1
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Almond PR, Biggs PJ, Coursey BM, Hanson WF, Huq MS, Nath R, Rogers DW. AAPM's TG-51 protocol for clinical reference dosimetry of high-energy photon and electron beams. Med Phys 1999; 26:1847-70. [PMID: 10505874 DOI: 10.1118/1.598691] [Citation(s) in RCA: 1137] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A protocol is prescribed for clinical reference dosimetry of external beam radiation therapy using photon beams with nominal energies between 60Co and 50 MV and electron beams with nominal energies between 4 and 50 MeV. The protocol was written by Task Group 51 (TG-51) of the Radiation Therapy Committee of the American Association of Physicists in Medicine (AAPM) and has been formally approved by the AAPM for clinical use. The protocol uses ion chambers with absorbed-dose-to-water calibration factors, N(60Co)D,w which are traceable to national primary standards, and the equation D(Q)w = MkQN(60Co)D,w where Q is the beam quality of the clinical beam, D(Q)w is the absorbed dose to water at the point of measurement of the ion chamber placed under reference conditions, M is the fully corrected ion chamber reading, and kQ is the quality conversion factor which converts the calibration factor for a 60Co beam to that for a beam of quality Q. Values of kQ are presented as a function of Q for many ion chambers. The value of M is given by M = PionP(TP)PelecPpolMraw, where Mraw is the raw, uncorrected ion chamber reading and Pion corrects for ion recombination, P(TP) for temperature and pressure variations, Pelec for inaccuracy of the electrometer if calibrated separately, and Ppol for chamber polarity effects. Beam quality, Q, is specified (i) for photon beams, by %dd(10)x, the photon component of the percentage depth dose at 10 cm depth for a field size of 10x10 cm2 on the surface of a phantom at an SSD of 100 cm and (ii) for electron beams, by R50, the depth at which the absorbed-dose falls to 50% of the maximum dose in a beam with field size > or =10x10 cm2 on the surface of the phantom (> or =20x20 cm2 for R50>8.5 cm) at an SSD of 100 cm. R50 is determined directly from the measured value of I50, the depth at which the ionization falls to 50% of its maximum value. All clinical reference dosimetry is performed in a water phantom. The reference depth for calibration purposes is 10 cm for photon beams and 0.6R50-0.1 cm for electron beams. For photon beams clinical reference dosimetry is performed in either an SSD or SAD setup with a 10x10 cm2 field size defined on the phantom surface for an SSD setup or at the depth of the detector for an SAD setup. For electron beams clinical reference dosimetry is performed with a field size of > or =10x10 cm2 (> or =20x20 cm2 for R50>8.5 cm) at an SSD between 90 and 110 cm. This protocol represents a major simplification compared to the AAPM's TG-21 protocol in the sense that large tables of stopping-power ratios and mass-energy absorption coefficients are not needed and the user does not need to calculate any theoretical dosimetry factors. Worksheets for various situations are presented along with a list of equipment required.
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26 |
1137 |
2
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Bignell GR, Warren W, Seal S, Takahashi M, Rapley E, Barfoot R, Green H, Brown C, Biggs PJ, Lakhani SR, Jones C, Hansen J, Blair E, Hofmann B, Siebert R, Turner G, Evans DG, Schrander-Stumpel C, Beemer FA, van Den Ouweland A, Halley D, Delpech B, Cleveland MG, Leigh I, Leisti J, Rasmussen S. Identification of the familial cylindromatosis tumour-suppressor gene. Nat Genet 2000; 25:160-5. [PMID: 10835629 DOI: 10.1038/76006] [Citation(s) in RCA: 527] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Familial cylindromatosis is an autosomal dominant genetic predisposition to multiple tumours of the skin appendages. The susceptibility gene (CYLD) has previously been localized to chromosome 16q and has the genetic attributes of a tumour-suppressor gene (recessive oncogene). Here we have identified CYLD by detecting germline mutations in 21 cylindromatosis families and somatic mutations in 1 sporadic and 5 familial cylindromas. All mutations predict truncation or absence of the encoded protein. CYLD encodes three cytoskeletal-associated-protein-glycine-conserved (CAP-GLY) domains, which are found in proteins that coordinate the attachment of organelles to microtubules. CYLD also has sequence homology to the catalytic domain of ubiquitin carboxy-terminal hydrolases (UCH).
