Genetics Home Reference: familial hypertrophic cardiomyopathy

MedlinePlus

... Savithri GR, Kumar MS, Narasimhan C, Nallari P. Molecular genetics of familial hypertrophic cardiomyopathy (FHC). J Hum Genet. ... 5(11):747. Citation on PubMed Kimura A. Molecular genetics and pathogenesis of cardiomyopathy. J Hum Genet. 2016 ...

The Prospect of Neutrinos with Gravitational Waves

NASA Astrophysics Data System (ADS)

Kohler, Susanna

2017-10-01

With the first detection of gravitational waves in 2015, scientists celebrated the opening of a new window to the universe. But multi-messenger astronomy astronomy based on detections of not just photons, but other signals as well was not a new idea at the time: we had already detected tiny, lightweight neutrinos emitted from astrophysical sources. Will we be able to combine observations of neutrinos and gravitational waves in the future to provide a deeper picture of astrophysical events?Signs of a MergerArtists impression of the first stage of a binary neutron star merger. [NASA, ESA, and A. Feild (STScI)]If the answer is yes, the key will probably be short gamma-ray bursts (SGRBs). Theory predicts that when a neutron star merges with another compact object (either another neutron star or a black hole), a number of signals may be observable. These include:gravitational waves as the binary spirals inward,a brief burst of gamma rays at merger (this is the SGRB),high-energy neutrino emission during the SGRB,optical and infrared emission after the merger in the form of a kilonova, andradio afterglows of the merger remnants.While weve observed the various electromagnetic components of this picture, the multi-messenger part is lacking: gravitational-wave detections havent been made in conjunction with electromagnetic counterparts thus far, and the only confirmed astrophysical sources of neutrinos are the Sun and Supernova 1987A.Pedicted neutrino fluxes during different stages of emission in an SGRB. [Kimura et al. 2017]Can we expect this to change in the future? A team of authors led by Shigeo Kimura (Pennsylvania State University) has now explored the likelihood that well be able to detect high-energy neutrinos in association with future gravitational-wave events.Detecting the SGRB NeutrinosKimura and collaborators first estimate the flux of high-energy neutrinos expected during various emission phases of an SGRB. They show that a period of late-time emission, known

JPRS Report, Science & Technology, Japan, Structure, Properties of Al Amorphous Alloys

DTIC Science & Technology

1990-12-04

present report, and to the members of the staff, particularly Masaji Nomura, Tetsuya Ishikawa , and Atsushi Koyama, of the High Energy Physics Laboratory...Aichi Educational University, and the research on Al-based quasicrystals was with Shin Takeuchi, and Kaoru Kimura, both of Tokyo University, and Takeshi

Collective Security in Europe and Asia

DTIC Science & Technology

1992-03-02

Minister Hisashi Owada carried by Kyodo, November 18, 1991, in Foreign Broadcast Information Service, (FBIS), Daily Report-East Asia, November 18, 1991...Report-Soviet Union, December 5, 1991, p. 54. For a Japanese view, see Hiroshi Kimura , "Gorbachev’s Japan Policy: The Northern Territories Issue

Resampling-Based Gap Analysis for Detecting Nodes with High Centrality on Large Social Network

DTIC Science & Technology

2015-05-22

University, Shiga, Japan kimura@rins.ryukoku.ac.jp 4 Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan 5 School of...second one is a network extracted from a Japanese word-of-mouth communication site for cosmetics , “@cosme”2, consist- ing of 45, 024 nodes

Effects of Attention on Dichotic Listening in Elderly and Patients with Dementia of the Alzheimer Type

ERIC Educational Resources Information Center

Bouma, Anke; Gootjes, Liselotte

2011-01-01

This article presents an overview of our studies in elderly and Alzheimer patients employing Kimura's dichotic digits paradigm as a measure for left hemispheric predominance for processing language stimuli. In addition to structural brain mechanisms, we demonstrated that attention modulates the direction and degree of ear asymmetry in dichotic…

Moving beyond the College-Preparatory High School Model to a College-Going Culture in Urban Catholic High Schools

ERIC Educational Resources Information Center

Aldana, Ursula S.

2014-01-01

A college-going culture has been found to improve academic outcomes for underrepresented high school students (Allen, Kimura-Walsh, & Griffin, 2009; Stanton-Salazar, 2010). The research on Catholic high schools shows their college-preparatory environment ability to produce successful outcomes for African-American and Latino students (Bryk,…

IFLA General Conference, 1986. Special Libraries Division. Section: Art Libraries. Papers.

ERIC Educational Resources Information Center

International Federation of Library Associations and Institutions, The Hague (Netherlands).

Papers on art libraries presented at the 1986 International Federation of Library Associations (IFLA) conference include: (1) "The Change of Illustrated Story Books in the Edo Period (1660-1880)" (Yaeko Kimura, Japan); (2) "History of Posters in Japan and the Present States of Their Documentation" (Itsuo Okubo, Japan); (3)…

[Angiolymphoid hyperplasia with eosinophilia with bilateral involvement of the lacrimal glands].

PubMed

Baráková, Drahomíra; Sâch, Josef; Kuchynka, Pavel; Rêdinová, Magdalena; Kocur, Ivo

2002-05-01

Angiolymphoid hyperplasia with eosinophilia (ALHE) and Kimura's disease are two rarely occurring disorders very similar to each other; however, they are individual nosological entities. For a long time they were considered as a single disease due to the frequency of similar characteristics. The majority of authors have recently considered these diseases as two individual entities with some reciprocal specifications, both clinical as well as morphological. We report on the case of a 76-year old male white European who had suffered for more than six years from subcutaneous tumour formations in different parts of the body. Eyelid oedema on the right side with palpable resistance under the upper temporal edge of the orbit initially occurred five years after the first symptoms of the disease. A similar finding occurred on the left side after eight months. The tumours on both sides were surgically removed and sent for histological analysis. A unilateral recurrence of the finding appeared after one year, followed by surgical intervention and histological examination. Tumour infiltrate in the first two orbita excisions was topically related to lacrimal gland structures; these structures were not found in the third excision. The case was histologically diagnosed as ALHE despite some similar characteristics with Kimura's disease. The diagnosis of ALHE was histologically supported, especially by the absence of lymphatic follicle formations and fibrotisation in the infiltrate, and the identification of the appearance of epitheloid up to histiocytoid of proliferating endothelium, which forms small lumens. The diagnosis of ALHE was additionally supported by the fact that the incidence of Kimura's disease in white Europeans is very rare. According to our findings, both entities overlap one another, even in some characteristics considered to be distinguishing. The question arises, therefore, whether the strict separation of these nosological entities can indeed be determined with

Generation of co-speech gestures based on spatial imagery from the right-hemisphere: evidence from split-brain patients.

PubMed

Kita, Sotaro; Lausberg, Hedda

2008-02-01

It has been claimed that the linguistically dominant (left) hemisphere is obligatorily involved in production of spontaneous speech-accompanying gestures (Kimura, 1973a, 1973b; Lavergne and Kimura, 1987). We examined this claim for the gestures that are based on spatial imagery: iconic gestures with observer viewpoint (McNeill, 1992) and abstract deictic gestures (McNeill, et al. 1993). We observed gesture production in three patients with complete section of the corpus callosum in commissurotomy or callosotomy (two with left-hemisphere language, and one with bilaterally represented language) and nine healthy control participants. All three patients produced spatial-imagery gestures with the left-hand as well as with the right-hand. However, unlike healthy controls and the split-brain patient with bilaterally represented language, the two patients with left-hemispheric language dominance coordinated speech and spatial-imagery gestures more poorly in the left-hand than in the right-hand. It is concluded that the linguistically non-dominant (right) hemisphere alone can generate co-speech gestures based on spatial imagery, just as the left-hemisphere can.

Finite Forward Acceptance Angles for Single Electron Capture by ^3He^2+ Ions in He and H_2

NASA Astrophysics Data System (ADS)

Mawhorter, Rj; Greenwood, J.; Smith; Chutjian, A.

2004-05-01

Perhaps surprisingly, electron capture scattering angles of a few degrees or more are observed for slow ions impacting light targets. Gas cells must be designed with this in mind. Indeed the difference between small acceptance angle results(W.L. Nutt, et al., J. Phys. B 8), 1457 (1978) and the larger acceptance-angle studies of both Kusakabe, et al.(T. Kusakabe, et al., J. Phys. Soc. Japan 59), 1218 (1990) and our group at JPL (presented here; energy range 0.33-4.67 keV/amu) for ^3He^2+ in H2 can be ascribed to this effect. Olson and Kimura(R. E. Olson and M. Kimura, J. Phys. B 15), 4231 (1982) have modeled the problem theoretically. We use existing differential cross section data(D. Bordenave-Montesquieu and R. Dagnac, J. Phys. B 27), 543 1994) for both H_2/ D2 and ^4He targets to calculate realistic acceptance angles. The resulting small total cross section corrections provide reliable absolute results for these benchmark systems. This work was carried out at JPL/Caltech, and was supported through agreement with NASA.

INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: Relaxation Property and Stability Analysis of the Quasispecies Models

NASA Astrophysics Data System (ADS)

Feng, Xiao-Li; Li, Yu-Xiao; Gu, Jian-Zhong; Zhuo, Yi-Zhong

2009-10-01

The relaxation property of both Eigen model and Crow-Kimura model with a single peak fitness landscape is studied from phase transition point of view. We first analyze the eigenvalue spectra of the replication mutation matrices. For sufficiently long sequences, the almost crossing point between the largest and second-largest eigenvalues locates the error threshold at which critical slowing down behavior appears. We calculate the critical exponent in the limit of infinite sequence lengths and compare it with the result from numerical curve fittings at sufficiently long sequences. We find that for both models the relaxation time diverges with exponent 1 at the error (mutation) threshold point. Results obtained from both methods agree quite well. From the unlimited correlation length feature, the first order phase transition is further confirmed. Finally with linear stability theory, we show that the two model systems are stable for all ranges of mutation rate. The Eigen model is asymptotically stable in terms of mutant classes, and the Crow-Kimura model is completely stable.

Neutral Theory: From Complex Population History to Natural Selection and Sociocultural Phenomena in Human Populations.

