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Vadim V Lozovoy,Xin Zhu,Tissa C Gunaratne,D Ahmasi Harris,Janelle C Shane,Marcos Dantus The possibility that chemical reactions may be controlled by tailored femtosecond laser pulses has inspired recent studies that take advantage of their short pulse duration, comparable to intramolecular dynamics, and high peak intensity to fragment and ionize molecules. In this article, we present ... ( view more )an experimental quest to control the chemical reactions that take place when isolated molecules interact with shaped near-infrared laser pulses with peak intensities ranging from 1013 to 1016 W/cm2. Through the exhaustive evaluation of hundreds of thousands of experiments, we methodically evaluated the molecular response of 16 compounds, including isomers, to the tailored light fields, as monitored by time-of-flight mass spectrometry. Analysis of the experimental data, taking into account its statistical significance, leads us to uncover important trends regarding the interaction of isolated molecules with an intense laser field. Despite the energetics involved in fragmentation and ionization, the integrated second-harmonic generation of a given laser pulse (ISHG), which was recorded as an independent diagnostic parameter, was found to be linearly proportional to the total ion yield (IMS) generated by that pulse in all of our pulse shaping measurements. Order of magnitude laser control over the relative yields of different fragment ions was observed for most of the molecules studied; the fragmentation yields were found to vary monotonically with IMS and/or ISHG. When the extensive changes in fragmentation yields as a function of IMS were compared for different phase functions, we found essentially identical results. This observation implies that fragmentation depends on a parameter that is responsible for IMS and independent from the particular time-frequency structure of the shaped laser pulse. With additional experiments, we found that individual ion yields depend only on the average pulse duration, implying that coherence does not play a role in the observed changes in yield as a function of pulse shaping. These findings were consistently observed for all molecules studied (p-, m-, o-nitrotoluene, 2,4-dinitrotoluene, benzene, toluene, naphthalene, azulene, acetone, acetyl chloride, acetophenone, p-chrolobenzonitrile, N,N-dimethylformamide, dimethyl phosphate, 2-chloroethyl ethyl sulfide, and tricarbonyl-[eta5-1-methyl-2,4-cyclopentadien-1-yl]-manganese). The exception to our conclusion is that the yield of small singly-charged fragments resulting from a multiple ionization process in a subset of molecules, were found to be highly sensitive to the phase structure of the intense pulses. This coherent process plays a minimal role in photofragmentation; therefore, we consider it an exception rather than a rule. Changes in the fragmentation process are dependent on molecular structure, as evidenced in a number of isomers, therefore femtosecond laser fragmentation could provide a practical dimension to analytical chemistry techniques. ( view less ) Paul W Bowyer,Ruwani S Gunaratne,Munira Grainger,Chrislaine Withers-Martinez,Sasala R Wickramsinghe,Edward W Tate,Robin J Leatherbarrow,Katherine A Brown,Anthony A Holder,Deborah F Smith Recombinant N-myristoyltransferase of Plasmodium falciparum (termed PfNMT) has been used in the development of a SPA (scintillation proximity assay) suitable for automation and high-throughput screening of inhibitors against this enzyme. The ability to use the SPA has been facilitated by developmen... ( view more )t of an expression and purification system which yields considerably improved quantities of soluble active recombinant PfNMT compared with previous studies. Specifically, yields of pure protein have been increased from 12 microg x l(-1) to >400 microg x l(-1) by use of a synthetic gene with codon usage optimized for expression in an Escherichia coli host. Preliminary small-scale 'piggyback' inhibitor studies using the SPA have identified a family of related molecules containing a core benzothiazole scaffold with IC50 values <50 microM, which demonstrate selectivity over human NMT1. Two of these compounds, when tested against cultured parasites in vitro, reduced parasitaemia by >80% at a concentration of 10 microM. ( view less ) Kevin E Bassler,Joseph L McCauley,Gemunu H Gunaratne Fat-tailed distributions have been reported in fluctuations of financial markets for more than a decade. Sliding interval techniques used in these studies implicitly assume that the underlying stochastic process has stationary increments. Through an analysis of intraday increments, we explicitly sh... ( view more )ow that this assumption is invalid for the Euro-Dollar exchange rate. We find several time intervals during the day where the standard deviation of increments exhibits power law behavior in time. Stochastic dynamics during these intervals is shown to be given by diffusion processes with a diffusion coefficient that depends on time and the exchange rate. We introduce methods to evaluate the dynamical scaling index and the scaling function empirically. In general, the scaling index is significantly smaller than previously reported values close to 0.5. We show how the latter as well as apparent fat-tailed distributions can occur only as artifacts of the sliding interval analysis. ( view less ) H Jayantha Gunaratne,Victor D Vacquier Whole genome sequence data permit the study of protein families regulating cellular homeostasis during development. Here we present a study of the sea urchin Ca(2+)-ATPases made possible by the Sea Urchin Genome Sequencing Project. This is of potential interest because adult sea urchins, their game... ( view more )tes and embryos live in the relatively high Ca(2+) concentration of 10 mM. Three Ca(2+)-ATPases regulate Ca(2+) levels in animal