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MESH Headings
- Amino Acid Sequence
- Catalytic Domain
- Chromosomes, Human, Pair 16/genetics
- Cloning, Molecular
- Contig Mapping
- Deubiquitinating Enzyme CYLD
- Exons/genetics
- Female
- Genes, Dominant/genetics
- Genes, Tumor Suppressor/genetics
- Genetic Predisposition to Disease/genetics
- Germ-Line Mutation/genetics
- Humans
- Loss of Heterozygosity/genetics
- Male
- Molecular Sequence Data
- Mutation/genetics
- Neoplasms, Multiple Primary/genetics
- Neoplasms, Multiple Primary/pathology
- Polymorphism, Genetic/genetics
- Proteins/chemistry
- Proteins/genetics
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- Sequence Homology, Amino Acid
- Sequence Tagged Sites
- Skin Neoplasms/genetics
- Skin Neoplasms/pathology
- Thiolester Hydrolases/chemistry
- Tumor Suppressor Proteins
- Ubiquitin Thiolesterase
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25 |
527 |
3
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Shipley WU, Verhey LJ, Munzenrider JE, Suit HD, Urie MM, McManus PL, Young RH, Shipley JW, Zietman AL, Biggs PJ. Advanced prostate cancer: the results of a randomized comparative trial of high dose irradiation boosting with conformal protons compared with conventional dose irradiation using photons alone. Int J Radiat Oncol Biol Phys 1995; 32:3-12. [PMID: 7721636 DOI: 10.1016/0360-3016(95)00063-5] [Citation(s) in RCA: 286] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
PURPOSE Following a thorough Phase I/II study, we evaluated by a Phase III trial high versus conventional dose external beam irradiation as mono-therapy for patients with Stage T3-T4 prostate cancer. Patient outcome following standard dose radiotherapy or following a 12.5% increase in total dose to 75.6 Cobalt Gray Equivalent (CGE) using a conformal perineal proton boost was compared for local tumor control, disease-free survival, and overall survival. METHODS AND MATERIALS Stage T3-T4, Nx, N0-2, M0 patients received 50.4 Gy by four-field photons and were randomized to receive either an additional 25.2 CGE by conformal protons (arm 1--the high dose arm, 103 patients, total dose 75.6 CGE) or an additional 16.8 Gy by photons (arm 2--the conventional dose arm, 99 patients, total dose 67.2 Gy). Actuarial overall survival (OS), disease-specific survival (DSS), total recurrence-free survival (TRFS), (clinically free, prostate specific antigen (PSA) less than 4ng/ml and a negative prostate rebiopsy, done in 38 patients without evidence of disease) and local control (digital rectal exam and rebiopsy negative) were evaluated. RESULTS The protocol completion rate was 90% for arm 1 and 97% for arm 2. With a median follow-up of 61 months (range 3 to 139 months) 135 patients are alive and 67 have died, 20 from causes other than prostate cancer. We found no significant differences in OS, DSS, TRFS or local control between the two arms. Among those completing randomized treatment (93 in arm 1 and 96 in arm 2), the local control at 5 and 8 years for arm 1 is 92% and 77%, respectively and is 80% and 60%, respectively for arm 2 (p = .089) and there are no significant differences in OS, DSS, and TRFS. The local control for the 57 patients with poorly differentiated (Gleason 4 or 5 of 5) tumors at 5 and 8 years for arm 1 is 94% and 84% and is 64% and 19% on arm 2 (p = 0.0014). In patients whose digital rectal exam had normalized following treatment and underwent prostate rebiopsy there was a lower positive rebiopsy rate for arm 1 versus arm 2 patients (28 vs. 45%) and also for those with well and moderately differentiated tumors versus poorly differentiated tumors (32 and 50%). These differences were not statistically significant. Grade 1 and 2 rectal bleeding is higher (32 vs. 12%, p = 0.002) as may be urethral stricture (19 vs. 8%, p = 0.07) in the arm 1 versus arm 2. CONCLUSIONS An increase in prostate tumor dose by external beam of 12.5% to 75.6 CGE by a conformal proton boost compared to a conventional dose of 67.2 Gy by a photon boost significantly improved local control only in patients with poorly differentiated tumors. It has increased late radiation sequelae, and as yet, has not increased overall survival, disease-specific survival, or total recurrence-free survival in any subgroup. These results have led us to test by a subsequent Phase III trial the potential beneficial effect on local control and disease-specific survival of a 12.5% increase in total dose relative to conventional dose in patients with T1, T2a, and T2b tumors.