PubMed

Austerlitz, Frédéric; Heyer, Evelyne

2018-06-01

Here, we present a synthetic view on how Kimura's Neutral theory has helped us gaining insight on the different evolutionary forces that shape human evolution. We put this perspective in the frame of recent emerging challenges: the use of whole genome data for reconstructing population histories, natural selection on complex polygenic traits, and integrating cultural processes in human evolution.

Piezoelectric and Electrostrictive Materials for Transducer Applications.

DTIC Science & Technology

1985-05-01

Engineering, May 1984. "Characteristics of Japanese Multilayer Ceramic Capacitors" Kevin Dietz B.S. Ceramic Science and Engineering, May 1984. "Leucite...Proer es." Waer Res Bull. I 8) 1007-19 � ,’ Kimura. K Dot. S Nanam . and T Kawamura. ’A New Pietoeiectntc ’k E. Newntuam. 0 P Skinner. and L. E

Oxygen and Other Atmospheric Gases

DTIC Science & Technology

1989-02-27

with a pulse width of approximately 8 ns and a repetition gen , (3so)’ l and , n. , have been identified and some mo- rate of I I Hz. The photoelectron...K. Kimura, J. Electron. Spectrosc.R-deerientphooioizaioncro,,.,,cion ThS, ,e in Relat. Pl’enom. 41, 325 (1986). the diaati aproxiat~n. tV-ia~oa Fanc

The Role of the Sonic Hedgehog Pathway for Prostate Cancer Progression

DTIC Science & Technology

2005-02-01

GY, Qi YP, Gysin S, Fernandez-Del Castillo C, Yalnik V, Antoniu and real-time PCR analyses. Sumnin Chi contributed to B, McMahon M, Warshaw AL, Hebrok... Romer JT, Kimura H, Magdaleno Set al:. 391(6662), 90-92 (1998). in a mouse model of prostate carcinogenesis. Suppression of the Shh pathway using a 10󈧘

The Role of the Sonic Hedgehog Pathway for Prostate Cancer Progression

DTIC Science & Technology

2005-02-01

analyses. Sumin Chi contributed to wers GY, Qi YP, Gysin S, Fernandez-Del Castillo C, Yajnik V. AntoniuB, McMahon M, Warshaw AL Hebrok M: Hedgehog is an...role for p27kiP, gene dosage • 15. Romer JT, Kimura H, Magdaleno S et at: 391(6662), 90-92 (1998). in a mouse model of prostate carcinogenesis

From Ear to Brain

ERIC Educational Resources Information Center

Kimura, Doreen

2011-01-01

In this paper Doreen Kimura gives a personal history of the "right-ear effect" in dichotic listening. The focus is on the early ground-breaking papers, describing how she did the first dichotic listening studies relating the effects to brain asymmetry. The paper also gives a description of the visual half-field technique for lateralized stimulus…

Evaluation and Management of Patients with Inhalation Injury

DTIC Science & Technology

1990-12-01

PRUITT, Jr., M.D., WILLIAM G. CIOFFI, M.D., TAKESHI SHIMAZU, M.D. HISASHI IKEUCHI, M.D., AND ARTHUR D. MASON, Jr., M.D. D T CO ELECTE" Inhalation...215, 1988. Do you think that there is some common pathway here 22. Kimura , R., Traber, L., Herndon, D., et al: Ibuprofen reduces the where there is

Independent Control of Grafting Density and Conformation of Single-Stranded DNA Brushes

DTIC Science & Technology

2007-01-02

Abstreiter G, Tornow M (2004) Langmuir 20:10086–10092. 20. Kimura-Suda H, Petrovykh DY, Tarlov MJ, Whitman LJ (2003) J Am Chem Soc 125:9014–9015. 21. Wolf...Tarlov MJ, Himpsel FJ, Whitman LJ (2006) J Am Chem Soc 128:2–3. 25. Rant U, Arinaga K, Fujiwara T, Fujita S, Tornow M, Yokoyama N, Abstreiter G (2003

Fractional quiver W-algebras

NASA Astrophysics Data System (ADS)

Kimura, Taro; Pestun, Vasily

2018-04-01

We introduce quiver gauge theory associated with the non-simply laced type fractional quiver and define fractional quiver W-algebras by using construction of Kimura and Pestun (Lett Math Phys, 2018. https://doi.org/10.1007/s11005-018-1072-1; Lett Math Phys, 2018. https://doi.org/10.1007/s11005-018-1073-0) with representation of fractional quivers.

Proceedings of the International Symposium on Multiple-Valued Logic (13th) Held at Kyoto, Japan on May 23-25, 1983.

DTIC Science & Technology

1983-05-01

would like to thank the members of the Organizing Committee of ISMVL-Japan, listed on page vii of this Proceedings, for their generous support. Hisashi ...8217 °. °- . ’. . 6% Organizing Commnittee I *Chairman: Hisashi Mine Department of Applied Mathematics and Physics Kcyoto University, Kyoto...Masayuki Kimura (Tohoku University, Japan) Tadahiro Kitahashi (Toyohashi University of Technology, Japan) Yoshiaki Koga (National Defense Academy, Japan

[Chronic atrophic gastritis: endoscopic and histological concordances, associated injuries and application of virtual chromoendoscopy].

PubMed

Liu Bejarano, Humberto

2011-01-01

Due to the poor agreement between endoscopy and histology, the gastric biopsy continues being the gold standard for the diagnosis of atrophic chronic gastritis. The Virtual chromoendoscopy system allows better observation of the gastric mucosa. Evaluate the agreement between the Kimura-Takemoto ´s endoscopic system classification and the histological system of OLGA (Operative for Link Assessment Gastritis), as well as to evaluate the application of the virtual chromoendoscopy. A prospective and longitudinal study of cohorts, 138 patients was include, using endoscopic system of atrophy by Kimura and Takemoto (K-T), with conventional optical and with the use of seventh filter of virtual chromoendoscopy ,then comparing with the histological findings of the OLGA pathology system, also were determinated injuries associated with respect to stage OLGA. The kappa index of agreement between conventional endoscopy and the system OLGA was 0.859 and with the system of virtual chromoendoscopy was 0.822, the preneoplasic and neoplastic gastric lesions were associate to stages III and IV of atrophy. The endoscopic and histological correlation with both systems isvery good, with or without the use of virtual chromoendoscopy. chronic atrophic gastritis, virtual chromoendoscopy, olga system, , kimuratakemoto system.

Neutral Theory is the Foundation of Conservation Genetics.

PubMed

Yoder, Anne D; Poelstra, Jelmer; Tiley, George P; Williams, Rachel

2018-04-16

Kimura's neutral theory of molecular evolution has been essential to virtually every advance in evolutionary genetics, and by extension, is foundational to the field of conservation genetics. Conservation genetics utilizes the key concepts of neutral theory to identify species and populations at risk of losing evolutionary potential by detecting patterns of inbreeding depression and low effective population size. In turn, this information can inform the management of organisms and their habitat providing hope for the long-term preservation of both. We expand upon Avise's "inventorial" and "functional" categories of conservation genetics by proposing a third category that is linked to the coalescent and that we refer to as "process-driven." It is here that connections between Kimura's theory and conservation genetics are strongest. Process-driven conservation genetics can be especially applied to large genomic datasets to identify patterns of historical risk, such as population bottlenecks, and accordingly, yield informed intuitions for future outcomes. By examining inventorial, functional, and process-driven conservation genetics in sequence, we assess the progression from theory, to data collection and analysis, and ultimately, to the production of hypotheses that can inform conservation policies.

Spectroscopic Characterization of Microplasmas

DTIC Science & Technology

2008-01-28

18th International Symposium on Plasma Chemistry , Kyoto, August, 2007. 3) H. Nakanishi, D.-S. Lee, O. Sakai and K. Tachibana: “Electron density and...collisional frequency in plasma with terahertz time-domain spectroscopy”, 18th International Symposium on Plasma Chemistry , Kyoto, August, 2007. 4) O...Symposium on Plasma Chemistry , Kyoto, August, 2007. 5) M. Kimura, T. Shirafuji, O. Sakai and K. Tachibana: “Discharge characteristics of the plasma in

Realization of New and Enhanced Materials Properties Through Nanostructural Control

DTIC Science & Technology

2009-08-14

repeated and verified by Paul Ashley at US Army RDECOM, Redstone Arsenal, ALand Warren Herman at the Laboratory for Physical Sciences (LPS), College...proposed in the following sections of this proposal. REFERENCES (AFOSR-FA9550-06-I-0042 relevant publications) I. Paul M. Wallace, Daniel R. B. Sluss...8. Fletcher Kimura, Gamal Khalil, Nobuyuki Zettsu, Younan Xi a, James B. Callis, Martin Goutennan, Larry R Dalton, Dana Dabin, and Miguel

Neutral theory, microbial practice: challenges in bacterial population genetics.

PubMed

Rocha, Eduardo P C

2018-04-19

Kimura's outstanding contributions to population genetics included many elegant theoretical results on the vagaries of alleles in populations. Once polymorphism data showed extensive variation in natural populations, these results led naturally to the Neutral Theory. In this article, I'll depart from some of these results to focus on four major open problems in microbial population genetics with direct implications to the study of molecular evolution: the lack of neutral polymorphism, the modeling of genetic exchanges, the population genetics of ill-defined populations, and the difficulty of untangling selection and demography in the light of the previous issues. Whilst studies in population genetics usually focus on single nucleotide polymorphism and allelic recombination, ignoring even small indels, a large fraction of genetic diversification in Bacteria results from horizontal gene transfer. Ignoring this fact defeats the purpose of population genetics: to characterize the genetic variation in populations and their adaptive effects. I'll argue that, following on Kimura's life work, one may need to develop new approaches to study microbes that reproduce asexually but are able to engage in gene exchanges with very distantly related organisms in a context where random sampling is often unachievable, populations are ill-defined, genetic linkage is strong, and random drift is rare.