cells: plasma membrane Ca(2+)-ATPase (PMCA), sarcoplasmic/endoplasmic reticulum Ca(2+)-ATPase (SERCA) and secretory pathway Ca(2+)-ATPase (SPCA). The primary structures of Sp-PMCA and Sp-SERCA in the sea urchin, Strongylocentrotus purpuratus (Sp), have been published. Here, we present the primary structure of Sp-SPCA, which is 912 amino acids and has 66% identity and 80% similarity to human SPCA1. Southern blots and genome analysis show that Sp-SPCA is a single copy gene. Each Sp Ca(2+)-ATPase is highly conserved when compared to its human ortholog, indicating that human and sea urchin share structurally similar energy driven Ca(2+) homeostasis mechanisms that have been maintained throughout the course of deuterostome evolution. Annotation using the assembled sea urchin genome reveals that Sp-SPCA, Sp-PMCA and Sp-SERCA have 23, 17 and 24 exons. RT-Q-PCR shows that transcripts of Sp-SPCA are at low levels compared to Sp-PMCA and Sp-SERCA. Gradual increases in Sp-PMCA and Sp-SERCA mRNA begin at the 18 hour hatched blastula stage and peak 4-5-fold higher by 25 h at the mid to late blastulae stage. ( view less ) Justin A Pachebat,Madhusudan Kadekoppala,Munira Grainger,Anton R Dluzewski,Ruwani S Gunaratne,Terence J Scott-Finnigan,Solabomi A Ogun,Irene T Ling,Lawrence H Bannister,Helen M Taylor,Graham H Mitchell,Anthony A Holder In Plasmodium falciparum, merozoite surface protein 7 (MSP7) was originally identified as a 22kDa protein on the merozoite surface and associated with the MSP1 complex shed during erythrocyte invasion. MSP7 is synthesised in schizonts as a 351-amino acid precursor that undergoes proteolytic process... ( view more )ing. During biosynthesis the MSP1 and MSP7 precursors form a complex that is targeted to the surface of developing merozoites. In the sequential proteolytic processing of MSP7, N- and C-terminal 20 and 33kDa products of primary processing, MSP7(20) and MSP7(33) are formed and MSP7(33) remains bound to full length MSP1. Later in the mature schizont, MSP7(20) disappears from the merozoite surface and on merozoite release MSP7(33) undergoes a secondary cleavage yielding the 22kDa MSP7(22) associated with MSP1. In free merozoites, both MSP7(22) and a further cleaved product, MSP7(19) present only in some parasite lines, were detected; these two derivatives are shed as part of the protein complex with MSP1 fragments during erythrocyte invasion. Primary processing of MSP7 is brefeldin A-sensitive while secondary processing is resistant to both calcium chelators and serine protease inhibitors. Primary processing of MSP7 occurs prior to that of MSP1 in a post-Golgi compartment, whereas the secondary cleavage occurs on the surface of the developing merozoite, possibly at the time of MSP1 primary processing and well before the secondary processing of MSP1. ( view less ) H Jayantha Gunaratne,Gary W Moy,Masashi Kinukawa,Shinji Miyata,Silvia A Mah,Victor D Vacquier BACKGROUND: Mutations in the human polycystic kidney disease-1 (hPKD1) gene result in ~85% of cases of autosomal dominant polycystic kidney disease, the most frequent human monogenic disease. PKD1 proteins are large multidomain proteins involved in a variety of signal transduction mechanisms. Obtai... ( view more )ning more information about members of the PKD1 family will help to clarify their functions. Humans have five hPKD1 proteins, whereas sea urchins have 10. The PKD1 proteins of the sea urchin, Strongylocentrotus purpuratus, are referred to as the Receptor for Egg Jelly, or SpREJ proteins. The SpREJ proteins form a subfamily within the PKD1 family. They frequently contain C-type lectin domains, PKD repeats, a REJ domain, a GPS domain, a PLAT/LH2 domain, 1-11 transmembrane segments and a C-terminal coiled-coil domain. RESULTS: The 10 full-length SpREJ cDNA sequences were determined. The secondary structures of their deduced proteins were predicted and compared to the five human hPKD1 proteins. The genomic structures of the 10 SpREJs show low similarity to each other. All 10 SpREJs are transcribed in either embryos or adult tissues. SpREJs show distinct patterns of expression during embryogenesis. Adult tissues show tissue-specific patterns of SpREJ expression. CONCLUSION: Possession of a REJ domain of about 600 residues defines this family. Except for SpREJ1 and 3, that are thought to be associated with the sperm acrosome reaction, the functions of the other SpREJ proteins remain unknown. The sea urchin genome is one-fourth the size of the human genome, but sea urchins have 10 SpREJ proteins, whereas humans have five. Determination of the tissue specific function of each of these proteins will be of interest to those studying echinoderm development. Sea urchins are basal deuterostomes, the line of evolution leading to the vertebrates. The study of individual PKD1 proteins will increase our knowledge of the importance of this gene family. ( view less ) P S Gunaratne,C N Wijeyaratne,P Chandrasiri,S Sivakumaran,K Sellahewa,P Perera,R Fernando,J Wanigasinghe,S Jayasinghe,R Ranawala,M T M Riffsy,H R Seneviratne An outbreak of Aspergillus fumigatus meningitis occurred in 5 women following spinal anaesthesia, performed between 21 June and 17 July 2005 for caesarean section, in Colombo, Sri Lanka. The patients' median age was 27 years. Different teams in 2 maternity hospitals gave spinal anaesthesia. Mean in... ( view more )cubation period was 11.2 days. Fever, headache and nuchal rigidity were common presentations. Remittent fever continued despite broad-spectrum intravenous antibiotics. Papilloedema, lateral rectus palsy, cerebral infarction and haemorrhage developed later. Three patients died. Cerebrospinal fluid pleocytosis with low glucose yielded negative PCR for fungi. Fungal cultures subsequently grew Aspergillus fumigatus. A post-mortem of the first patient confirmed Aspergillus meningitis, followed by treatment with amphotericin B and voriconazole, that