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Clinical Trial |
30 |
286 |
4
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Nath R, Biggs PJ, Bova FJ, Ling CC, Purdy JA, van de Geijn J, Weinhous MS. AAPM code of practice for radiotherapy accelerators: report of AAPM Radiation Therapy Task Group No. 45. Med Phys 1994; 21:1093-121. [PMID: 7968843 DOI: 10.1118/1.597398] [Citation(s) in RCA: 174] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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Guideline |
31 |
174 |
5
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Abstract
Originally described and most frequently reported in association with the kidney, the malignant rhabdoid tumor (MRT) is a highly aggressive neoplasm with distinctive morphologic features. Extrarenal sites reported for this neoplasm include the liver, thymus, and various soft tissue sites. Young infants are affected with rare exceptions. We report the case of a 3-month-old boy who presented with hyperirritability and increasing head size over several weeks. The patient died following a two-week hospital stay marked by development of seizures, paralysis, and apnea. At autopsy, significant findings were limited to the central nervous system. The subarachnoid space contained neoplasm throughout, with multiple areas of parenchymal invasion. A predominating intraparenchymal mass was present in the inferior cerebellum contiguous with the neoplasm in the subarachnoid space and probably represented the site of origin. Microscopically, the neoplasm was composed of a highly cellular monomorphic population of polygonal cells with roughly ovoid vesicular nuclei and conspicuous nucleoli. Variable amounts of cytoplasm were present, and many cells contained a single, well-demarcated eosinophilic hyaline globule adjacent to the nucleus. Ultrastructurally, the cytoplasmic globules were composed of whorled aggregates of intermediate filaments. Immunoperoxidase studies confirmed that the filaments were composed, at least in part, of vimentin. The morphologic and immunohistochemical features are diagnostic of MRT, an entity of unknown histogenesis that has not been reported previously as a primary neoplasm of the CNS.
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Case Reports |
38 |
161 |
6
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Purcell RV, Visnovska M, Biggs PJ, Schmeier S, Frizelle FA. Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancer. Sci Rep 2017; 7:11590. [PMID: 28912574 PMCID: PMC5599497 DOI: 10.1038/s41598-017-11237-6] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 08/21/2017] [Indexed: 12/21/2022] Open
Abstract
Colorectal cancer (CRC) is a heterogeneous disease and recent advances in subtype classification have successfully stratified the disease using molecular profiling. The contribution of bacterial species to CRC development is increasingly acknowledged, and here, we sought to analyse CRC microbiomes and relate them to tumour consensus molecular subtypes (CMS), in order to better understand the relationship between bacterial species and the molecular mechanisms associated with CRC subtypes. We classified 34 tumours into CRC subtypes using RNA-sequencing derived gene expression and determined relative abundances of bacterial taxonomic groups using 16S rRNA amplicon metabarcoding. 16S rRNA analysis showed enrichment of Fusobacteria and Bacteroidetes, and decreased levels of Firmicutes and Proteobacteria in CMS1. A more detailed analysis of bacterial taxa using non-human RNA-sequencing reads uncovered distinct bacterial communities associated with each molecular subtype. The most highly enriched species associated with CMS1 included Fusobacterium hwasookii and Porphyromonas gingivalis. CMS2 was enriched for Selenomas and Prevotella species, while CMS3 had few significant associations. Targeted quantitative PCR validated these findings and also showed an enrichment of Fusobacterium nucleatum, Parvimonas micra and Peptostreptococcus stomatis in CMS1. In this study, we have successfully associated individual bacterial species to CRC subtypes for the first time.
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research-article |
8 |
152 |
7
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Biggs PJ, Wooster R, Ford D, Chapman P, Mangion J, Quirk Y, Easton DF, Burn J, Stratton MR. Familial cylindromatosis (turban tumour syndrome) gene localised to chromosome 16q12-q13: evidence for its role as a tumour suppressor gene. Nat Genet 1995; 11:441-3. [PMID: 7493027 DOI: 10.1038/ng1295-441] [Citation(s) in RCA: 125] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The human skin is a complex organ composed of the surface epidermis, the subjacent dermis (in which blood vessels, lymphatics and nerves are located) and the skin appendages. The latter include hair follicles, sebaceous glands (which secrete lipids that may serve as a permeability barrier, emollient or antimicrobial agent), apocrine glands (which secrete scents) and eccrine glands (which produce sweat for temperature control). Hereditary cylindromatosis (MIM 123850) is a rare autosomal dominant disease characterised by the development of multiple neoplasms originating from the skin appendages. These neoplasms have been termed cylindromas due to their characteristic microscopic architecture and are believed to exhibit apocrine or eccrine differentiation. We have carried out a genome search using two families with this disease, which has provided strong evidence for linkage of cylindromatosis to loci on chromosome 16q12-q13. Using markers close to the cylindromatosis gene, consistent loss of the wild-type allele was observed in 19 tumours from four individuals in the two families, indicating that the gene is likely to be a tumour suppressor gene.
