairwise r 2 of 0.30, decaying rapidly from 0.50 to 0.20 at 800 bp. No apparent LD among genes was found.  ...  Gill, R. J. Kuntz, J. Beal, and J. Manares provided technical assistance in the lab. We thank A. Soto and M. T. Cervera, and P.  ...  -Linkage disequilibrium (as estimated by r 2 ) plots for five drought-response candidate genes, including three (dhn-1, sams-2, and ppap-12) that map in the same linkage group (LG 8; see Brown et al.  ... 
doi:10.1534/genetics.105.047126 pmid:16387885 pmcid:PMC1456261 fatcat:dauxiamsfrbgngkieohiixa2v4

What everybody should know about the rat genome and its online resources

Simon N Twigger, Kim D Pruitt, Xosé M Fernández-Suárez, Donna Karolchik, Kim C Worley, Donna R Maglott, Garth Brown, George Weinstock, Richard A Gibbs, Jim Kent, Ewan Birney, Howard J Jacob
2008 Nature Genetics  
The Y chromosome was originally sequenced only to about twofold coverage as a consequence of the unusually large size of the Brown Norway Y chromosome.  ...  The previous rat SNP map was based on cDNA from four strains (SHRSP, Brown Norway, WKY and Sprague-Dawley) and had 12,395 interstrain polymorphic sites 4 .  ... 
doi:10.1038/ng0508-523 pmid:18443589 pmcid:PMC2505193 fatcat:k5rnfgkj6ngzpkieh27xgwkgpa

Gut Microbe-Targeted Choline Trimethylamine Lyase Inhibition Improves Obesity Via Rewiring of Host Circadian Rhythms [article]

Rebecca C Schugar, Christy M Gliniak, Robert N Helsley, Amanda L Brown, Amy Burrows, Chelsea Finney, Kevin K Fung, Frederick M Allen, Daniel Ferguson, Anthony D Gromovsky, Chase Neumann, Amy McMillan (+14 others)
2020 bioRxiv   pre-print
All other plots were carried out using R (r-project.org).  ...  Raw counts were loaded into R (http://www.R-project.org/) (R Development Core Team, 2015) and edgeR 69 was used to perform upper quantile, betweenlane normalization, and DE analysis.  ... 
doi:10.1101/2020.12.04.411546 fatcat:lu3gyrzmx5c2tmd6s4ea3mq7ua

ClinVar: improving access to variant interpretations and supporting evidence

Melissa J Landrum, Jennifer M Lee, Mark Benson, Garth R Brown, Chen Chao, Shanmuga Chitipiralla, Baoshan Gu, Jennifer Hart, Douglas Hoffman, Wonhee Jang, Karen Karapetyan, Kenneth Katz (+10 others)
2017 Nucleic Acids Research  
ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/) is a freely available, public archive of human genetic variants and interpretations of their significance to disease, maintained at the National Institutes of Health. Interpretations of the clinical significance of variants are submitted by clinical testing laboratories, research laboratories, expert panels and other groups. ClinVar aggregates data by variant-disease pairs, and by variant (or set of variants). Data aggregated by variant are
more » ... ble on the website, in an improved set of variant call format files and as a new comprehensive XML report. ClinVar recently started accepting submissions that are focused primarily on providing phenotypic information for individuals who have had genetic testing. Submissions may come from clinical providers providing their own interpretation of the variant ('provider interpretation') or from groups such as patient registries that primarily provide phenotypic information from patients ('phenotyping only'). ClinVar continues to make improvements to its search and retrieval functions. Several new fields are now indexed for more precise searching, and filters allow the user to narrow down a large set of search results.
doi:10.1093/nar/gkx1153 pmid:29165669 pmcid:PMC5753237 fatcat:ngbthvyavvejjdkin52xwrjmua

Identification of quantitative trait loci influencing wood property traits in loblolly pine (Pinus taeda L.). III. QTL Verification and candidate gene mapping