saved the lives of others. Visual and hearing impairment in one and complete recovery in the other were observed a year after treatment. Examination of unused plastic syringes, needles, cannulae, and ampoules of anaesthetic agents confirmed that 43 syringes from three different manufactures were contaminated with Aspergillus fumigatus. The stores for drugs and devices of the Ministry of Health were examined and found to be full of tsunami donations, while regular procurements of the Ministry were kept in a poorly maintained humid warehouse. Inadequate space for tsunami donations was identified as the most plausible explanation for sub-optimal storage. Withdrawal and incineration of all unused syringes controlled the outbreak. The survival of those aggressively treated for Aspergillus meningitis suggests in hindsight that the availability of diagnostic tests and specific treatment, and early recognition of the outbreak could have saved the lives of victims who died. Early life-threatening side-effects and permanent long term sequelae of antifungal medication stress the need to be cautious with empirical treatment in immuno-competent low-risk individuals. ( view less ) Michelle M Roux,Ian K Townley,Michael Raisch,Anna Reade,Cynthia Bradham,Glen Humphreys,Herath Jayantha Gunaratne,Christopher E Killian,Gary Moy,Yi-Hsien Su,Charles A Ettensohn,Fred Wilt,Victor D Vacquier,Robert D Burke,Gary Wessel,Kathy R Foltz The sea urchin egg has a rich history of contributions to our understanding of fundamental questions of egg activation at fertilization. Within seconds of sperm-egg interaction, calcium is released from the egg endoplasmic reticulum, launching the zygote into the mitotic cell cycle and the developm... ( view more )ental program. The sequence of the Strongylocentrotus purpuratus genome offers unique opportunities to apply functional genomic and proteomic approaches to investigate the repertoire and regulation of Ca(2+) signaling and homeostasis modules present in the egg and zygote. The sea urchin "calcium toolkit" as predicted by the genome is described. Emphasis is on the Ca(2+) signaling modules operating during egg activation, but the Ca(2+) signaling repertoire has ramifications for later developmental events and adult physiology as well. Presented here are the mechanisms that control the initial release of Ca(2+) at fertilization and additional signaling components predicted by the genome and found to be expressed and operating in eggs at fertilization. The initial release of Ca(2+) serves to coordinate egg activation, which is largely a phenomenon of post-translational modifications, especially dynamic protein phosphorylation. Functional proteomics can now be used to identify the phosphoproteome in general and specific kinase targets in particular. This approach is described along with findings to date. Key outstanding questions regarding the activation of the developmental program are framed in the context of what has been learned from the genome and how this knowledge can be applied to functional studies. ( view less ) Sea Urchin Genome Sequencing Consortium ,Erica Sodergren,George M Weinstock,Eric H Davidson,R Andrew Cameron,Richard A Gibbs,Robert C Angerer,Lynne M Angerer,Maria Ina Arnone,David R Burgess,Robert D Burke,James A Coffman,Michael Dean,Maurice R Elphick,Charles A Ettensohn,Kathy R Foltz,Amro Hamdoun,Richard O Hynes,William H Klein,William Marzluff,David R McClay,Robert L Morris,Arcady Mushegian,Jonathan P Rast,L Courtney Smith,Michael C Thorndyke,Victor D Vacquier,Gary M Wessel,Greg Wray,Lan Zhang,Christine G Elsik,Olga Ermolaeva,Wratko Hlavina,Gretchen Hofmann,Paul Kitts,Melissa J Landrum,Aaron J Mackey,Donna Maglott,Georgia Panopoulou,Albert J Poustka,Kim Pruitt,Victor Sapojnikov,Xingzhi Song,Alexandre Souvorov,Victor Solovyev,Zheng Wei,Charles A Whittaker,Kim Worley,K James Durbin,Yufeng Shen,Olivier Fedrigo,David Garfield,Ralph Haygood,Alexander Primus,Rahul Satija,Tonya Severson,Manuel L Gonzalez-Garay,Andrew R Jackson,Aleksandar Milosavljevic,Mark Tong,Christopher E Killian,Brian T Livingston,Fred H Wilt,Nikki Adams,Robert Bellé,Seth Carbonneau,Rocky Cheung,Patrick Cormier,Bertrand Cosson,Jenifer Croce,Antonio Fernandez-Guerra,Anne-Marie Genevière,Manisha Goel,Hemant Kelkar,Julia Morales,Odile Mulner-Lorillon,Anthony J Robertson,Jared V Goldstone,Bryan Cole,David Epel,Bert Gold,Mark E Hahn,Meredith Howard-Ashby,Mark Scally,John J Stegeman,Erin L Allgood,Jonah Cool,Kyle M Judkins,Shawn S McCafferty,Ashlan M Musante,Robert A Obar,Amanda P Rawson,Blair J Rossetti,Ian R Gibbons,Matthew P Hoffman,Andrew Leone,Sorin Istrail,Stefan C Materna,Manoj P Samanta,Viktor Stolc,Waraporn Tongprasit,Qiang Tu,Karl-Frederik Bergeron,Bruce P Brandhorst,James Whittle,Kevin Berney,David J Bottjer,Cristina Calestani,Kevin Peterson,Elly Chow,Qiu Autumn Yuan,Eran Elhaik,Dan Graur,Justin T Reese,Ian Bosdet,Shin Heesun,Marco A Marra,Jacqueline Schein,Michele K Anderson,Virginia Brockton,Katherine M Buckley,Avis H Cohen,Sebastian D Fugmann,Taku Hibino,Mariano Loza-Coll,Audrey J Majeske,Cynthia Messier,Sham V Nair,Zeev Pancer,David P Terwilliger,Cavit Agca,Enrique Arboleda,Nansheng Chen,Allison M Churcher,F Hallböök,Glen W Humphrey,Mohammed M Idris,Takae Kiyama,Shuguang Liang,Dan Mellott,Xiuqian Mu,Greg Murray,Robert P Olinski,Florian Raible,Matthew Rowe,John S Taylor,Kristin Tessmar-Raible,D Wang,Karen H Wilson,Shunsuke Yaguchi,Terry Gaasterland,Blanca E Galindo,Herath J Gunaratne,Celina Juliano,Masashi Kinukawa,Gary W Moy,Anna T Neill,Mamoru Nomura,Michael Raisch,Anna Reade,Michelle M Roux,Jia L Song,Yi-Hsien Su,Ian K Townley,Ekaterina Voronina,Julian L Wong,Gabriele Amore,Margherita Branno,Euan R Brown,Vincenzo Cavalieri,Véronique Duboc,Louise Duloquin,Constantin Flytzanis,Christian Gache,François Lapraz,Thierry Lepage,Annamaria Locascio,Pedro Martinez,Giorgio Matassi,Valeria Matranga,Ryan Range,Francesca Rizzo,Eric Röttinger,Wendy