The Effect of Preheat Temperature and Inter-Pass Reheating on Microstructure and Texture Evolution During Hot Rolling of Ti-6Al-4V (Preprint)

DTIC Science & Technology

2008-02-01

three broad types of microstructures can be developed in alpha/beta titanium alloys by TMP [2- 4 ], namely, fully lamellar, fully equiaxed, and...32-45. 4 . M. Peters, G. Luetjering, in: Titanium 80: Science and Technology, ed. H. Kimura and O. Izumi, Kyoto, Japan, 1980, pp. 925-938. 5. G...Lutjering, J.C. Williams, in: Titanium , Springer-Verlag, Berlin, Germany, 2003, pp.220- 224. 6 . A.A. Salem, M.G. Glavicic, S.L. Semiatin, Materials

Capsule Depolymerase Overexpression Reduces Bacillus anthracis Virulence

DTIC Science & Technology

2010-01-01

protein that autocatalytically forms a heterodimer consisting of 35 kDa and 15 kDa subunits. CapD shares 32 % identity with the Bacillus subtilis GGT and 35...Immun 49, 291–297. Kimura, K., Tran, L. S., Uchida, I. & Itoh, Y. (2004). Characterization of Bacillus subtilis gamma-glutamyltransferase and its...Capsule depolymerase overexpression reduces Bacillus anthracis virulence Angelo Scorpio,3 Donald J. Chabot, William A. Day,4 Timothy A. Hoover and

JPRS Report Science and Technology, Japan: Atomic Energy Society 1989 Annual Meeting.

DTIC Science & Technology

1989-10-13

Control Rod Hole in VHTRC-1 Core [F, Akino, T, Yamane, et al.] ,,, 5 Measurement of MEU [Medium Enriched Uranium ] Fuel Element Characteristics in...K. Yoshida, K. Kobayashi, I. Kimura , C. Yamanaka, and S. Nakai, Laser Laboratory,, Osaka University. Nuclear Reactor Laboratory, Kyoto University...1 core loaded with 278 fuel rods (4 percent enriched uranium ). The PNS target was placed at the back center of the 1/2 assembly on the fixed side

Exact solutions for the selection-mutation equilibrium in the Crow-Kimura evolutionary model.

PubMed

Semenov, Yuri S; Novozhilov, Artem S

2015-08-01

We reformulate the eigenvalue problem for the selection-mutation equilibrium distribution in the case of a haploid asexually reproduced population in the form of an equation for an unknown probability generating function of this distribution. The special form of this equation in the infinite sequence limit allows us to obtain analytically the steady state distributions for a number of particular cases of the fitness landscape. The general approach is illustrated by examples; theoretical findings are compared with numerical calculations. Copyright © 2015. Published by Elsevier Inc.

Density Optimization of Lithium Lanthanum Titanate Ceramics for Lightweight Lithium-Air Batteries

DTIC Science & Technology

2014-11-01

Thangadurai V, Weppner W. Lithium lanthanum titanates: a review. Chemistry of Materials. 2003;15:3974–3990. 4. Knauth P. Inorganic solid Li ion conductors...an overview. Solid State Ionics. 2009;180:911–916. 5. Ban CW, Choi GM. The effect of sintering on the grain boundary conductivity of lithium ...lanthanum titanates. Solid State Ionics. 2001;140:285–292. 6. Inada R, Kimura K, Kusakabe K, Tojo T, Sakurai Y. Synthesis and lithium -ion conductivity

The Evaluation of Novel Bioactive Ingredients for Combat Ration Intermediate Moisture (IM) Products to Assure the Microbiological Safety

DTIC Science & Technology

2008-10-01

bacterial inactivation ( Hiraki , 2000 and Hiraki et al., 2003). The exact mechanism of action is not well understood. Purasal®P is a combination of...coli O157:H7, Slamonella typhimurium and Listeria monocytogenes Journal of Food Science 70: M404-M408. Hiraki J. 2000. ε-polylysine; its...development and utilization. Fine Chem 29: 18-25. Hiraki J., Takafumi I., Ninomiya S., Seki H., Uohama K., Seki H., Kimura S., Yangimoto Y. and Barnett J

The Effects of Hydrodynamic Stretch on the Flame Propagation Enhancement of Ethylene by Addition of Ozone

DTIC Science & Technology

2015-07-13

2004.08.272) 13. Ohisa H, Kimura I, Horisawa H. 1999 Control of soot emission of a turbulent diffusion flame by DC or AC corona discharges . Combust. Flame 116...References 1. Bozhenkov SA, Starikovskaia SM, Starikovskii AY. 2003 Nanosecond gas discharge ignition of H2- and CH4-containing mixtures. Combust. Flame...s10573-005-0047-6) 7. Kim W, Do H, Mungal MG, Cappelli MA. 2008 Optimal discharge placement in plasma-assisted combustion of a methane jet in cross

Wave Data Acquisition and Hindcast for Saginaw Bay, Michigan.

DTIC Science & Technology

1983-06-01

Bretschneider (1952) and Mitsuyasu and Kimura (1965) for f the peak fre- %m quency (where fm = f g/U) while the total energy decay rate follows that mm...Spectra of Wind-Generated Gravity Waves," Journal of Physical Oceanography, Vol 5, pp 410-420. Mitsuyasu, Hisashi . 1968. "On the Growth of the...8217 . , / . - . ’ -’ -. .. ’ . .. _..- -’ - Mitsuyasu, Hisashi , and Kirmura, Hisao. 1965. "Wind Wave in Decay Area," Coastal Engineering in Japan, Vol 8, pp 221-35. Ou, Shan-Hwei. 1980 (Sep

International Conference on Crystal Growth (10th) (ICCG-10) Held in San Diego, California on August 16 - 21, 1992

DTIC Science & Technology

1992-08-21

Synthetic Crystals. China82 The Growth of LaMgA],,O,,:Nd Large Crystals with High Quality B16 G, Wu. X Ma.* J. Xu. X Zhang and Y. Shen Crystal Growth and...Stolchlometry Problems of ZnSe for High Power Laser Y. ShIralshl Optical Components Kimura Metamelt Project. Japan E~ Kjause.* A. Moseal and H. Harmnn...Maki- Shanghai Institute of Ceramics. China Yokohama City University. Japa 023 CS Growth of High -CluaI~ty TI:A1202 Crystals for Solid-State Lase In

On spatial mutation-selection models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kondratiev, Yuri, E-mail: kondrat@math.uni-bielefeld.de; Kutoviy, Oleksandr, E-mail: kutoviy@math.uni-bielefeld.de, E-mail: kutovyi@mit.edu; Department of Mathematics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139

2013-11-15

We discuss the selection procedure in the framework of mutation models. We study the regulation for stochastically developing systems based on a transformation of the initial Markov process which includes a cost functional. The transformation of initial Markov process by cost functional has an analytic realization in terms of a Kimura-Maruyama type equation for the time evolution of states or in terms of the corresponding Feynman-Kac formula on the path space. The state evolution of the system including the limiting behavior is studied for two types of mutation-selection models.

Physical Characterization of Clostridium Botulinum Neurotoxin Genes

DTIC Science & Technology

1993-10-01

Acid Res. 14, 7809-78 12. 10 Fujii, N., Kimura, K., Murakami, T ., Indoh, I., Yashiki, T ., Tsuzuki, K., Yokosawa , N. & Oguma, K. (1990) Microbiol...from Clostridium spp. whose genomic DNA is of a high A+ T content (greater than 70% A+ T ), exhibit an extremely strong discrimination against all...BoNT/E, 4-12 Sathyamoorthy T T et al. (1985) H E L I H S L H G LE2 YES 5’-CACGAACTTATACATTCTCTACATGG-3’ 861-886 BoNT/E, 212-220 Wernars & T T A AT

International Conference on Liquid and Amorphous Metals (5th) Held at Los Angeles, California on August 15-19, 1983. Abstract.

DTIC Science & Technology

1983-08-19

Wang : CORROSION RESISTANCE OF AMORPHOUS AND CRYSTALLIZED Fe-Ni-Cr-W ALLOYS " 12:25 am M4 A. Yokoyama, H. Komiyama, H. Inoue, T. Masunoto, and H.M. Kimura...ENTHALPY RELAXATION IN PdNi ALLOY GLASSES 2:30 pm N3 A.I. Taub and J.L. Walter: SCALING THE COMPOSITION DEPENDENCE OF ATOMIC TRANSPORT AND STRUCTURAL...Cnn, L.Q. Wang , Y. Obi, and K. Fukamichi: LOW- TEMPERATURE SPECIFIC HEAT OF Fe-Zr AND Ni-Zr AMORPHOUS ALLOYS 2:15 pm 02 S.J. Poon: FLUX FLOW RESISTIVITY

Vortex pairs on surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koiller, Jair; Boatto, Stefanella

2009-05-06

A pair of infinitesimally close opposite vortices moving on a curved surface moves along a geodesic, according to a conjecture by Kimura. We outline a proof. Numerical simulations are presented for a pair of opposite vortices at a close but nonzero distance on a surface of revolution, the catenoid. We conjecture that the vortex pair system on a triaxial ellipsoid is a KAM perturbation of Jacobi's geodesic problem. We outline some preliminary calculations required for this study. Finding the surfaces for which the vortex pair system is integrable is in order.

Structural drift: the population dynamics of sequential learning.

PubMed

Crutchfield, James P; Whalen, Sean

2012-01-01

We introduce a theory of sequential causal inference in which learners in a chain estimate a structural model from their upstream "teacher" and then pass samples from the model to their downstream "student". It extends the population dynamics of genetic drift, recasting Kimura's selectively neutral theory as a special case of a generalized drift process using structured populations with memory. We examine the diffusion and fixation properties of several drift processes and propose applications to learning, inference, and evolution. We also demonstrate how the organization of drift process space controls fidelity, facilitates innovations, and leads to information loss in sequential learning with and without memory.

[Identification of pyrrosiae folium and its adulterants based on psbA-trnH sequence].

PubMed

Zhang, Ya-Qin; Shi, Yue; Song, Ming; Lin, Yun-Han; Ma, Xiao-Xi; Sun, Wei; Xiang, Li; Liu, Xi

2014-06-01

In this study, the psbA-trnH sequence as DNA barcode was used to evaluate the accuracy and stability for identification pteridophyte medicinal material Pyrrosiae Foliumas from adulterants. Genomic DNA from 106 samples were extracted successfully. The Kimura 2-Parameter (K2P) distances and ML tree were calculated using software MEGA 6.0. The intra-specific genetic distances of 3 original plants were lower than inter-specific genetic distances of adulterants. The ML tree indicated that Pyrrosiae Folium can be distinguished from its adulterants obviously. Therefore, the psbA-trnH sequence as a barcode of the pteridophyte, can accurately and stably distinguish Pyrrosiae Folium from its adulterants.