Garth R Brown, Daniel L Bassoni, Geoffrey P Gill, Joseph R Fontana, Nicholas C Wheeler, Robert A Megraw, Mark F Davis, Mitchell M Sewell, Gerald A Tuskan, David B Neale
2003 Genetics  
. , 2002 Brown et al. 2001) . markers (Figure 1 ).  ... 
pmid:12930758 pmcid:PMC1462646 fatcat:ob3z5hqs4je3lhezos3fqcemei

ClinVar: public archive of interpretations of clinically relevant variants

Melissa J. Landrum, Jennifer M. Lee, Mark Benson, Garth Brown, Chen Chao, Shanmuga Chitipiralla, Baoshan Gu, Jennifer Hart, Douglas Hoffman, Jeffrey Hoover, Wonhee Jang, Kenneth Katz (+7 others)
2015 Nucleic Acids Research  
Interpretations are submitted by clinical testing laboratories, research laboratories, locus-specific databases, OMIM R , GeneReviews TM , UniProt, expert panels and practice guidelines.  ...  Submissions are accessioned and versioned (SCV) In its initial release (2013), ClinVar was largely seeded with records based on allelic variants described in OMIM R ; variants described in GeneReviews  ...  Today, ClinVar staff continue to process variants from OMIM R and GeneReviews TM ; they also regularly process direct submissions from clinical testing laboratories, research groups, UniProt and locus-specific  ... 
doi:10.1093/nar/gkv1222 pmid:26582918 pmcid:PMC4702865 fatcat:x4b6xdfj65ebtnpinz3m2mcm6u

RefSeq: an update on mammalian reference sequences

Kim D. Pruitt, Garth R. Brown, Susan M. Hiatt, Françoise Thibaud-Nissen, Alexander Astashyn, Olga Ermolaeva, Catherine M. Farrell, Jennifer Hart, Melissa J. Landrum, Kelly M. McGarvey, Michael R. Murphy, Nuala A. O'Leary (+17 others)
2013 Nucleic Acids Research  
The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database is a collection of annotated genomic, transcript and protein sequence records derived from data in public sequence archives and from computation, curation and collaboration (http://www.ncbi.nlm. nih.gov/refseq/). We report here on growth of the mammalian and human subsets, changes to NCBI's eukaryotic annotation pipeline and modifications affecting transcript and protein records. Recent changes to
more » ... s eukaryotic genome annotation pipeline provide higher throughput, and the addition of RNAseq data to the pipeline results in a significant expansion of the number of transcripts and novel exons annotated on mammalian RefSeq genomes. Recent annotation changes include reporting supporting evidence for transcript records, modification of exon feature annotation and the addition of a structured report of gene and sequence attributes of biological interest. We also describe a revised protein annotation policy for alternatively spliced transcripts with more divergent predicted proteins and we summarize the current status of the RefSeqGene project.
doi:10.1093/nar/gkt1114 pmid:24259432 pmcid:PMC3965018 fatcat:wid54lruqrdzndb4oghwltdrqa

Protocol of a 12-month multifactorial eHealth programme targeting balance, dual-tasking and mood to prevent falls in older people: the StandingTall+ randomised controlled trial