Beane,Cynthia Bradham,Christine Byrum,Tom Glenn,Sofia Hussain,Gerard Manning,Esther Miranda,Rebecca Thomason,Katherine Walton,Athula Wikramanayke,Shu-Yu Wu,Ronghui Xu,C Titus Brown,Lili Chen,Rachel F Gray,Pei Yun Lee,Jongmin Nam,Paola Oliveri,Joel Smith,Donna Muzny,Stephanie Bell,Joseph Chacko,Andrew Cree,Stacey Curry,Clay Davis,Huyen Dinh,Shannon Dugan-Rocha,Jerry Fowler,Rachel Gill,Cerrissa Hamilton,Judith Hernandez,Sandra Hines,Jennifer Hume,Laronda Jackson,Angela Jolivet,Christie Kovar,Sandra Lee,Lora Lewis,George Miner,Margaret Morgan,Lynne V Nazareth,Geoffrey Okwuonu,David Parker,Ling-Ling Pu,Rachel Thorn,Rita Wright We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by ... ( view more )a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes. ( view less ) J Reddy Challa,Tissa C Gunaratne,M Cather Simpson The temporally overlapping, ultrafast electronic and vibrational dynamics of a model five-coordinate, high-spin heme in a nominally isotropic solvent environment has been studied for the first time with three complementary ultrafast techniques: transient absorption, time-resolved resonance Raman St... ( view more )okes, and time-resolved resonance Raman anti-Stokes spectroscopies. Vibrational dynamics associated with an evolving ground-state species dominate the observations. Excitation into the blue side of the Soret band led to very rapid S2 --> S1 decay (sub-100 fs), followed by somewhat slower (800 fs) S1 --> S0 nonradiative decay. The initial vibrationally excited, non-Boltzmann S0 state was modeled as shifted to lower energy by 300 cm(-1) and broadened by 20%. On a approximately 10 ps time scale, the S0 state evolved into its room-temperature, thermal distribution S0 profile largely through VER. Anti-Stokes signals disappear very rapidly, indicating that the vibrational energy redistributes internally in about 1-3 ps from the initial accepting modes associated with S1 --> S0 internal conversion to the rest of the macrocycle. Comparisons of anti-Stokes mode intensities and lifetimes from TRARRS studies in which the initial excited state was prepared by ligand photolysis [Mizutani, T.; Kitagawa, T. Science 1997, 278, 443, and Chem. Rec. 2001, 1, 258] suggest that, while transient absorption studies appear to be relatively insensitive to initial preparation of the electronic excited state, the subsequent vibrational dynamics are not. Direct, time-resolved evaluation of vibrational lifetimes provides insight into fast internal conversion in hemes and the pathways of subsequent vibrational energy flow in the ground state. The overall similarity of the model heme electronic dynamics to those of biological systems may be a sign that the protein's influence upon the dynamics of the heme active site is rather subtle. ( view less ) Seiichi Nakata,Yukio Sato,Pujitha Gunaratne,Yoshiro Suzuki,Saiko Sugiura,Tsutomu Nakashima OBJECTIVE: To estimate asymmetry in normal and pathological facial functions using an established computer generated objective evaluation technique. METHODS: Analysis was performed on three-dimensional (3-D) data captured using a specially designed 3-D face shape measurement system. Six healthy vol... ( view more )unteers and six patients with Bell's palsy were analyzed for forced eye closure and grinning actions. The asymmetry was computed at locations that had the greatest effect in each action on both the left and right sides of the face, in reference to a relaxed condition. The patients' data were captured and analyzed repeatedly for a period of three days for an average interval of four weeks, and the results were compared with the Yanagihara scale. RESULTS: The control set of a normal sample exhibited a low standard deviation and a high correlation coefficient in both facial actions, and this contributed to a robust evaluation. The patients showed a higher standard deviation than the healthy subjects because of the larger degree of scatter of the data points in their respective data distributions. During the three clinical examinations, our proposed quantification method produced a continuous grading scheme, as opposed to the discrete scheme of the House-Brackmann grading. CONCLUSION: Our proposed system shows advantages over the existing methods in that it does not rely on reference points nor does it use markers to analyze facial deformation. In addition, our estimations are very robust and accurate because our approach directly evaluates 3-D spatial variations in normal and pathological facial functions. ( view less ) Yan Song,Gemunu H Gunaratne Large bones from many anatomical locations of the human skeleton consist of an outer shaft (cortex) surrounding a highly porous internal region (trabecular bone) whose structure is reminiscent of a disordered cubic network. Age related degradation of cortical and trabecular bone takes different for... ( view more )ms. Trabecular bone weakens primarily by loss of connectivity of the porous network, and recent studies have shown that vibrational response can be used to obtain reliable estimates for loss of its strength. In contrast, cortical bone degrades via the accumulation of long fractures and changes in the level of mineralization of the bone tissue. In this paper, we model cortical bone by an initially solid specimen with uniform density to which long fractures are introduced; we find that, as in the case of trabecular bone, vibrational assessment provides more reliable estimates of residual strength in cortical bone than is possible using measurements of density or porosity. ( view less ) Herath Jayantha Gunaratne,Victor D VacquierPlasma membrane, sarco-endoplasmic reticulum and secretory pathway Ca2+-ATPases (designated PMCA, SERCA and SPCA) regulate intracellular Ca2+ in animal cells. The presence of PMCA, and the absence of SERCA, in sea urchin sperm is known. By using inhibitors of Ca2+-ATPases, we now show the presence ... ( view more )of SPCA