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30 |
125 |
8
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Adams DJ, Biggs PJ, Cox T, Davies R, van der Weyden L, Jonkers J, Smith J, Plumb B, Taylor R, Nishijima I, Yu Y, Rogers J, Bradley A. Mutagenic insertion and chromosome engineering resource (MICER). Nat Genet 2004; 36:867-71. [PMID: 15235602 DOI: 10.1038/ng1388] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2004] [Accepted: 05/06/2004] [Indexed: 11/09/2022]
Abstract
Embryonic stem cell technology revolutionized biology by providing a means to assess mammalian gene function in vivo. Although it is now routine to generate mice from embryonic stem cells, one of the principal methods used to create mutations, gene targeting, is a cumbersome process. Here we describe the indexing of 93,960 ready-made insertional targeting vectors from two libraries. 5,925 of these vectors can be used directly to inactivate genes with an average targeting efficiency of 28%. Combinations of vectors from the two libraries can be used to disrupt both alleles of a gene or engineer larger genomic changes such as deletions, duplications, translocations or inversions. These indexed vectors constitute a public resource (Mutagenic Insertion and Chromosome Engineering Resource; MICER) for high-throughput, targeted manipulation of the mouse genome.
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Research Support, Non-U.S. Gov't |
21 |
110 |
9
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Ahmed I, Biggs PJ, Matthews PJ, Collins LJ, Hendy MD, Lockhart PJ. Mutational dynamics of aroid chloroplast genomes. Genome Biol Evol 2013. [PMID: 23204304 PMCID: PMC3542561 DOI: 10.1093/gbe/evs110] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
A characteristic feature of eukaryote and prokaryote genomes is the co-occurrence of nucleotide substitution and insertion/deletion (indel) mutations. Although similar observations have also been made for chloroplast DNA, genome-wide associations have not been reported. We determined the chloroplast genome sequences for two morphotypes of taro (Colocasia esculenta; family Araceae) and compared these with four publicly available aroid chloroplast genomes. Here, we report the extent of genome-wide association between direct and inverted repeats, indels, and substitutions in these aroid chloroplast genomes. We suggest that alternative but not mutually exclusive hypotheses explain the mutational dynamics of chloroplast genome evolution.
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Research Support, Non-U.S. Gov't |
12 |
100 |
10
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Warren W, Biggs PJ, el-Baz M, Ghoneim MA, Stratton MR, Venitt S. Mutations in the p53 gene in schistosomal bladder cancer: a study of 92 tumours from Egyptian patients and a comparison between mutational spectra from schistosomal and non-schistosomal urothelial tumours. Carcinogenesis 1995; 16:1181-9. [PMID: 7767983 DOI: 10.1093/carcin/16.5.1181] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Much of bladder cancer in East Africa and the Middle East is attributed to chronic urinary infection with Schistosoma haematobium ('schistosomiasis'). Most schistosomal bladder cancer (SBC) is squamous cell carcinoma (SCC) and occurs in the fifth decade of life. In contrast, nonschistosomal bladder cancer (NSBC) in Western countries usually occurs in the seventh decade of life and is largely transitional cell carcinoma (TCC). To shed light on the mechanisms underlying these different patterns of bladder cancer we looked for mutations in the p53 gene in SBC from 92 patients in Egypt, where schistosomiasis is hyperendemic. Patients' mean age at presentation of bladder cancer was 49.4 +/- 9.9 years and 90% had a clinical history of schistosomiasis and/or histological evidence of schistosomal eggs adjacent to the carcinoma. There were 53 SCC, 23 TCC, 13 adenocarcinomas and three other carcinomas. Thirty patients had tumours with mutations in exons 5-8 of the p53 gene: 17/53 SCC, 8/23 TCC, 4/13 adenocarcinomas and 1/3 other tumours. Of 19 mutations in SCC, 16 were base pair substitutions (BPS), two were deletions and one an insertion. Two tumours each contained two mutations. Of the BPS, nine were transitions at CpG dinucleotides and two were G-->T transversions. All the mutations in TCC were BPS: four were transitions at CpG dinucleotides and three were G-->C transversions. One TCC had two mutations. Of four adenocarcinomas with mutations, two had transitions at CpG dinucleotides. Of the 30 BPS mutations, 16 were transitions at CpG dinucleotides, of which 12 were C-->T. We combined these 33 mutations with six obtained from Egyptian SCC reported by Habuchi et al. (Cancer Res., 53, 3795-3799, 1993) to compile a mutational spectrum. This was compared with a NSBC spectrum assembled from 118 mutations reported in the literature. The proportion of BPS at CpG dinucleotides was significantly higher in SBC than in NSBC (18/34 versus 25/103, P = 0.003). There was also a bias away from mutations in exons 7 and 8 towards mutations in exons 5 and 6. We suggest that the excess of transitions at CpG dinucleotides in SBC results from nitric oxide (NO) produced by the inflammatory response provoked by schistosomal eggs. NO could produce such mutations directly, by deamination of 5-methylcytosine, and indirectly, following conversion to nitrate, bacterial reduction to nitrite and endogenous formation of urinary N-nitroso compounds. These produce O6-alkylguanines in DNA, leading to very high rates of G:C-->A:T transitions, a process possibly augmented by inefficient repair of alkylated bases at CpG dinucleotides.