Updates and achievements in virology.

PubMed

Buonaguro, Franco M; Campadelli-Fiume, Gabriella; De Giuli Morghen, Carlo; Palù, Giorgio

2010-07-01

The 4th European Congress of Virology, hosted by the Italian Society for Virology, attracted approximately 1300 scientists from 46 countries worldwide. It also represented the first conference of the European Society for Virology, which was established in Campidoglio, Rome, Italy in 2009. The main goal of the meeting was to share research activities and results achieved in European virology units/institutes and to strengthen collaboration with colleagues from both western and developing countries. The worldwide representation of participants is a testament to the strength and attraction of European virology. The 5-day conference brought together the best of current virology; topics covered all three living domains (bacteria, archaea and eucarya), with special sessions on plant and veterinary virology as well as human virology, including two oral presentations on mimiviruses. The conference included five plenary sessions, 31 workshops, one hepatitis C virus roundtable, ten special workshops and three poster sessions, as well as 45 keynote lectures, 191 oral presentations and 845 abstracts. Furthermore, the Gesellschaft fur Virologie Loeffler-Frosch medal award was given to Peter Vogt for his long-standing career and achievements; the Gardner Lecture of the European Society for Clinical Virology was presented by Yoshihiro Kawaoka, and the Pioneer in Virology Lecture of the Italian Society for Virology was presented by Ulrich Koszinowski.

Development of the Nonobese Diabetic Mouse and Contribution of Animal Models for Understanding Type 1 Diabetes.

PubMed

Mullen, Yoko

2017-04-01

In 1974, the discovery of a mouse and a rat that spontaneously developed hyperglycemia led to the development of 2 autoimmune diabetes models: nonobese diabetic (NOD) mouse and Bio-Breeding rat. These models have contributed to our understanding of autoimmune diabetes, provided tools to dissect autoimmune islet damage, and facilitated development of early detection, prevention, and treatment of type 1 diabetes. The genetic characterization, monoclonal antibodies, and congenic strains have made NOD mice especially useful.Although the establishment of the inbred NOD mouse strain was documented by Makino et al (Jikken Dobutsu. 1980;29:1-13), this review will focus on the not-as-well-known history leading to the discovery of a glycosuric female mouse by Yoshihiro Tochino. This discovery was spearheaded by years of effort by Japanese scientists from different disciplines and dedicated animal care personnel and by the support of the Shionogi Pharmaceutical Company, Osaka, Japan. The history is based on the early literature, mostly written in Japanese, and personal communications especially with Dr Tochino, who was involved in diabetes animal model development and who contributed to the release of NOD mice to the international scientific community. This article also reviews the scientific contributions made by the Bio-Breeding rat to autoimmune diabetes.

Geochemical models of melting and magma storage conditions for basalt lava from Santorini Volcano, Greece

NASA Astrophysics Data System (ADS)

Baziotis, Ioannis; Kimura, Jun-Ichi; Pantazidis, Avgoustinos; Klemme, Stephan; Berndt, Jasper; Asimow, Paul

2017-04-01

. Observed mineralogy and major element chemistry suggest fractionation in a shallow magma chamber. Using the major element chemistry and PRIMACALC2 (Kimura & Ariskin 2014) back-calculator, inferred crystallization conditions are P=0.02 GPa, oxidized (fO2=QFM+2), and ˜1 wt% H2O in the primary basalt. The source mantle conditions are estimated at P=2.1 GPa, T=1350˚ C, and degree of melting F=8%. We also used trace elements to estimate the incompatible element budget of the primary basalt using the forward trace-element mass-balance model of ARC BASALT SIMULATOR ver.4 (Kimura et al. 2014). Preliminary results suggest that the slab flux was derived from ˜150 km depth, and fluxed mantle melting occurred at P=2.3 GPa, T=1380˚ C, F=8%. The estimated slab depth is consistent with the seismic observations and mantle conditions are consistent with the PRIMACALC2 major element modelling. Our intent is to extend our analytical data with precise trace element and isotope analyses in order to reveal more detailed source conditions and richer information about processes from the slab through the mantle and up to the shallow magma chamber. References Andújar, J. et al. (2015). JPET, 56 (4), 765-794. Druitt, et al. (1999). Geological Society Memoir, 19. Huijsmans, J. P., & Barton, M. (1989). JPET, 30(3), 583-625. Kimura, J. I., & Ariskin, A. A. (2014). G3, 15, 1494-1514. Kimura, J. I. et al. (2014). G3, 15, 691-739. Mortazavi, M., & Sparks, R. S. J. (2004). Con Min Pet, 146(4), 397-413. Papazachos, et al. (2000). Tectonophysics, 319(4), 275-300.

The Charging of Dust Grains in the Inner Heliosheath

NASA Astrophysics Data System (ADS)

Avinash, K.; Slavin, J.; Zank, G. P.; Frisch, P.

2008-12-01

Equilibrium electric charge and surface potential on a dust grain in the heliosheath are calculated. The grain is charged due to heliosheath plasma flux, photo electrons flux, secondary electron emission flux and transmission flux. Realistically, the heliosheath plasma consists of solar electrons, solar wind ions [SWI] and pick up ions [PUI]. These species interact differently with TS and thus have different characteristics down stream in the heliosheath. The PUI suffer multiple reflections at TS and are accelerated to high energies in the range of ~ 106 K. The solar electrons, on the other hand, are heated adiabatically through the TS and have temperature in the range ~ 5x105 K. The SWI may have a smaller temperature typically in the range 1-5x104 K The density of electrons could be in the range ~5 x 10-4 cm-3, while the ratio of PUI to SWI density could range from 0.1 to 0.5. Taking into account these parameters, grain charging due to different plasma species and other fluxes mentioned earlier, is calculated. Our results show that (a) surface potential is very sensitive to electron temp. It goes through a maxima and for realistic values close to or less than 5x105 K it can be as big as 26V which is twice the value calculated by Kimura and Mann1. This may have implications for electrostatic disruption and the size distribution of dust particles in the heliosheath. With PUI density the surface potential increases about 10 to 20 %. Though temperature of PUI is significantly larger than that of electrons, it is not large enough to make up for the mass ratio of electrons to protons. On account small temperature and electron/proton mass ratio, the effect of SWI on dust charge is very weak. (1) H. Kimura and I. Mann, Ap.J. 499, 454 (1998).

"The Theory was Beautiful Indeed": Rise, Fall and Circulation of Maximizing Methods in Population Genetics (1930-1980).

PubMed

Grodwohl, Jean-Baptiste

2017-08-01

Describing the theoretical population geneticists of the 1960s, Joseph Felsenstein reminisced: "our central obsession was finding out what function evolution would try to maximize. Population geneticists used to think, following Sewall Wright, that mean relative fitness, W, would be maximized by natural selection" (Felsenstein 2000). The present paper describes the genesis, diffusion and fall of this "obsession", by giving a biography of the mean fitness function in population genetics. This modeling method devised by Sewall Wright in the 1930s found its heyday in the late 1950s and early 1960s, in the wake of Motoo Kimura's and Richard Lewontin's works. It seemed a reliable guide in the mathematical study of deterministic effects (the study of natural selection in populations of infinite size, with no drift), leading to powerful generalizations presenting law-like properties. Progress in population genetics theory, it then seemed, would come from the application of this method to the study of systems with several genes. This ambition came to a halt in the context of the influential objections made by the Australian mathematician Patrick Moran in 1963. These objections triggered a controversy between mathematically- and biologically-inclined geneticists, with affected both the formal standards and the aims of population genetics as a science. Over the course of the 1960s, the mean fitness method withered with the ambition of developing the deterministic theory. The mathematical theory became increasingly complex. Kimura re-focused his modeling work on the theory of random processes; as a result of his computer simulations, Lewontin became the staunchest critic of maximizing principles in evolutionary biology. The mean fitness method then migrated to other research areas, being refashioned and used in evolutionary quantitative genetics and behavioral ecology.

Comparative study of quantal and semiclassical treatments of charge transfer between O+ and He

NASA Astrophysics Data System (ADS)

Zhao, L. B.; Joseph, D. C.; Saha, B. C.; Liebermann, H. P.; Funke, P.; Buenker, R. J.

2009-03-01

A comparative study for the electron capture process O+(S40,D20,P20)+He→O(P3)+He+ is reported. The cross sections are calculated using fully quantal and semiclassical molecular-orbital close-coupling (MOCC) approaches in the adiabatic representation. Detailed comparison of transition probabilities and cross sections is made from both MOCC approaches and displays close agreement above ˜125eV/u . The remarkable discrepancies between the earlier semiclassical and quantal MOCC approaches may be attributed to the insufficient step-size resolution in their semiclassical calculation [M. Kimura , Phys. Rev. A 50, 4854 (1994)]. Our results have also been compared with experiment and found to be in good agreement.

Ship Production Symposium Held in Long Beach, California on September 11-13, 1985. Volume 2 (The National Shipbuilding Research Program)

DTIC Science & Technology

1985-09-01

t h e long- term we are comple te ly redes ign ing the Weapon Systems F i le c o m p u t e r s o f t w a r e s o t h a t i t i s f u l l y ...sidewall 6) ability to repair surface defects by carbon arcing and grinding -572- LIST OF REFERENCES 1) Kimura, S., Ichihara, I., and Nagai, Y ...5.5 inch/min) (50/60 Hz) Stroke: 350mm (I 3.8 inch) electric inching method M o u n t i n g A s s e m b l y ) Vertical Head adjustment Slide speed

Transdermal nicotine patches for eosinophilic pustular folliculitis.

PubMed

Yoshifuku, Asuka; Higashi, Yuko; Matsushita, Shigeto; Kawai, Kazuhiro; Kanekura, Takuro

2013-09-01

We previously reported the clinical effectiveness of transdermal nicotine patches for the treatment of skin disorders with eosinophilic infiltration such as Kimura's disease, erythema nodosum and eosinophilic pustular folliculitis (EPF). We assessed the efficacy and safety of transdermal nicotine patches for EPF. We treated eight patients with EPF with transdermal nicotine patches and evaluated the treatment response by performing overall lesional assessment. Excellent 77and good responses were obtained in five and one patient(s), respectively. In the other two patients, the lesions remained unchanged. No severe adverse effects were observed. Our results suggest that transdermal nicotine patches may be useful and safe in the treatment of EPF. © 2013 Japanese Dermatological Association.