and Ca2+ store in sea urchin sperm, which refills by SPCA-type pumps. Immunofluorescence shows SPCA localizes to the mitochondrion. Ca2+ measurements reveal that approximately 75% of Ca2+ extrusion is by Ca2+ ATPases and 25% by Na+ dependent Ca2+ exchanger/s. Bisphenol, a Ca2+ ATPase inhibitor, completely blocks the acrosome reaction, indicating the importance of Ca2+-ATPases in fertilization. ( view less ) Herath Jayantha Gunaratne,Anna T Neill,Victor D Vacquier Plasma membrane Ca2+ATPases (PMCAs) export Ca2+ from cells in a highly regulated manner, providing fine-tuning to the maintenance of intracellular Ca2+ concentrations. There are few studies of PMCAs in spermatozoa, which is surprising considering the importance of this enzyme in all cell types. Her... ( view more )e we describe the primary structure and localization of the PMCA of sea urchin spermatozoa (suPMCA). The suPMCA is 1,154 amino acids and has 56% identity and 76% similarity to all 4 human PMCA isoforms. The suPMCA shares the features of a typical PMCA, including domains for calmodulin binding, ATP binding, ATPase phosphorylation, and 10 putative transmembrane segments with two large cytoplasmic loops. Southern blots show that suPMCA is a single copy gene. Treatment of live sea urchin sperm with the PMCA inhibitor, 5-(-6)-carboxyeosin, results in elevations of intracellular Ca2+ and loss of flagellar motility. Immunoblotting and immunoflorescence show that suPMCA is concentrated in the sperm head plasma membrane. In previous work, we showed that a plasma membrane K+ dependent Na+/Ca2+ exchanger (suNCKX), which also keeps Ca2+ low in these cells, is concentrated in the sperm flagellum. Thus, the sperm head and flagellum localize different gene products, both functioning to keep intracellular Ca2+ low, while the sperm swims in seawater containing 10 mM Ca2+. ( view less ) Donna M Muzny,Steven E Scherer,Rajinder Kaul,Jing Wang,Jun Yu,Ralf Sudbrak,Christian J Buhay,Rui Chen,Andrew Cree,Yan Ding,Shannon Dugan-Rocha,Rachel Gill,Preethi Gunaratne,R Alan Harris,Alicia C Hawes,Judith Hernandez,Anne V Hodgson,Jennifer Hume,Andrew Jackson,Ziad Mohid Khan,Christie Kovar-Smith,Lora R Lewis,Ryan J Lozado,Michael L Metzker,Aleksandar Milosavljevic,George R Miner,Margaret B Morgan,Lynne V Nazareth,Graham Scott,Erica Sodergren,Xing-Zhi Song,David Steffen,Sharon Wei,David A Wheeler,Mathew W Wright,Kim C Worley,Ye Yuan,Zhengdong Zhang,Charles Q Adams,M Ali Ansari-Lari,Mulu Ayele,Mary J Brown,Guan Chen,Zhijian Chen,James Clendenning,Kerstin P Clerc-Blankenburg,Runsheng Chen,Zhu Chen,Clay Davis,Oliver Delgado,Huyen H Dinh,Wei Dong,Heather Draper,Stephen Ernst,Gang Fu,Manuel L Gonzalez-Garay,Dawn K Garcia,Will Gillett,Jun Gu,Bailin Hao,Eric Haugen,Paul Havlak,Xin He,Steffen Hennig,Songnian Hu,Wei Huang,Laronda R Jackson,Leni S Jacob,Susan H Kelly,Michael Kube,Ruth Levy,Zhangwan Li,Bin Liu,Jing Liu,Wen Liu,Jing Lu,Manjula Maheshwari,Bao-Viet Nguyen,Geoffrey O Okwuonu,Anthony Palmeiri,Shiran Pasternak,Lesette M Perez,Karen A Phelps,Farah J H Plopper,Boqin Qiang,Christopher Raymond,Ruben Rodriguez,Channakhone Saenphimmachak,Jireh Santibanez,Hua Shen,Yan Shen,Sandhya Subramanian,Paul E Tabor,Daniel Verduzco,Lenee Waldron,Jian Wang,Jun Wang,Qiaoyan Wang,Gabrielle A Williams,Gane K-S Wong,Zhijian Yao,JingKun Zhang,Xiuqing Zhang,Guoping Zhao,Jianling Zhou,Yang Zhou,David Nelson,Hans Lehrach,Richard Reinhardt,Susan L Naylor,Huanming Yang,Maynard Olson,George Weinstock,Richard A Gibbs After the completion of a draft human genome sequence, the International Human Genome Sequencing Consortium has proceeded to finish and annotate each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chrom... ( view more )osomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest unbroken stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also includes a chemokine receptor gene cluster as well as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion that occurred some time after the split of Homininae from Ponginae, and propose an evolutionary history of the inversion. ( view less ) Steven E Scherer,Donna M Muzny,Christian J Buhay,Rui Chen,Andrew Cree,Yan Ding,Shannon Dugan-Rocha,Rachel Gill,Preethi Gunaratne,R Alan Harris,Alicia C Hawes,Judith Hernandez,Anne V Hodgson,Jennifer Hume,Andrew Jackson,Ziad Mohid Khan,Christie Kovar-Smith,Lora R Lewis,Ryan J Lozado,Michael L Metzker,Aleksandar Milosavljevic,George R Miner,Kate T Montgomery,Margaret B Morgan,Lynne V Nazareth,Graham Scott,Erica Sodergren,Xing-Zhi Song,David Steffen,Ruth C Lovering,David A Wheeler,Kim C Worley,Yi Yuan,Zhengdong Zhang,Charles Q Adams,M Ali Ansari-Lari,Mulu Ayele,Mary J Brown,Guan Chen,Zhijian Chen,Kerstin P Clerc-Blankenburg,Clay Davis,Oliver Delgado,Huyen H Dinh,Heather Draper,Manuel L Gonzalez-Garay,Paul Havlak,Laronda R Jackson,Leni S Jacob,Susan H Kelly,Li Li,Zhangwan Li,Jing Liu,Wen Liu,Jing Lu,Manjula Maheshwari,Bao-Viet Nguyen,Geoffrey O Okwuonu,Shiran Pasternak,Lesette M Perez,Farah J H Plopper,Jireh Santibanez,Hua Shen,Paul E Tabor,Daniel Verduzco,Lenee Waldron,Qiaoyan Wang,Gabrielle A Williams,Jingkun Zhang,Jianling Zhou,Carlana C Allen,Anita G Amin,Vivian Anyalebechi,Michael Bailey,Joseph A Barbaria,Kesha E Bimage,Nathaniel P Bryant,Paula E Burch,Carrie E Burkett,Kevin L Burrell,Eliana Calderon,Veronica Cardenas,Kelvin Carter,Kristal Casias,Iracema Cavazos,Sandra R Cavazos,Heather Ceasar,Joseph Chacko,Sheryl N Chan,Dean Chavez,Constantine Christopoulos,Joseph Chu,Raynard Cockrell,Caroline D Cox,Michelle Dang,Stephanie R Dathorne,Robert David,Candi Mon'Et Davis,Latarsha Davy-Carroll,Denise R Deshazo,Jeremy E Donlin,Lisa D'Souza,Kristy A Eaves,Amy Egan,Alexandra J Emery-Cohen,Michael Escotto,Nicole Flagg,Lisa D Forbes,Abdul M Gabisi,Melissa Garza,Cerissa Hamilton,Nicholas Henderson,Omar Hernandez,Sandra Hines,Marilyn E Hogues,Mei Huang,DeVincent G Idlebird,Rudy Johnson,Angela Jolivet,Sally Jones,Ryan Kagan,Laquisha M King,Belita