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Comparative Study |
30 |
90 |
11
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Beatty J, Biggs PJ, Gall K, Okunieff P, Pardo FS, Harte KJ, Dalterio MJ, Sliski AP. A new miniature x-ray device for interstitial radiosurgery: dosimetry. Med Phys 1996; 23:53-62. [PMID: 8700033 DOI: 10.1118/1.597791] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
A miniature, battery operated 40 kV x-ray device has been developed for the interstitial treatment of small tumors ( < 3 cm diam) in humans. X rays are emitted from the tip of a 10 cm long, 3 mm diameter probe that is stereotactically inserted into the tumor. The beam, characterized by half-value layer (HVL), spectrum analysis, and isodose contours, behaves essentially as a point isotropic source with an effective energy of 20 keV at a depth of 10 mm in water. The absolute output from the device was measured using a parallel plate ionization chamber, modified with a platinum aperture. The dose rate in water determined from these chamber measurements was found to be nominally 150 cGy/min at a distance of 10 mm for a beam current of 40 microA and voltage of 40 kV. The dose in water falls off approximately as the third power of the distance. To date, 14 patients have been treated with this device in a phase I clinical trial.
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Clinical Trial |
29 |
79 |
12
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Zhong B, Deusch O, Goremykin VV, Penny D, Biggs PJ, Atherton RA, Nikiforova SV, Lockhart PJ. Systematic error in seed plant phylogenomics. Genome Biol Evol 2011; 3:1340-8. [PMID: 22016337 PMCID: PMC3237385 DOI: 10.1093/gbe/evr105] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Resolving the closest relatives of Gnetales has been an enigmatic problem in seed plant phylogeny. The problem is known to be difficult because of the extent of divergence between this diverse group of gymnosperms and their closest phylogenetic relatives. Here, we investigate the evolutionary properties of conifer chloroplast DNA sequences. To improve taxon sampling of Cupressophyta (non-Pinaceae conifers), we report sequences from three new chloroplast (cp) genomes of Southern Hemisphere conifers. We have applied a site pattern sorting criterion to study compositional heterogeneity, heterotachy, and the fit of conifer chloroplast genome sequences to a general time reversible + G substitution model. We show that non-time reversible properties of aligned sequence positions in the chloroplast genomes of Gnetales mislead phylogenetic reconstruction of these seed plants. When 2,250 of the most varied sites in our concatenated alignment are excluded, phylogenetic analyses favor a close evolutionary relationship between the Gnetales and Pinaceae—the Gnepine hypothesis. Our analytical protocol provides a useful approach for evaluating the robustness of phylogenomic inferences. Our findings highlight the importance of goodness of fit between substitution model and data for understanding seed plant phylogeny.
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Research Support, Non-U.S. Gov't |
14 |
76 |
13
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Gunderson LL, Shipley WU, Suit HD, Epp ER, Nardi G, Wood W, Cohen A, Nelson J, Battit G, Biggs PJ, Russell A, Rockett A, Clark D. Intraoperative irradiation: a pilot study combining external beam photons with "boost" dose intraoperative electrons. Cancer 1982; 49:2259-66. [PMID: 7074541 DOI: 10.1002/1097-0142(19820601)49:11<2259::aid-cncr2820491110>3.0.co;2-q] [Citation(s) in RCA: 73] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Intraoperative "boost" dose electron beam therapy given in combination with 4500--5000 rad (45--50 Gray) external beam irradiation has been demonstrated as a practical therapeutic modality at the MGH. This procedure has been employed thus far in 58 patients; the results in the initial 36 are analyzed in detail in this paper. Thirty-four of the 36 patients had locally advanced lesions--unresectable, recurrent, or residual disease. Results achieved to date are in full agreement with our expectations: high radiation doses have been delivered to the primary intra-abdominal and pelvic tumors, excluding the sensitive structures from irradiation. This has been accomplished by a truly multidisciplinary effort comprising surgery, anesthesiology, OR nursing, administration, engineers, physicists, therapy technologists, and radiation therapists. Although follow-up is not yet sufficient to judge ultimate efficacy, acute and chronic severe morbidity is low and local control is good. There is justified enthusiasm for continuing the procedure.
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43 |
73 |
14
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Biggs PJ, Ling CC. Electrons as the cause of the observed dmax shift with field size in high energy photon beams. Med Phys 1979; 6:291-5. [PMID: 113656 DOI: 10.1118/1.594580] [Citation(s) in RCA: 69] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
For megavoltage x-ray beams, it is well known that the percent depth-dose increases considerably with field size in the buildup region, resulting in a significant shift in the apparent position of maximum dose, dmax. The nature of this increase has been investigated using a sweeping magnet placed just below the treatment head of a 25-MV linac. Measurements show that for increasing magnetic fields the dose in the buildup region is continually reduced, until a point is reached beyond which no additional reduction is observed. Here the buildup curve is essentially field size independent. These results clearly show that electrons are the primary cause of dose increase with field size in the buildup region, in contrast to a recent publication claiming that scattered photons are the cause. Further measurements were made by blocking out the primary beam at the level of the jaws and measuring the depth dose of the scattered electrons originating from the jaws. The results show that a thickness of approximately 1 gcm-2, of either polystyrene or lead, reduces the dose by a factor of two, providing further evidence that the scattered component of the beam consists of low energy electrons.