Evolution of N-species Kimura/voter models towards criticality, a surrogate for general models of accidental pathogens

NASA Astrophysics Data System (ADS)

Ghaffari, Peyman; Stollenwerk, Nico

2012-09-01

In models for accidental pathogens, with the paradigmatic epidemiological system of bacterial meningitis, there was evolution towards states exhibiting critical fluctuations with power law behaviour observed [1]. This is a model with many possibly pathogenic strains essentially evolving independently to low pathogenicity. A first and previous study had shown that in the limit of vanishing pathogenicity there are critical fluctuations with power law distributions observed, already when only two strains interact [2]. This earlier version of a two strain model was very recently reinvestigated [3] and named as Stollenwerk-Jansen model (SJ). Muñoz et al. demonstrated that this two-strain model for accidental pathogens is in the universality class of the so-called voter model. Though this model clearly shows criticality, its control parameter, the pathogenicity, is not self-tuning towards criticality. However, the multi-strain version mentioned above [1] is well evolving towards criticality, as well as a spatially explicit version of this, shown in [4] p. 155. These models of multi-strain type including explicitly mutations of the pathogenicity can be called SJ-models of type II [5]. Since the original epidemiological model is of SIRYX-type, the evolution to zero pathogenicity is slow and perturbed by large population noise. In the present article we now show on the basis of the notion of the voter-model universality classes the evolution of n-voter models with mutaion towards criticality, now much less perturbed by population noise, hence demonstrating a clear mechanism of self-organized criticality in the sense of [6, 7]. The present results have wide implications for many diseases in which a large proportion of infections is asymptomatic, meaning that the system has already evolved towards an average low pathogenicity. This holds not only for the original paradigmatic case of bacterial meningitis, but was reecently also suggested for example for dengue fever (DENFREE project).

Positron scattering from carbon dioxide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zecca, Antonio; Perazzolli, Chiara; Moser, Norberto

2006-07-15

We report total cross section measurements for positron scattering from carbon dioxide (CO{sub 2}). The energy range of the present measurements is 0.1-20.0 eV. The present study is undertaken to both try and resolve a discrepancy in the literature between the earlier low-energy works of Hoffman et al. [Phys. Rev. A 25, 1393 (1982)] and Kimura et al. [J. Chem. Phys. 107, 6616 (1997)], and to extend the available data to lower energies. We find generally good agreement with the data of Hoffman et al. over the common experimental energy range. A comparison of the present data with available calculationsmore » is also made, as is a comparison with corresponding electron total cross section data.« less

Biologically inspired adaptive walking of a quadruped robot.

PubMed

Kimura, Hiroshi; Fukuoka, Yasuhiro; Cohen, Avis H

2007-01-15

We describe here the efforts to induce a quadruped robot to walk with medium-walking speed on irregular terrain based on biological concepts. We propose the necessary conditions for stable dynamic walking on irregular terrain in general, and we design the mechanical and the neural systems by comparing biological concepts with those necessary conditions described in physical terms. PD-controller at joints constructs the virtual spring-damper system as the viscoelasticity model of a muscle. The neural system model consists of a central pattern generator (CPG), reflexes and responses. We validate the effectiveness of the proposed neural system model control using the quadruped robots called 'Tekken1&2'. MPEG footage of experiments can be seen at http://www.kimura.is.uec.ac.jp.

The oxytocin receptor gene (OXTR) localizes to human chromosome 3p25 by fluorescence in situ hybridization and PCR analysis of somatic cell hybrids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Simmons, C.F. Jr.; Clancy, T.E.; Quan, R.

1995-04-10

The human oxytocin receptor regulates parturition and myometrial contractility, breast milk let-down, and reproductive behaviors in the mammalian central nervous system. Kimura et al. recently identified a human oxytocin receptor cDNA by means of expression cloning from a human myometrial cDNA library. To elucidate further the molecular mechanisms that regulate oxytocin receptor gene expression and to define the expected Mendelian inheritance of possible human disease states, we must determine the number of genes, their localization, and their organization and structure. We summarize below our data indicating that the human oxytocin receptor gene is localized to 3p25 and exists as amore » single copy in the haploid genome. 9 refs., 2 figs.« less

Neutral evolution of proteins: The superfunnel in sequence space and its relation to mutational robustness

NASA Astrophysics Data System (ADS)

Noirel, Josselin; Simonson, Thomas

2008-11-01

Following Kimura's neutral theory of molecular evolution [M. Kimura, The Neutral Theory of Molecular Evolution (Cambridge University Press, Cambridge, 1983) (reprinted in 1986)], it has become common to assume that the vast majority of viable mutations of a gene confer little or no functional advantage. Yet, in silico models of protein evolution have shown that mutational robustness of sequences could be selected for, even in the context of neutral evolution. The evolution of a biological population can be seen as a diffusion on the network of viable sequences. This network is called a "neutral network." Depending on the mutation rate μ and the population size N, the biological population can evolve purely randomly (μN ≪1) or it can evolve in such a way as to select for sequences of higher mutational robustness (μN ≫1). The stringency of the selection depends not only on the product μN but also on the exact topology of the neutral network, the special arrangement of which was named "superfunnel." Even though the relation between mutation rate, population size, and selection was thoroughly investigated, a study of the salient topological features of the superfunnel that could affect the strength of the selection was wanting. This question is addressed in this study. We use two different models of proteins: on lattice and off lattice. We compare neutral networks computed using these models to random networks. From this, we identify two important factors of the topology that determine the stringency of the selection for mutationally robust sequences. First, the presence of highly connected nodes ("hubs") in the network increases the selection for mutationally robust sequences. Second, the stringency of the selection increases when the correlation between a sequence's mutational robustness and its neighbors' increases. The latter finding relates a global characteristic of the neutral network to a local one, which is attainable through experiments or molecular

Neutral evolution of proteins: The superfunnel in sequence space and its relation to mutational robustness.

PubMed

Noirel, Josselin; Simonson, Thomas

2008-11-14

Following Kimura's neutral theory of molecular evolution [M. Kimura, The Neutral Theory of Molecular Evolution (Cambridge University Press, Cambridge, 1983) (reprinted in 1986)], it has become common to assume that the vast majority of viable mutations of a gene confer little or no functional advantage. Yet, in silico models of protein evolution have shown that mutational robustness of sequences could be selected for, even in the context of neutral evolution. The evolution of a biological population can be seen as a diffusion on the network of viable sequences. This network is called a "neutral network." Depending on the mutation rate mu and the population size N, the biological population can evolve purely randomly (muN<1) or it can evolve in such a way as to select for sequences of higher mutational robustness (muN>1). The stringency of the selection depends not only on the product muN but also on the exact topology of the neutral network, the special arrangement of which was named "superfunnel." Even though the relation between mutation rate, population size, and selection was thoroughly investigated, a study of the salient topological features of the superfunnel that could affect the strength of the selection was wanting. This question is addressed in this study. We use two different models of proteins: on lattice and off lattice. We compare neutral networks computed using these models to random networks. From this, we identify two important factors of the topology that determine the stringency of the selection for mutationally robust sequences. First, the presence of highly connected nodes ("hubs") in the network increases the selection for mutationally robust sequences. Second, the stringency of the selection increases when the correlation between a sequence's mutational robustness and its neighbors' increases. The latter finding relates a global characteristic of the neutral network to a local one, which is attainable through experiments or molecular

Origin of the eclogitic clasts with graphite-bearing and graphite-free lithologies in the Northwest Africa 801 (CR2) chondrite: Possible origin from a Moon-sized planetary body inferred from chemistry, oxygen isotopes and REE abundances

NASA Astrophysics Data System (ADS)

Hiyagon, H.; Sugiura, N.; Kita, N. T.; Kimura, M.; Morishita, Y.; Takehana, Y.

2016-08-01

In order to clarify the origin of the eclogitic clasts found in the NWA801 (CR2) chondrite (Kimura et al., 2013), especially, that of the high pressure and temperature (P-T) condition (∼3 GPa and ∼1000 °C), we conducted ion microprobe analyses of oxygen isotopes and rare earth element (REE) abundances in the clasts. Oxygen isotopic compositions of the graphite-bearing lithology (GBL) and graphite-free lithology (GFL) show a slope ∼0.6 correlation slightly below the CR-CH-CB chondrites field in the O three-isotope-diagram, with a large variation for the former and almost homogeneous composition for the latter. The average REE abundances of the two lithologies show almost unfractionated patterns. Based on these newly obtained data, as well as mineralogical observations, bulk chemistry, and considerations about diffusion timescales for various elements, we discuss in detail the formation history of the clasts. Consistency of the geothermobarometers used by Kimura et al. (2013), suggesting equilibration of various elements among different mineral pairs, provides a strong constraint for the duration of the high P-T condition. We suggest that the high P-T condition lasted 102-103 years. This clearly precludes a shock high pressure (HP) model, and hence, strongly supports a static HP model. A static HP model requires a Moon-sized planetary body of ∼1500 km in radius. Furthermore, it implies two successive violent collisions, first at the formation of the large planetary body, when the clasts were placed its deep interior, and second, at the disruption of the large planetary body, when the clasts were expelled out of the parent body and later on transported to the accretion region of the CR chondrites. We also discuss possible origin of O isotopic variations in GBL, and presence/absence of graphite in GBL/GFL, respectively, in relation to smelting possibly occurred during the igneous process(es) which formed the two lithologies. Finally we present a possible

The origin and evolution of seahorses (genus Hippocampus): a phylogenetic study using the cytochrome b gene of mitochondrial DNA.