Leal,Heather Lebow,Sandra Lee,Jaclyn M LeVan,Lakeshia C Lewis,Pamela London,Lorna M Lorensuhewa,Hermela Loulseged,Demetria A Lovett,Alice Lucier,Raymond L Lucier,Jie Ma,Renita C Madu,Patricia Mapua,Ashley D Martindale,Evangelina Martinez,Elizabeth Massey,Samantha Mawhiney,Michael G Meador,Sylvia Mendez,Christian Mercado,Iracema C Mercado,Christina E Merritt,Zachary L Miner,Emmanuel Minja,Teresa Mitchell,Farida Mohabbat,Khatera Mohabbat,Baize Montgomery,Niki Moore,Sidney Morris,Mala Munidasa,Robin N Ngo,Ngoc B Nguyen,Elizabeth Nickerson,Ogechi O Nwaokelemeh,Stanley Nwokenkwo,Melissa Obregon,Maryann Oguh,Njideka Oragunye,Rodolfo J Oviedo,Bridgette J Parish,David N Parker,Julia Parrish,Kenya L Parks,Heidie A Paul,Brett A Payton,Agapito Perez,William Perrin,Adam Pickens,Eltrick L Primus,Ling-Ling Pu,Maria Puazo,Miyo M Quiles,Juana B Quiroz,Dina Rabata,Kacy Reeves,San Juana Ruiz,Hongmei Shao,Ida Sisson,Titilola Sonaike,Richard P Sorelle,Angelica E Sutton,Amanda F Svatek,Leah Anne Svetz,Kavitha S Tamerisa,Tineace R Taylor,Brian Teague,Nicole Thomas,Rachel D Thorn,Zulma Y Trejos,Brenda K Trevino,Ogechi N Ukegbu,Jeremy B Urban,Lydia I Vasquez,Virginia A Vera,Donna M Villasana,Ling Wang,Stephanie Ward-Moore,James T Warren,Xuehong Wei,Flower White,Angela L Williamson,Regina Wleczyk,Hailey S Wooden,Steven H Wooden,Jennifer Yen,Lillienne Yoon,Vivienne Yoon,Sara E Zorrilla,David Nelson,Raju Kucherlapati,George Weinstock,Richard A Gibbs,Baylor College of Medicine Human Genome Sequencing Center Sequence Production Team  Human chromosome 12 contains more than 1,400 coding genes and 487 loci that have been directly implicated in human disease. The q arm of chromosome 12 contains one of the largest blocks of linkage disequilibrium found in the human genome. Here we present the finished sequence of human chromosome 12... ( view more ), which has been finished to high quality and spans approximately 132 megabases, representing approximately 4.5% of the human genome. Alignment of the human chromosome 12 sequence across vertebrates reveals the origin of individual segments in chicken, and a unique history of rearrangement through rodent and primate lineages. The rate of base substitutions in recent evolutionary history shows an overall slowing in hominids compared with primates and rodents. ( view less ) Teresa V Bowman,Andrew J McCooey,Akil A Merchant,Carlos A Ramos,Patricia Fonseca,Alan Poindexter,Steven B Bradfute,Daniela M Oliveira,Rahshaana Green,Yayun Zheng,Kathyjo A Jackson,Stuart M Chambers,Shannon L McKinney-Freeman,Kevin G Norwood,Gretchen Darlington,Preethi H Gunaratne,David Steffen,Margaret A Goodell Hematopoietic stem cells (HSCs) maintain tissue homeostasis by rapidly responding to environmental changes. Although this function is well understood, the molecular mechanisms governing this characteristic are largely unknown. We used a sequenced-based strategy to explore the role of both transcrip... ( view more )tional and post-transcriptional regulation in HSC biology. We characterized the gene expression differences between HSCs, both quiescent and proliferating, and their differentiated progeny. This analysis revealed a large fraction of sequence tags aligned to intronic sequences, which we showed were derived from unspliced transcripts. A comparison of the biological properties of the observed spliced versus unspliced transcripts in HSCs showed that the unspliced transcripts were enriched in genes involved in DNA binding and RNA processing. In addition, levels of unspliced message decreased in a transcript-specific fashion after HSC activation in vivo. This change in unspliced transcript level coordinated with increases in gene expression of splicing machinery components. Combined, these results suggest that post-transcriptional regulation is important in HSC activation in vivo. ( view less ) Herath Jayantha Gunaratne,Victor D Vacquier Sarco/endoplasmic reticulum Ca2+ ATPase (SERCA), a vesicular integral membrane protein, is the best-characterized member of the P-type ion translocating ATPase superfamily. Here we describe the cloning and structural analysis of a sea urchin SERCA (suSERCA) cloned from testis cDNA. The approximatel... ( view more )y 112 kDa suSERCA is 1022 amino acids with approximately 70% identity and 80% similarity to all known mammalian SERCA isoforms. suSERCA shares all the structural features of mammalian SERCAs, including domains: A, actuator; N, nucleotide-binding; and P, phosphorylation, and also 10 transmembrane helices. Like human SERCA2, the suSERCA has a possible 11th transmembrane segment in its extreme C-terminus. The alignment of three sequences (suSERCA, human SERCA2, and rabbit SERCA1a) shows that the Ca2+ binding residues and kinks (required to form the ion-binding pocket) are 100% conserved. The annotated suSERCA gene consists of 24 exons separated by 23 introns and is approximately 30 kb. Western blots show that suSERCA is present in sea urchin eggs and testis, but not in mature spermatozoa. Treatment of live sperm with SERCA inhibitors has no effect on intracellular calcium, suggesting the absence of SERCA in sea urchin spermatozoa. ( view less ) Shaowen Hu,Girish Nathan,Donald J Kouri,David K Hoffman,Gemunu H GunaratneTwo families of statistical measures are used for quantitative characterization of nonequilibrium patterns and their evolution. The first quantifies the disorder in labyrinthine patterns, and captures features like the domain size, defect density, variations in wave number, etc. The second class of... ( view more ) characteristics can be used to quantify the disorder in more general nonequilibrium structures, including those observed during domain growth. The presence of distinct stages of relaxation in spatiotemporal dynamics under the Swift-Hohenberg equation is analyzed using both classes of measures. ( view less ) Michael A K Liebschner,Ralph Müller,Sunil J Wimalawansa,Chamith S