Kimberley S van Schooten, Michele L Callisaya, Bridianne O'Dea, Thomas Lung, Kaarin Anstey, Stephen R Lord, Helen Christensen, Alicia Brown, Jessica Chow, Garth McInerney, Lillian Miles, Michelle Ngo (+2 others)
2021 BMJ Open  
IntroductionFalls have a multifactorial aetiology, which may limit the effectiveness of the common approach of exercise as the sole intervention strategy. Multifactorial interventions could be more effective in people at high risk of falling; however, the focus of such interventions has traditionally been quite narrow. This paper describes the design of a randomised controlled trial that will evaluate the effectiveness of an eHealth programme, which addresses cumulative effects of key fall-risk
more » ... factors across the triad of physical, affective and cognitive functions on falls in older people.Methods and analysis518 older people aged 65 years and over with high fall risk, defined as having a history of falls in the past 6 months, self-reported fear of falling or being aged 80 years or over, will be recruited via local advertisements, newsletters and presentations, and randomised to an intervention or health education control group. The intervention comprises balance exercise, cognitive-motor exercise and cognitive–behavioural therapy, with their dosage based on participant's baseline balance, executive function and mood. The primary outcome is the rate of falls in the 12 months after randomisation. Secondary outcomes at 6 and 12 months comprise programme adherence, healthcare use, physical activity, balance and mobility, cognitive function, psychological well-being, quality of life, health literacy and user experience and attitudes towards the programme. Data will be analysed following intention to treat to gauge real-world effectiveness. We will further determine complier averaged causal effects to correct for varying adherence and conduct economic analyses to gain insight into cost-effectiveness and cost–utility.Ethics and disseminationEthical approval was obtained from the University of New South Wales (UNSW) Human Research Ethics Committee in December 2017. Outcomes will be disseminated via peer-reviewed articles, conference presentations, community events and media releases.Trial registration numberACTRN12619000540112.
doi:10.1136/bmjopen-2021-051085 pmid:33858875 fatcat:ipsiqrjxpnakrhomu72ggq7b5i

Strong‐Lensing Analysis of A1689 from Deep Advanced Camera Images

Tom Broadhurst, Narciso Benitez, Dan Coe, Keren Sharon, Kerry Zekser, Rick White, Holland Ford, Rychard Bouwens, John Blakeslee, Marc Clampin, Nick Cross, Marijn Franx (+30 others)
2005 Astrophysical Journal  
The projected mass profile flattens steadily towards the center with a shallow mean slope of dΣ/d r ≃ -0.55±0.1, over the observed range, r<250kpc/h, matching well an NFW profile, but with a relatively  ...  The resulting mass map is more circular in projection than the clumpy distribution of cluster galaxies and the light is more concentrated than the mass within r<50kpc/h.  ...  Integrating the mass along a column, z, where r 2 = (ξ r r s ) 2 + z 2 gives: M(ξ r ) = ρ s r 3 s (ξ r ) ξr o d 2 ξ r ∞ −∞ 1 (r/r s )(1 + r/r s ) 2 dz r s , (22) Using this mass, a bend-angle of α = 4GM  ... 
doi:10.1086/426494 fatcat:qyqhtpcvqvhmhihypz7oz3j5am

Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis

Marta F. Nabais, Tian Lin, Beben Benyamin, Kelly L. Williams, Fleur C. Garton, Anna A. E. Vinkhuyzen, Futao Zhang, Costanza L. Vallerga, Restuadi Restuadi, Anna Freydenzon, Ramona A. J. Zwamborn, Paul J. Hop (+25 others)
2020 npj Genomic Medicine  
10 −3 ), compared to both MOA (r b MOA adj ¼ 0:99, s.e. = 1.6 × 10 −3 ) and MOMENT (r b MOMENT adj ¼ 0:97, s. e. = 5.7 × 10 −3 , Supplementary Fig. 6e, f, respectively) .  ...  Interestingly, the correlation of effect sizes is much higher between standard linear regression models and MOA (Supplementary Fig. 1 ,r b ¼ 1, s.e. = 3 × 10 −3 ) than with MOMENT (r b ¼ À0:2, s.e. =  ... 
doi:10.1038/s41525-020-0118-3 pmid:32140259 pmcid:PMC7046630 fatcat:wciwalvrh5ax3gqsh7jdlidr7y

A large population of 'Lyman-break' galaxies in a protocluster at redshift z ≈ 4.1

George K. Miley, Roderik A. Overzier, Zlatan I. Tsvetanov, Rychard J. Bouwens, Narciso Benítez, John P. Blakeslee, Holland C. Ford, Garth D. Illingworth, Marc Postman, Piero Rosati, Mark Clampin, George F. Hartig (+26 others)
2004 Nature  
1.1, (r − i) ≤ 1 and i < 27.  ...  1.1, (r − i) ≤ 1 and i < 27.  ... 
doi:10.1038/nature02125 pmid:14702079 fatcat:ogyyyvqkxrewrbuugwvvjpvkbu
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