PubMed

Casey, Stephen P; Hall, Heather J; Stanley, Helen F; Vincent, Amanda C J

2004-02-01

Phylogenetic relationships among 93 specimens of 22 species of seahorses (genus Hippocampus) from the Atlantic and Indo-Pacific Oceans were analysed using cytochrome b gene sequence data. A maximum sequence divergence of 23.2% (Kimura 2-parameter model) suggests a pre-Tethyan origin for the genus. Despite a greater number of seahorse species in the Indo-Pacific than in the Atlantic Ocean, there was no compelling genetic evidence to support an Indo-Pacific origin for the genus Hippocampus. The phylogenetic data suggest that high diversity in the Indo-Pacific results from speciation events dating from the Pleistocene to the Miocene, or earlier. Both vicariance and dispersal events in structuring the current global distribution of seahorses. The results suggested that several species designations need re-evaluating, and further phylogeographic studies are required to determine patterns and processes of seahorse dispersal.

[Beginnings of the study of Western sciences, "Rangaku," in Kyoto and Osaka in close relations with the Edo school].

PubMed

Murata, T

2001-01-01

Beginnings of the study of Western sciences, "Rangaku," in Kyoto and Osaka in the late 18th century are reviewed. Profiles and achievements of several active learners are briefly described; they include Koishi Genzui (Osaka-Kyoto), Tsuji Ranshitsu (Kyoto), Kimura Kenkadō (Osaka), and Hashimoto Sōkichi (Osaka). Genzui, after having successfully made good relations with Sugita Genpaku and Ohtsuki Gentaku, leading masters of the Edo school, played a role of an advocator for promoting "Rangaku" in Osaka and Kyoto. As a result, Kenkadō attained the publication of his book "Ikkaku Sankō," a monograph of the Western crude drug unicorn, with the help of Gentaku, who had translated a Dutch reference into Japanese for him. Ranshitsu and Sōkichi were taught the Dutch language by Gentaku; Sōkichi is known as the founder of "Rangaku" in Osaka.

Projection of Summer Climate on Tokyo Metropolitan Area using Pseudo Global Warming Method

NASA Astrophysics Data System (ADS)

Adachi, S. A.; Kimura, F.; Kusaka, H.; Hara, M.

2010-12-01

:10.1002/joc.2142 (2010). 2. Kusaka, H., H. Kondo, Y. Kikegawa, and F. Kimura, Bound.-Layer Meteor., 101, 329-358 (2001). 3. Sato, T., F. Kimura, and A. Kitoh, J. Hydrology, 144-154 (2007).

Keyhole approach for repair of congenital duodenal obstruction.

PubMed

Kozlov, Y; Novogilov, V; Yurkov, P; Podkamenev, A; Weber, I; Sirkin, N

2011-03-01

We report on our experience of repair of congenital duodenal obstruction using a circumumbilical incision. The aim of this report is to describe how a Bianchi approach provides a safe and invisible alternative to transverse abdominal incision for the repair of duodenal atresia. Between January 2005 and December 2009, we treated 13 cases with congenital duodenal obstruction using a circumumbilical incision (Group I) and 14 cases with this condition repaired using a standard transverse right upper abdominal incision (Group II). Surgical procedures included a diamond-shaped duodenoduodenostomy as originally described by Kimura and standard duodenal web excision. The circumumbilical incision utilized at our institution is a classic Bianchi procedure. The 2 groups were compared with regard to patient demographics, operative reports and postoperative outcomes. There were no differences in preoperative parameters such as gestational age, age at surgery, or body weight at operation between the 2 groups. The circumumbilical cohort and transverse incision cohort had similar rates of congenital anomalies (61.54% vs. 64.29%), Kimura diamond-shaped anastomosis (61.54% vs. 64.29%) with only a slight female predominance in Group I. The mean operating time in Group I was 65.0 min while mean duration of the operation in Group II was 64.64 min. The difference between groups was statistically not significant (p>0.05). The mean time to full enteral feeding for patients with an umbilical incision was significantly shorter (p<0.0001) compared to patients with a standard incision (6.92 days vs. 11.86 days). Mean postoperative hospital stay was longer for patients in Group II (19.71 days vs. 12.38 days; p<0.0001). The postoperative course was uneventful for all patients. There were no intra- or postoperative complications. We report on a first series comparing umbilical and transverse right upper abdominal incision for the treatment of congenital duodenal obstruction. Our results suggest

Collisions of O+ with He at low energies

NASA Astrophysics Data System (ADS)

Joseph, Dwayne C.; Saha, B. C.; Zhao, L. B.

2009-05-01

We have investigated the following charge transfer processO^+( ^4S^0, ^2D^0, ^2P^0)+He->O( ^3P)+He^+-δE using the full quantum [1] and semi-classical molecular [2]orbital close-coupling (MOCC) approximations. The quantum MOCC equations are solved numerically in the adiabatic representation [3]. Using MRD-CI package [4] the ab initio configuration interaction calculation is carried out for potential energies. Details of our findings will be reported in the conference. [1] B. H. Bransden and M. R. C. McDowell, ``Charge Exchange and the Theory of Ion-Atom Collisions'', Clarendon Press, Oxford, 1992. [2] M. Kimura and N. F. Lane, At. Mol. Opt. Phys 26, 79 (1990). [3] J. P. Braga and J. C. Belchoir, J. Comput. Chem 17, 1559 (1996). [4] R. J. Buenker, ``Current Aspects of Quantum Chemistry 1981, Vol 21, edited by R. Carbo (Elsevier, Amsterdam), p 17.

Intercorporeality and aida: Developing an interaction theory of social cognition.

PubMed

Tanaka, Shogo

2017-06-01

The aim of this article is to develop an interaction theory (IT) of social cognition. The central issue in the field of social cognition has been theory of mind (ToM), and there has been debate regarding its nature as either theory-theory or as simulation theory. Insights from phenomenology have brought a second-person perspective based on embodied interactions into the debate, thereby forming a third position known as IT. In this article, I examine how IT can be further elaborated by drawing on two phenomenological notions-Merleau-Ponty's intercorporeality and Kimura's aida . Both of these notions emphasize the sensory-motor, perceptual, and non-conceptual aspects of social understanding and describe a process of interpersonal coordination in which embodied interaction gains autonomy as an emergent system. From this perspective, detailed and nuanced social understanding is made possible through the embodied skill of synchronizing with others.

DNA barcoding and phylogeny of Calidris and Tringa (Aves: Scolopacidae).

PubMed

Huang, Zuhao; Tu, Feiyun

2017-07-01

The avian genera Calidris and Tringa are the largest of the widespread family of Scolopacidae. The phylogeny of members of the two genera is still a matter of controversial. Mitochondrial cytochrome c oxidase subunit I (COI) can serve as a fast and accurate marker for the identification and phylogeny of animal species. In this study, we analyzed the COI barcodes of thirty-one species of the two genera. All the species had distinct COI sequences. Two hundred and twenty-one variable sites were identified. Kimura two-parameter distances were calculated between barcodes. Neighbor-joining and maximum likelihood methods were used to construct phylogenetic trees. All the species could be discriminated by their distinct clades in the phylogenetic trees. The phylogenetic trees grouped all the species of Calidris and Tringa into different monophyletic clade, respectively. COI data showed a well-supported phylogeny for Calidris and Tringa species.

Charge exchange in slow collisions of Si3+ with H

NASA Astrophysics Data System (ADS)

Joseph, D. C.; Saha, B. C.

2010-10-01

Low energy electron capture from atomic hydrogen by multi-charged ions continues to be of interest and has wide applications including both magnetically confined^ fusion and astrophysical plasmas. The charge exchange process reported here, Si^3+ + H -- Si^2+ + H^+ is an important destruction mechanism of Si^3+ in photo-ionized gas. The soft X-ray emission from comets has been explained by charge transfer of solar wind ions, among them Si^3+, with neutrals in the cometary gas vapor. The state selective cross sections are evaluated using the semi-classical molecular orbital close coupling (MOCC) [1] methods. Adiabatic potentials and wave functions for a number of low-lying singlet and triplet states are calculated using the MRD-CI package [2]. Details will be presented at the conference. [1] M. Kimura and N. F. Lane, At. Mol. Opt. Phys 26, 79 (1990). [3] R. J. Buenker, ``Current Aspects of Quantum Chemistry'' 1981, Vol 21, edited by R. Carbo (Elsevier, Amsterdam) p 17.

Quasispecies theory for finite populations

PubMed Central

Park, Jeong-Man; Muñoz, Enrique; Deem, Michael W.

2015-01-01

We present stochastic, finite-population formulations of the Crow-Kimura and Eigen models of quasispecies theory, for fitness functions that depend in an arbitrary way on the number of mutations from the wild type. We include back mutations in our description. We show that the fluctuation of the population numbers about the average values are exceedingly large in these physical models of evolution. We further show that horizontal gene transfer reduces by orders of magnitude the fluctuations in the population numbers and reduces the accumulation of deleterious mutations in the finite population due to Muller’s ratchet. Indeed the population sizes needed to converge to the infinite population limit are often larger than those found in nature for smooth fitness functions in the absence of horizontal gene transfer. These analytical results are derived for the steady-state by means of a field-theoretic representation. Numerical results are presented that indicate horizontal gene transfer speeds up the dynamics of evolution as well. PMID:20365394

DNA barcoding Indian freshwater fishes.

PubMed

Lakra, Wazir Singh; Singh, M; Goswami, Mukunda; Gopalakrishnan, A; Lal, K K; Mohindra, V; Sarkar, U K; Punia, P P; Singh, K V; Bhatt, J P; Ayyappan, S

2016-11-01

DNA barcoding is a promising technique for species identification using a short mitochondrial DNA sequence of cytochrome c oxidase I (COI) gene. In the present study, DNA barcodes were generated from 72 species of freshwater fish covering the Orders Cypriniformes, Siluriformes, Perciformes, Synbranchiformes, and Osteoglossiformes representing 50 genera and 19 families. All the samples were collected from diverse sites except the species endemic to a particular location. Species were represented by multiple specimens in the great majority of the barcoded species. A total of 284 COI sequences were generated. After amplification and sequencing of 700 base pair fragment of COI, primers were trimmed which invariably generated a 655 base pair barcode sequence. The average Kimura two-parameter (K2P) distances within-species, genera, families, and orders were 0.40%, 9.60%, 13.10%, and 17.16%, respectively. DNA barcode discriminated congeneric species without any confusion. The study strongly validated the efficiency of COI as an ideal marker for DNA barcoding of Indian freshwater fishes.