Rajapakse,Gemunu H Gunaratne Aging induces several types of architectural changes in trabecular bone including thinning, increased levels of anisotropy, and perforation. It has been determined, on the basis of analysis of mathematical models, that reduction in fracture load caused by perforation is significantly higher than th... ( view more )ose due to equivalent levels of thinning or anisotropy. The analysis has also provided an expression which relates the fractional reduction of strength tau to the fraction of elements nu that have been removed from a network. Further, it was proposed that the ratio Gamma of the elastic constant of a sample and its linear response at resonance can be used as a surrogate for tau. Experimental validation of these predictions requires following architectural changes in a given sample of trabecular bone; techniques to study such changes using microcomputed tomography are only beginning to be available. In the present study, we use anatomically accurate computer models constructed from digitized images of bone samples for the purpose. Images of healthy bone are subjected to successive levels of synthetic degradation via surface erosion. Computer models constructed from these images are used to calculate their fracture load and other mechanical properties. Results from these computations are shown to be consistent with predictions derived from the analysis of mathematical models. Although the form of tau(nu) is known, parameters in the expression are expected to be sample-specific, and hence nu is not a reliable predictor of strength. We provide an example to demonstrate this. In contrast, analysis of model networks shows that the linear part of tau(Gamma) depends only on the structure of trabecular bone. Computations on models constructed from samples of iliac crest trabecular bone are shown to be in agreement with this assertion. Since Gamma can be computed from a vibrational assessment of bone, we argue that the latter can be used to introduce new surrogates for bone strength and hence diagnostic tools for osteoporosis. ( view less ) Tissa Gunaratne,J Reddy Challa,M Cather Simpson para-Nitroaniline (PNA) plays an essential role as the prototype model of push-pull chromophores. The nature and degree of participation of vibrational degrees of freedom in the charge-transfer and internal-conversion processes are current issues of great theoretical and practical importance. Ultra... ( view more )fast time-resolved anti-Stokes resonance Raman spectroscopy (TRARRS) experiments on PNA in dimethyl sulfoxide with three different excitation wavelengths were performed to probe these dynamical influences. The vibrational dynamics associated with S0 were independent of incident wavelength, and this supports the picture that the S1 dynamics are fast relative to the rate of intersystem crossing. The phenyl breathing mode nu(19) (860 cm(-1)) and the symmetric NO2 stretch nu(29) (1310 cm(-1)) exhibited vibrational lifetimes in S0 of 8.1 and 5.2 ps, respectively. No evidence for inhomogeneous broadening of the charge-transfer band in the UV/Vis absorption spectrum was found. ( view less ) Tissa C Gunaratne,Alexey V Gusev,Xinzhan Peng,Angela Rosa,Giampaolo Ricciardi,Evert Jan Baerends,Corrado Rizzoli,Malcolm E Kenney,Michael A J Rodgers Reported herein is a combination of experimental and DFT/TDDFT theoretical investigations of the ground and excited states of 1,4,8,11,15,18,22,25-Octabutoxyphthalocyaninato-nickel(II), NiPc(BuO)(8), and the dynamics of its deactivation after excitation into the S(1)(pi,pi) state in toluene solutio... ( view more )n. According to X-ray crystallographic analysis NiPc(BuO)(8) has a highly saddled structure in the solid state. However, DFT studies suggest that in solution the complex is likely to flap from one D(2)(d)-saddled conformation to the opposite one through a D(4)(h)-planar structure. The spectral and kinetic changes for the complex in toluene are understood in terms of the 730 nm excitation light generating a primarily excited S(1) (pi,pi) state that transforms initially into a vibrationally hot (3)(d(z)2,d(x)2(-)(y)2) state. Cooling to the zeroth state is complete after ca. 8 ps. The cold (d,d) state converted to its daughter state, the (3)LMCT (pi,d(x)2(-)(y)2), which itself decays to the ground state with a lifetime of 640 ps. The proposed deactivation mechanism applies to the D(2)(d)-saddled and the D(4)(h)-planar structure as well. The results presented here for NiPc(BuO)(8) suggest that in nickel phthalocyanines the (1,3)LMCT (pi,d(x)2(-)(y)2) states may provide effective routes for radiationless deactivation of the (1,3)(pi,pi) states. ( view less ) Mark T Ross,Darren V Grafham,Alison J Coffey,Steven Scherer,Kirsten McLay,Donna Muzny,Matthias Platzer,Gareth R Howell,Christine Burrows,Christine P Bird,Adam Frankish,Frances L Lovell,Kevin L Howe,Jennifer L Ashurst,Robert S Fulton,Ralf Sudbrak,Gaiping Wen,Matthew C Jones,Matthew E Hurles,T Daniel Andrews,Carol E Scott,Stephen Searle,Juliane Ramser,Adam Whittaker,Rebecca Deadman,Nigel P Carter,Sarah E Hunt,Rui Chen,Andrew Cree,Preethi Gunaratne,Paul Havlak,Anne Hodgson,Michael L Metzker,Stephen Richards,Graham Scott,David Steffen,Erica Sodergren,David A Wheeler,Kim C Worley,Rachael Ainscough,Kerrie D Ambrose,M Ali Ansari-Lari,Swaroop Aradhya,Robert I S Ashwell,Anne K Babbage,Claire L Bagguley,Andrea Ballabio,Ruby Banerjee,Gary E Barker,Karen F Barlow,Ian P Barrett,Karen N Bates,David M Beare,Helen Beasley,Oliver Beasley,Alfred Beck,Graeme Bethel,Karin Blechschmidt,Nicola Brady,Sarah Bray-Allen,Anne M Bridgeman,Andrew J Brown,Mary J Brown,David Bonnin,Elspeth A Bruford,Christian Buhay,Paula Burch,Deborah Burford,Joanne Burgess,Wayne Burrill,John Burton,Jackie M Bye,Carol Carder,Laura Carrel,Joseph Chako,Joanne C Chapman,Dean Chavez,Ellson Chen,Guan Chen,Yuan Chen,Zhijian Chen,Craig Chinault,Alfredo Ciccodicola,Sue Y Clark,Graham