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46 |
69 |
15
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Palta JR, Biggs PJ, Hazle JD, Huq MS, Dahl RA, Ochran TG, Soen J, Dobelbower RR, McCullough EC. Intraoperative electron beam radiation therapy: technique, dosimetry, and dose specification: report of task force 48 of the Radiation Therapy Committee, American Association of Physicists in Medicine. Int J Radiat Oncol Biol Phys 1995; 33:725-46. [PMID: 7558965 DOI: 10.1016/0360-3016(95)00280-c] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Intraoperative radiation therapy (IORT) is a treatment modality whereby a large single dose of radiation is delivered to a surgically open, exposed cancer site. Typically, a beam of megavoltage electrons is directed at an exposed tumor or tumor bed through a specially designed applicator system. In the last few years, IORT facilities have proliferated around the world. The IORT technique and the applicator systems used at these facilities vary greatly in sophistication and design philosophy. The IORT beam characteristics vary for different designs of applicator systems. It is necessary to document the existing techniques of IORT, to detail the dosimetry data required for accurate delivery of the prescribed dose, and to have a uniform method of dose specification for cooperative clinical trials. The specific charge to the task group includes the following: (a) identify the multidisciplinary IORT team, (b) outline special considerations that must be addressed by an IORT program, (c) review currently available IORT techniques, (d) describe dosimetric measurements necessary for accurate delivery of prescribed dose, (e) describe dosimetric measurements necessary in documenting doses to the surrounding normal tissues, (f) recommend quality assurance procedures for IORT, (g) review methods of treatment documentation and verification, and (h) recommend methods of dose specification and recording for cooperative clinical trials.
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30 |
67 |
16
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Petti PL, Goodman MS, Sisterson JM, Biggs PJ, Gabriel TA, Mohan R. Sources of electron contamination for the Clinac-35 25-MV photon beam. Med Phys 1983; 10:856-61. [PMID: 6419032 DOI: 10.1118/1.595348] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
A detailed Monte Carlo approach has been employed to investigate the sources of electron contamination for the 25-MV photon beam generated by Varian's Clinac-35. Three sources of contamination were examined: (a) the flattening filter and beam monitor chamber, (b) the fixed primary collimators downstream from the monitor chamber and the adjustable photon jaws, and (c) the air volume separating the treatment head from the observation point. Five source-to-surface distances (SSDs) were considered for a single field size, 28 cm in diameter at 80 cm SSD. It was found that for small SSDs (80-100 cm), the dominant sources of electron contamination were the flattening filter and the beam monitor chamber which accounted for 70% of the unwanted electrons. Thirteen percent of the remaining electrons originated in the downstream primary collimators and the photon jaws, and 17% were produced in air. At larger SSDs, the fraction of unwanted electrons originating in air increased. At 400 cm SSD, 61% of the contaminating electrons present in the beam were produced in air, 34% originated in the flattening filter and beam monitor chamber, and 5% were due to interactions in the fixed collimators downstream from the monitor chamber and the adjustable photon jaws. These calculated results are substantiated by recent experiments.
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42 |
66 |
17
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Mountcastle RB, Roof BS, Mayfield RK, Mordes DB, Sagel J, Biggs PJ, Rawe SE. Pituitary adenocarcinoma in an acromegalic patient: response to bromocriptine and pituitary testing: a review of the literature on 36 cases of pituitary carcinoma. Am J Med Sci 1989; 298:109-18. [PMID: 2669475 DOI: 10.1097/00000441-198908000-00007] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
There are 36 reported cases of metastatic pituitary carcinoma and almost half (44%) of these were associated with syndromes of hormonal hypersecretion. The case of a 56-year-old acromegalic man with cervical lymphatic and spinal metastases from a primary pituitary carcinoma is described. Elevated basal levels of plasma growth hormone (GH) and insulin growth factor-1/Somatomedin C (IGF-1/SmC) were found. GH levels did not increase after TRH or LHRH administration but decreased after L-Dopa and glucose. Immunostaining of the metastatic tumor for GH and electron microscopy findings confirmed the diagnosis of pituitary GH-secreting carcinoma. Striking clinical improvement and a 46% decrease in plasma GH levels were observed with bromocriptine treatment, although IGF-1/SmC levels increased during therapy. The clinical course of most reported cases of pituitary adenocarcinoma has been one of progressive intracranial expansion of a pituitary neoplasm. In only 25% were metastatic lesions discovered antemortem, and disabling symptomatology caused by metastases was rare. Only four previously reported patients of 36 with pituitary carcinoma had acromegaly.