DNA barcoding of five common stored-product pest species of genus Cryptolestes (Coleoptera: Laemophloeidae).

PubMed

Wang, Y J; Li, Z H; Zhang, S F; Varadínová, Z; Jiang, F; Kučerová, Z; Stejskal, V; Opit, G; Cao, Y; Li, F J

2014-10-01

Several species of the genus Cryptolestes Ganglbauer, 1899 (Coleoptera: Laemophloeidae) are commonly found in stored products. In this study, five species of Cryptolestes, with almost worldwide distribution, were obtained from laboratories in China, Czech Republic and the USA: Cryptolestes ferrugineus (Stephens, 1831), Cryptolestes pusillus (Schönherr, 1817), Cryptolestes turcicus (Grouvelle, 1876), Cryptolestes pusilloides (Steel & Howe, 1952) and Cryptolestes capensis (Waltl, 1834). Molecular identification based on a 658 bp fragment from the mitochondrial DNA cytochrome c oxidase subunit I (COI) was adopted to overcome some problems of morphological identification of Cryptolestes species. The utility of COI sequences as DNA barcodes in discriminating the five Cryptolestes species was evaluated on adults and larvae by analysing Kimura 2-parameter distances, phylogenetic tree and haplotype networks. The results showed that molecular approaches based on DNA barcodes were able to accurately identify these species. This is the first study using DNA barcoding to identify Cryptolestes species and the gathered DNA sequences will complement the biological barcode database.

Quantifying evolutionary dynamics from variant-frequency time series.

PubMed

Khatri, Bhavin S

2016-09-12

From Kimura's neutral theory of protein evolution to Hubbell's neutral theory of biodiversity, quantifying the relative importance of neutrality versus selection has long been a basic question in evolutionary biology and ecology. With deep sequencing technologies, this question is taking on a new form: given a time-series of the frequency of different variants in a population, what is the likelihood that the observation has arisen due to selection or neutrality? To tackle the 2-variant case, we exploit Fisher's angular transformation, which despite being discovered by Ronald Fisher a century ago, has remained an intellectual curiosity. We show together with a heuristic approach it provides a simple solution for the transition probability density at short times, including drift, selection and mutation. Our results show under that under strong selection and sufficiently frequent sampling these evolutionary parameters can be accurately determined from simulation data and so they provide a theoretical basis for techniques to detect selection from variant or polymorphism frequency time-series.

Evolution Models with Conditional Mutation Rates: Strange Plateaus in Population Distribution

NASA Astrophysics Data System (ADS)

Saakian, David B.

2017-08-01

Cancer is related to clonal evolution with a strongly nonlinear, collective behavior. Here we investigate a slightly advanced version of the popular Crow-Kimura evolution model, suggested recently, by simply assuming a conditional mutation rate. We investigated the steady-state solution and found a highly intriguing plateau in the distribution. There are selective and nonselective phases, with a rather narrow plateau in the distribution at the peak in the first phase, and a wide plateau for many Hamming classes (a collection of genomes with the same number of mutations from the reference genome) in the second phase. We analytically solved the steady state distribution in the selective and nonselective phases, calculating the widths of the plateaus. Numerically, we also found an intermediate phase with several plateaus in the steady-state distribution, related to large finite-genome-length corrections. We assume that the newly observed phenomena should exist in other versions of evolution dynamics when the parameters of the model are conditioned to the population distribution.

The Development of Astronomy and Emergence of Astrophysics in Japan

NASA Astrophysics Data System (ADS)

Nakamura, Tsuko

This chapter overviews the emergence and development phases of modern astronomy and astrophysics in Japan, mainly before WWII. In the beginning of the nineteenth century under the samurai regime of the Tokugawa Shogunate, shogunal astronomers started to learn Western astronomy through a Dutch translation of the book Astronomie by J.J. Lalande. After the Meiji Restoration (1868) the new government founded the University of Tokyo (1877), the first modern university in Japan, in which Tokyo Astronomical Observatory (TAO) also started in 1888. Terao Hisashi, who had gone to Paris to study the modern astronomy, became the first Director of TAO in 1888. The astronomy introduced by Terao into Japan was so-called classical astronomy. Two of Terao's early students made Japan's first internationally recognized achievements in astronomy, the discovery of the Z-term in the polar motion of the Earth by Kimura (Astronomische Nachrichten, 158, 234-240, 1902) and the discovery of asteroid families by Hirayama (Astronomical Journal, 31, 185-188, 1918).

Molecular diversity of some species belonging to the genus Daphnia O. F. Müller, 1785 (Crustacea: Cladocera) in Turkey.

PubMed

Özdemir, Ebru; Altındağ, Ahmet; Kandemir, İrfan

2017-05-01

Daphnia is a freshwater zooplankton species with controversial taxonomy due to its high morphological variation linked to environmental factors and inter-specific hybridization and polyploidy in some groups. The aim of the present study is to examine molecular diversity of some Daphnia species in Turkey and to establish DNA barcodes of Turkish Daphnia species. Sequence analysis was performed using 540 bp region of cytochrome oxidase subunit I gene of mitochondrial DNA. A total of 34 haplotypes have been identified for Turkey. Daphnia pulex complex was divided into two clades with 16.1% sequence divergence according to molecular taxonomy based on Kimura 2-parameter. The clade which was molecularly diverged from Daphnia pulex with 16.1% sequence divergence was found to show 99% similarity with Daphnia cf. pulicaria (sensu Alonso 1996) instead of Daphnia pulicaria Forbes, 1893. Furthermore, this study has contributed to Turkish zoogeography by demonstrating the distribution of Daphnia species in Turkey.

Multi-q crystal and magnetic structure in TbMnO3: Evidence for a Soliton-lattice

NASA Astrophysics Data System (ADS)

Aliouane, N.; Strempfer, J.; Caliebe, W.

2005-03-01

In TbMnO3, Mn-spins order with a sinusoidal antiferromagnetic (AF) propagation wave vector QMn=[0,k+/-q,l] (q˜0.288b^*) at TN(Mn)=41K. The propagation vector QMn varies with temperature on cooling until TLock(Mn) ˜30K, which coincides with a ferroelectric transition. In addition to QMn reflections we find magnetic reflections at 3QMn. Our X-ray measurements show that the magneto-elastic coupling gives rise to a structural modulation at twice the magnetic wavevector (2QMn). Field cooling the sample under a magnetic field oriented along the a-direction with H>9T shows that all magnetic wavevectors for Mn and Tb collapse to a single q structure with Q=[0,1/4,0], an up-up, down-down phase, and coincide with anomalies in the polarization. We argue that the temperature and field dependence of the magnetic and superlattice reflections are consistent with a soliton formalism which predicts a stable commensurate single q=1/4 phase [1]. [1] Kimura et al., PRB 68, 60403(2003).

[Identification of Tibetan medicine "Dida" of Gentianaceae using DNA barcoding].

PubMed

Liu, Chuan; Zhang, Yu-Xin; Liu, Yue; Chen, Yi-Long; Fan, Gang; Xiang, Li; Xu, Jiang; Zhang, Yi

2016-02-01

The ITS2 barcode was used toidentify Tibetan medicine "Dida", and tosecure its quality and safety in medication. A total of 13 species, 151 experimental samples for the study from the Tibetan Plateau, including Gentianaceae Swertia, Halenia, Gentianopsis, Comastoma, Lomatogonium ITS2 sequences were amplified, and purified PCR products were sequenced. Sequence assembly and consensus sequence generation were performed using the CodonCode Aligner V3.7.1. The Kimura 2-Parameter (K2P) distances were calculated using MEGA 6.0. The neighbor-joining (NJ) phylogenetic trees were constructed. There are 31 haplotypes among 231 bp after alignment of all ITS2 sequence haplotypes, and the average G±C content of 61.40%. The NJ tree strongly supported that every species clustered into their own clade and high identification success rate, except that Swertia bifolia and Swertia wolfangiana could not be distinguished from each other based on the sequence divergences. DNA barcoding could be used as a fast and accurate identification method to distinguish Tibetan medicine "Dida" to ensure its safe use. Copyright© by the Chinese Pharmaceutical Association.

Exact Markov chain and approximate diffusion solution for haploid genetic drift with one-way mutation.

PubMed

Hössjer, Ola; Tyvand, Peder A; Miloh, Touvia

2016-02-01

The classical Kimura solution of the diffusion equation is investigated for a haploid random mating (Wright-Fisher) model, with one-way mutations and initial-value specified by the founder population. The validity of the transient diffusion solution is checked by exact Markov chain computations, using a Jordan decomposition of the transition matrix. The conclusion is that the one-way diffusion model mostly works well, although the rate of convergence depends on the initial allele frequency and the mutation rate. The diffusion approximation is poor for mutation rates so low that the non-fixation boundary is regular. When this happens we perturb the diffusion solution around the non-fixation boundary and obtain a more accurate approximation that takes quasi-fixation of the mutant allele into account. The main application is to quantify how fast a specific genetic variant of the infinite alleles model is lost. We also discuss extensions of the quasi-fixation approach to other models with small mutation rates. Copyright © 2015 Elsevier Inc. All rights reserved.

Mitochondrial DNA variation and phylogenetic relationships among five tuna species based on sequencing of D-loop region.

PubMed

Kumar, Girish; Kocour, Martin; Kunal, Swaraj Priyaranjan

2016-05-01

In order to assess the DNA sequence variation and phylogenetic relationship among five tuna species (Auxis thazard, Euthynnus affinis, Katsuwonus pelamis, Thunnus tonggol, and T. albacares) out of all four tuna genera, partial sequences of the mitochondrial DNA (mtDNA) D-loop region were analyzed. The estimate of intra-specific sequence variation in studied species was low, ranging from 0.027 to 0.080 [Kimura's two parameter distance (K2P)], whereas values of inter-specific variation ranged from 0.049 to 0.491. The longtail tuna (T. tonggol) and yellowfin tuna (T. albacares) were found to share a close relationship (K2P = 0.049) while skipjack tuna (K. pelamis) was most divergent studied species. Phylogenetic analysis using Maximum-Likelihood (ML) and Neighbor-Joining (NJ) methods supported the monophyletic origin of Thunnus species. Similarly, phylogeny of Auxis and Euthynnus species substantiate the monophyly. However, results showed a distinct origin of K. pelamis from genus Thunnus as well as Auxis and Euthynnus. Thus, the mtDNA D-loop region sequence data supports the polyphyletic origin of tuna species.