Clarke,Chris M Clee,Sheila Clegg,Kerstin Clerc-Blankenburg,Karen Clifford,Vicky Cobley,Charlotte G Cole,Jen S Conquer,Nicole Corby,Richard E Connor,Robert David,Joy Davies,Clay Davis,John Davis,Oliver Delgado,Denise Deshazo,Pawandeep Dhami,Yan Ding,Huyen Dinh,Steve Dodsworth,Heather Draper,Shannon Dugan-Rocha,Andrew Dunham,Matthew Dunn,K James Durbin,Ireena Dutta,Tamsin Eades,Matthew Ellwood,Alexandra Emery-Cohen,Helen Errington,Kathryn L Evans,Louisa Faulkner,Fiona Francis,John Frankland,Audrey E Fraser,Petra Galgoczy,James Gilbert,Rachel Gill,Gernot Glöckner,Simon G Gregory,Susan Gribble,Coline Griffiths,Russell Grocock,Yanghong Gu,Rhian Gwilliam,Cerissa Hamilton,Elizabeth A Hart,Alicia Hawes,Paul D Heath,Katja Heitmann,Steffen Hennig,Judith Hernandez,Bernd Hinzmann,Sarah Ho,Michael Hoffs,Phillip J Howden,Elizabeth J Huckle,Jennifer Hume,Paul J Hunt,Adrienne R Hunt,Judith Isherwood,Leni Jacob,David Johnson,Sally Jones,Pieter J de Jong,Shirin S Joseph,Stephen Keenan,Susan Kelly,Joanne K Kershaw,Ziad Khan,Petra Kioschis,Sven Klages,Andrew J Knights,Anna Kosiura,Christie Kovar-Smith,Gavin K Laird,Cordelia Langford,Stephanie Lawlor,Margaret Leversha,Lora Lewis,Wen Liu,Christine Lloyd,David M Lloyd,Hermela Loulseged,Jane E Loveland,Jamieson D Lovell,Ryan Lozado,Jing Lu,Rachael Lyne,Jie Ma,Manjula Maheshwari,Lucy H Matthews,Jennifer McDowall,Stuart McLaren,Amanda McMurray,Patrick Meidl,Thomas Meitinger,Sarah Milne,George Miner,Shailesh L Mistry,Margaret Morgan,Sidney Morris,Ines Müller,James C Mullikin,Ngoc Nguyen,Gabriele Nordsiek,Gerald Nyakatura,Christopher N O'Dell,Geoffery Okwuonu,Sophie Palmer,Richard Pandian,David Parker,Julia Parrish,Shiran Pasternak,Dina Patel,Alex V Pearce,Danita M Pearson,Sarah E Pelan,Lesette Perez,Keith M Porter,Yvonne Ramsey,Kathrin Reichwald,Susan Rhodes,Kerry A Ridler,David Schlessinger,Mary G Schueler,Harminder K Sehra,Charles Shaw-Smith,Hua Shen,Elizabeth M Sheridan,Ratna Shownkeen,Carl D Skuce,Michelle L Smith,Elizabeth C Sotheran,Helen E Steingruber,Charles A Steward,Roy Storey,R Mark Swann,David Swarbreck,Paul E Tabor,Stefan Taudien,Tineace Taylor,Brian Teague,Karen Thomas,Andrea Thorpe,Kirsten Timms,Alan Tracey,Steve Trevanion,Anthony C Tromans,Michele d'Urso,Daniel Verduzco,Donna Villasana,Lenee Waldron,Melanie Wall,Qiaoyan Wang,James Warren,Georgina L Warry,Xuehong Wei,Anthony West,Siobhan L Whitehead,Mathew N Whiteley,Jane E Wilkinson,David L Willey,Gabrielle Williams,Leanne Williams,Angela Williamson,Helen Williamson,Laurens Wilming,Rebecca L Woodmansey,Paul W Wray,Jennifer Yen,Jingkun Zhang,Jianling Zhou,Huda Zoghbi,Sara Zorilla,David Buck,Richard Reinhardt,Annemarie Poustka,André Rosenthal,Hans Lehrach,Alfons Meindl,Patrick J Minx,Ladeana W Hillier,Huntington F Willard,Richard K Wilson,Robert H Waterston,Catherine M Rice,Mark Vaudin,Alan Coulson,David L Nelson,George Weinstock,John E Sulston,Richard Durbin,Tim Hubbard,Richard A Gibbs,Stephan Beck,Jane Rogers,David R Bentley The human X chromosome has a unique biology that was shaped by its evolution as the sex chromosome shared by males and females. We have determined 99.3% of the euchromatic sequence of the X chromosome. Our analysis illustrates the autosomal origin of the mammalian sex chromosomes, the stepwise proc... ( view more )ess that led to the progressive loss of recombination between X and Y, and the extent of subsequent degradation of the Y chromosome. LINE1 repeat elements cover one-third of the X chromosome, with a distribution that is consistent with their proposed role as way stations in the process of X-chromosome inactivation. We found 1,098 genes in the sequence, of which 99 encode proteins expressed in testis and in various tumour types. A disproportionately high number of mendelian diseases are documented for the X chromosome. Of this number, 168 have been explained by mutations in 113 X-linked genes, which in many cases were characterized with the aid of the DNA sequence. ( view less ) Girish Nathan,Gemunu GunaratneWe present a class of statistical measures that can be used to quantify nonequilibrium surface growth. They are used to deduce information about spatiotemporal dynamics of model systems for spinodal decomposition and surface deposition. Pattern growth in the Cahn-Hilliard equation (used to model sp... ( view more )inodal decomposition) are shown to exhibit three distinct stages. Two models of surface growth, namely, the continuous Kardar-Parisi-Zhang model and the discrete restricted-solid-on-solid model are shown to have different saturation exponents. ( view less ) Akifumi Fukumura,Masahiro Endo,Tatsuaki Kanai,Mitsue Takeshita,Makoto Sakama,Akira Ito,Yutaka Takahashi,Masao Hoshina,Yohsuke Kusano,Eisuke Takase,Jayantha Gunaratne A Japanese code of practice for clinical dosimetry, titled "Standard Dosimetry of Absorbed Dose in External Beam Radiotherapy" was published by the Japan Society of Medical Physics (JSMP) in 2002. It mostly followed IAEA Technical Reports Series No. 398, which was based on N(D,w), i.e., the calibra... ( view more )tion factor in terms of absorbed dose to water for a dosimeter. The Japanese primary standard dosimetry laboratory, however, has not supplied N(D,w) but N(X), as the calibration factor in terms of exposure. The unique feature of the Japanese code was provision of a data table of calculated conversion factors, N(D,w) / N(X) values, for many types of ionization chambers, excluding new plane-parallel ionization chambers. This paper describes the experimental evaluation of the conversion factors for the new plane-parallel ionization chambers, such as the Roos-type and Advanced Markus chambers. The obtained N(D,w) / N(X) values for PTW 34001, Wellhöfer PPC 40 and PTW 34045 were 37.96 +/- 0.19, 37.85 +/- 0.36 and 37.90 +/- 0.26 (Gy/C kg(-1)), respectively. They agreed with estimations based on Monte Carlo calculations. ( view less )
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