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Case Reports |
36 |
62 |
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Biggs PJ, Warren W, Venitt S, Stratton MR. Does a genotoxic carcinogen contribute to human breast cancer? The value of mutational spectra in unravelling the aetiology of cancer. Mutagenesis 1993; 8:275-83. [PMID: 8377645 DOI: 10.1093/mutage/8.4.275] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The p53 tumour suppressor gene is turning out to be a useful reporter for the stigmata of past genotoxic exposure. About half of all human cancers contain p53 mutations most of which occur in those regions (exons 5-8) of the gene that are highly conserved during evolution. Mutations are mainly of the missense type and their frequency and distribution vary among different kinds of cancer. The ability to detect all six possible base-substitution mutations in the p53 gene in human tumours makes it possible to construct mutational spectra for different cancers at a locus clearly implicated in carcinogenesis. Transitions at one particular hotspot--the CpG dinucleotide--occur frequently in many cancers and may reflect endogenous mutation. A reduction in the proportion of CpG mutations at the expense, for example, of an increase in GC to TA transversions may signal the effect of an exogenous mutagen. We exploited these features of the p53 gene to examine the evidence that a previously unsuspected genotoxic exposure may contribute to the high incidence of breast cancer in women living in rich industrialized countries. We compiled a mutational spectrum of p53 from 120 breast cancers and compared it with the spectrum from 145 colorectal cancers and 246 lung cancers. A germline p53 spectrum was constructed using data from 27 patients. Two hundred germline mutations in the haemophilia B gene served as a 'background' spectrum.(ABSTRACT TRUNCATED AT 250 WORDS)
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Review |
32 |
62 |
19
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Goremykin VV, Nikiforova SV, Biggs PJ, Zhong B, Delange P, Martin W, Woetzel S, Atherton RA, McLenachan PA, Lockhart PJ. The evolutionary root of flowering plants. Syst Biol 2012; 62:50-61. [PMID: 22851550 DOI: 10.1093/sysbio/sys070] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Correct rooting of the angiosperm radiation is both challenging and necessary for understanding the origins and evolution of physiological and phenotypic traits in flowering plants. The problem is known to be difficult due to the large genetic distance separating flowering plants from other seed plants and the sparse taxon sampling among basal angiosperms. Here, we provide further evidence for concern over substitution model misspecification in analyses of chloroplast DNA sequences. We show that support for Amborella as the sole representative of the most basal angiosperm lineage is founded on sequence site patterns poorly described by time-reversible substitution models. Improving the fit between sequence data and substitution model identifies Trithuria, Nymphaeaceae, and Amborella as surviving relatives of the most basal lineage of flowering plants. This finding indicates that aquatic and herbaceous species dominate the earliest extant lineage of flowering plants. [; ; ; ; ; .].
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Research Support, Non-U.S. Gov't |
13 |
57 |
20
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Gunderson LL, Tepper JE, Biggs PJ, Goldson A, Martin JK, McCullough EC, Rich TA, Shipley WU, Sindelar WF, Wood WC. Intraoperative +/- external beam irradiation. Curr Probl Cancer 1983; 7:1-69. [PMID: 6352189 DOI: 10.1016/s0147-0272(83)80021-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Review |
42 |
57 |
21
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Ahmed I, Matthews PJ, Biggs PJ, Naeem M, McLenachan PA, Lockhart PJ. Identification of chloroplast genome loci suitable for high‐resolution phylogeographic studies of
C
olocasia esculenta
(
L
.)
S
chott (
A
raceae) and closely related taxa. Mol Ecol Resour 2013; 13:929-37. [DOI: 10.1111/1755-0998.12128] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 04/25/2013] [Accepted: 04/30/2013] [Indexed: 11/28/2022]
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12 |
56 |
22
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Toombs-Ruane LJ, Benschop J, French NP, Biggs PJ, Midwinter AC, Marshall JC, Chan M, Drinković D, Fayaz A, Baker MG, Douwes J, Roberts MG, Burgess SA. Carriage of Extended-Spectrum-Beta-Lactamase- and AmpC Beta-Lactamase-Producing Escherichia coli Strains from Humans and Pets in the Same Households. Appl Environ Microbiol 2020; 86:e01613-20. [PMID: 33036993 PMCID: PMC7688229 DOI: 10.1128/aem.01613-20] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 09/29/2020] [Indexed: 12/13/2022] Open
Abstract
Extended-spectrum-beta-lactamase (ESBL)- or AmpC beta-lactamase (ACBL)-producing Escherichia coli bacteria are the most common cause of community-acquired multidrug-resistant urinary tract infections (UTIs) in New Zealand. The carriage of antimicrobial-resistant bacteria has been found in both people and pets from the same household; thus, the home environment may be a place where antimicrobial-resistant bacteria are shared between humans and pets. In this study, we sought to determine whether members (pets and people) of the households of human index cases with a UTI caused by an ESBL- or ACBL-producing E. coli strain also carried an ESBL- or ACBL-producing Enterobacteriaceae strain and, if so, whether it was a clonal match to the index case clinical strain. Index cases with a community-acquired UTI were recruited based on antimicrobial susceptibility testing of urine isolates. Fecal samples were collected from 18 non-index case people and 36 pets across 27 households. Eleven of the 27 households screened had non-index case household members (8/18 people and 5/36 animals) positive for ESBL- and/or ACBL-producing E. coli strains. Whole-genome sequence analysis of 125 E. coli isolates (including the clinical urine isolates) from these 11 households showed that within seven households, the same strain of ESBL-/ACBL-producing E. coli was cultured from both the index case and another person (5/11 households) or pet dog (2/11 households). These results suggest that transmission within the household may contribute to the community spread of ESBL- or ACBL-producing E. coliIMPORTANCEEnterobacteriaceae that produce extended-spectrum beta-lactamases (ESBLs) and AmpC beta-lactamases (ACBLs) are important pathogens and can cause community-acquired illnesses, such as urinary tract infections (UTIs). Fecal carriage of these resistant bacteria by companion animals may pose a risk for transmission to humans. Our work evaluated the sharing of ESBL- and ACBL-producing E. coli isolates between humans and companion animals. We found that in some households, dogs carried the same strain of ESBL-producing E. coli as the household member with a UTI. This suggests that transmission events between humans and animals (or vice versa) are likely occurring within the home environment and, therefore, the community as a whole. This is significant from a health perspective, when considering measures to minimize community transmission, and highlights that in order to manage community spread, we need to consider interventions at the household level.
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research-article |
5 |
53 |
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Biggs PJ, Russell MD. An investigation into the presence of secondary electrons in megavoltage photon beams. Phys Med Biol 1983; 28:1033-43. [PMID: 6415682 DOI: 10.1088/0031-9155/28/9/003] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The presence of secondary electrons in photon beams of 60Co and 4, 8, 10, 15 and 25 MV x-rays has been studied by measuring surface charge using thin window ionisation chambers. Measurements have been made for square fields from 4 X 4 cm2 to 35 X 35 cm2 for locations from the collimator head to a distance of 4 m from the target. In addition, measurements have been made for rectangular fields at 10 MV and 25 MV for fields of equivalent area from 5 X 5 cm2 to 25 X 25 cm2. By eliminating the inverse square effect, the presence of contaminants from the head and the effect of build-up in air are clearly seen and well separated. Comparison between the curves at different energies indicates an increasing effect of contamination from the head with energy and a decreasing effect of electron production in air with increasing energy.
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42 |
52 |
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Biggs PJ, Epp ER, Ling CC, Novack DH, Michaels HB. Dosimetry, field shaping and other considerations for intra-operative electron therapy. Int J Radiat Oncol Biol Phys 1981; 7:875-84. [PMID: 6796550 DOI: 10.1016/0360-3016(81)90003-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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44 |
48 |
25
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DeLaney TF, Shipley WU, O'Leary MP, Biggs PJ, Prout GR. Preoperative irradiation, lymphadenectomy, and 125iodine implantation for patients with localized carcinoma of the prostate. Int J Radiat Oncol Biol Phys 1986; 12:1779-85. [PMID: 3759530 DOI: 10.1016/0360-3016(86)90319-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Fifty-four patients with clinically and surgically localized prostatic carcinoma were treated with low-dose preoperative irradiation (1,050 cGy), pelvic lymphadenectomy, and interstitial 125Iodine implantation. The follow-up range is 2 to 9 years with a median follow-up of 5 years. Overall local tumor control is 92%. Actuarial 5-year survival is 86% and the actuarial disease-free survival at 5 years is 73%. Patients with poorly differentiated tumors have a significantly worse actuarial survival (62%) at 5 years than patients with well (95%) or moderately well differentiated tumors (93%), p = 0.04. Disease-free survival at 5 years was influenced by grade: well (100%), moderate (60%), and poor (48%), p = 0.03. Multivariate regression analysis indicates that only the degree of differentiation (p = 0.05) significantly impacts on survival. Both degree of differentiation (p = 0.04) and nodal status (p = 0.03) significantly influence disease-free survival. Potency has been maintained in 71% of patients potent at the time of implantation. Late reactions have been acceptable to date: bladder outlet obstruction (13%), mild proctitis (13%), cystourethritis (6%), incontinence (2%), and prostatic calculi (2%).
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39 |
47 |