Molecular identification of Taenia mustelae cysts in subterranean rodent plateau zokors (Eospalax baileyi)

PubMed Central

ZHAO, Fang; ZHANG, Ming-Xia; MA, Jun-Ying; CAI, Hui-Xia; SU, Jian-Ping; CAI, Hui-Xia; HOU, Zhi-Bin; ZHANG, Tong-Zuo; LIN, Gong-Hua

2014-01-01

Cestode larvae spend one phase of their two-phase life cycle in the viscera of rodents, but cases of cestodes infecting subterranean rodents have only been rarely observed. To experimentally gain some insight into this phenomenon, we captured approximately 300 plateau zokors (Eospalax baileyi), a typical subterranean rodent inhabiting the Qinghai-Tibet Plateau, and examined their livers for the presence of cysts. Totally, we collected five cysts, and using a mitochondrial gene (cox1) and two nuclear genes (pepck and pold) as genetic markers, we were able to analyze the taxonomy of the cysts. Both the maximum likelihood and Bayesian methods showed that the cysts share a monophyly with Taenia mustelae, while Kimura 2-parameter distances and number of different sites between our sequences and T. mustelae were far less than those found between the examined sequences and other Taeniidae species. These results, alongside supporting paraffin section histology, imply that the cysts found in plateau zokors can be regarded as larvae of T. mustelae, illustrating that zokors are a newly discovered intermediate host record of this parasite. PMID:25017751

Method of Electroporation for the Early Chick Embryo

NASA Astrophysics Data System (ADS)

Hatakeyama, Jun; Shimamura, Kenji

Chick embryos have long been one of the favored model systems in the field of embryology and developmental biology. Recent advances in the gene manipulation technologies (Muramatsu et al., 1997; Nakamura et al., 2004) make this model system even more attractive for the developmental biologists (see review by Stern, 2005). Thanks to its two dimensional geometry, easiness in accessibility and observation, and well-established fate maps (e.g. Couly and Le Douarin, 1988; Garcia-Martinez et al., 1993; Hatada and Stern, 1994; Psychoyos and Stern, 1996; Sawada and Aoyama, 1999; Cobos et al., 2001; Lopez-Sanchez et al., 2001; Redkar et al., 2001; Fernandez-Garre et al., 2002; Kimura et al., 2006; Matsushita et al., 2008), it has great advantages especially for studies at the early embryonic stages, such as the processes of gastrulation, neural induction, left-right patterning, etc. For such purposes, a whole embryo culture system, originally invented by Dennis A. T. New (New, 1955), and its derivatives (Flamme, 1987; Sundin and Eichele, 1992; Stern, 1993; Chapman et al., 2001) have been widely used.

Molecular identification of Taenia mustelae cysts in subterranean rodent plateau zokors (Eospalax baileyi).

PubMed

Zhao, Fang; Ma, Jun-Ying; Cai, Hui-Xia; Su, Jian-Ping; Hou, Zhi-Bin; Zhang, Tong-Zuo; Lin, Gong-Hua

2014-07-01

Cestode larvae spend one phase of their two-phase life cycle in the viscera of rodents, but cases of cestodes infecting subterranean rodents have only been rarely observed. To experimentally gain some insight into this phenomenon, we captured approximately 300 plateau zokors (Eospalax baileyi), a typical subterranean rodent inhabiting the Qinghai-Tibet Plateau, and examined their livers for the presence of cysts. Totally, we collected five cysts, and using a mitochondrial gene (cox1) and two nuclear genes (pepck and pold) as genetic markers, we were able to analyze the taxonomy of the cysts. Both the maximum likelihood and Bayesian methods showed that the cysts share a monophyly with Taenia mustelae, while Kimura 2-parameter distances and number of different sites between our sequences and T. mustelae were far less than those found between the examined sequences and other Taeniidae species. These results, alongside supporting paraffin section histology, imply that the cysts found in plateau zokors can be regarded as larvae of T. mustelae, illustrating that zokors are a newly discovered intermediate host record of this parasite.

DNA Barcoding in Pencilfishes (Lebiasinidae: Nannostomus) Reveals Cryptic Diversity across the Brazilian Amazon

PubMed Central

Benzaquem, Denise Corrêa; Oliveira, Claudio; da Silva Batista, Jaqueline; Zuanon, Jansen; Porto, Jorge Ivan Rebelo

2015-01-01

Nannostomus is comprised of 20 species. Popularly known as pencilfishes the vast majority of these species lives in the flooded forests of the Amazon basin and are popular in the ornamental trade. Among the lebiasinids, it is the only genus to have undergone more than one taxonomic revision. Even so, it still possesses poorly defined species. Here, we report the results of an application of DNA barcoding to the identification of pencilfishes and highlight the deeply divergent clades within four nominal species. We surveyed the sequence variation in the mtDNA cytochrome c oxidase subunit I gene among 110 individuals representing 14 nominal species that were collected from several rivers along the Amazon basin. The mean Kimura-2-parameter distances within species and genus were 2% and 19,0%, respectively. The deep lineage divergences detected in N. digrammus, N. trifasciatus, N. unifasciatus and N. eques suggest the existence of hidden diversity in Nannostomus species. For N. digrammus and N. trifasciatus, in particular, the estimated divergences in some lineages were so high that doubt about their conspecific status is raised. PMID:25658694

Influence of Iron Oxide Particles on the Strength of Ball-Milled Iron

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lesuer, D R; Syn, C K; Sherby, O D

2005-12-07

Detailed microstructural and mechanical property studies of ball-milled iron, in the powder and consolidated states, are reviewed and assessed. The analyses cover three and one-half orders of magnitude of grain size (from 6 nm to 20 mm) and focus on the influence of oxide particles on the strength. The study includes the early work of Koch and Yang, Kimura and Takaki and continues with the more recent work of Umemoto et al and Belyakov, Sakai et al. It is shown that the major contributors to strength are the nanooxide particles. These particles are created by adiabatic shear banding during ball-millingmore » leading to a bimodal distribution of particles. The predicted strength from particles, {sigma}{sub p}, is given by {sigma}{sub p} = B {center_dot} (D*{sub S}){sup -1/2} where D*{sub S} is the surface-to-surface interparticle spacing, and B = 395 MPa {center_dot} {micro}m{sup -1/2}. A model is proposed that accounts for the influence of the bimodal particle size distribution on strength.« less

DNA barcodes effectively identify the morphologically similar Common Opossum (Didelphis marsupialis) and Virginia Opossum (Didelphis virginiana) from areas of sympatry in Mexico.

PubMed

Cervantes, Fernando A; Arcangeli, Jésica; Hortelano-Moncada, Yolanda; Borisenko, Alex V

2010-12-01

Two morphologically similar species of opossum from the genus Didelphis-Didelphis virginiana and Didelphis marsupialis-cooccur sympatrically in Mexico. High intraspecific variation complicates their morphological discrimination, under both field and museum conditions. This study aims to evaluate the utility and reliability of using DNA barcodes (short standardized genome fragments used for DNA-based identification) to distinguish these two species. Sequences of the cytochrome c oxidase subunit I (Cox1) mitochondrial gene were obtained from 12 D. marsupialis and 29 D. virginiana individuals and were compared using the neighbor-joining (NJ) algorithm with Kimura's two-parameter (K2P) model of nucleotide substitution. Average K2P distances were 1.56% within D. virginiana and 1.65% in D. marsupialis. Interspecific distances between D. virginiana and D. marsupialis varied from 7.8 to 9.3% and their barcode sequences formed distinct non-overlapping clusters on NJ trees. All sympatric specimens of both species were effectively discriminated, confirming the utility of Cox1 barcoding as a tool for taxonomic identification of these morphologically similar taxa.

[Identification of medicinal plant Dendrobium based on the chloroplast psbK-psbI intergenic spacer].

PubMed

Yao, Hui; Yang, Pei; Zhou, Hong; Ma, Shuang-jiao; Song, Jing-yuan; Chen, Shi-lin

2015-06-01

In this paper, the chloroplast psbK-psbI intergenic spacers of 18 species of Dendrobium and their adulterants were amplified and sequenced, and then the sequence characteristics were analyzed. The sequence lengths of chloroplast psbK-psbI regions of Dendrobium ranged from 474 to 513 bp and the GC contents were 25.4%-27.6%. The variable sites were 71 while the informative sites were 46. The inter-specific genetic distances calculated by Kimura 2-parameter (K2P) of Dendrobium were 0.006 1-0.058 1, with an average of 0.028 4. The K2P genetic distances between Dendrobium species and Bulbophyllum odoratissimum were 0.093 2-0.120 4. The NJ tree showed that the Dendrobium species can be easily differentiated from each other and 6 samples of the inspected Dendrobium species were identified successfully through sequencing the psbK-psbI intergenic spacer. Therefore, the chloroplast psbK-psbI intergenic spacer can be used as a candidate marker to identify Dendrobium species and its adulterants.

Identification of Neoceratitis asiatica (Becker) (Diptera: Tephritidae) based on morphological characteristics and DNA barcode.

PubMed

Guo, Shaokun; He, Jia; Zhao, Zihua; Liu, Lijun; Gao, Liyuan; Wei, Shuhua; Guo, Xiaoyu; Zhang, Rong; Li, Zhihong

2017-12-12

Neoceratitis asiatica (Becker), which especially infests wolfberry (Lycium barbarum L.), could cause serious economic losses every year in China, especially to organic wolfberry production. In some important wolfberry plantings, it is difficult and time-consuming to rear the larvae or pupae to adults for morphological identification. Molecular identification based on DNA barcode is a solution to the problem. In this study, 15 samples were collected from Ningxia, China. Among them, five adults were identified according to their morphological characteristics. The utility of mitochondrial DNA (mtDNA) cytochrome c oxidase I (COI) gene sequence as DNA barcode in distinguishing N. asiatica was evaluated by analysing Kimura 2-parameter distances and phylogenetic trees. There were significant differences between intra-specific and inter-specific genetic distances according to the barcoding gap analysis. The uncertain larval and pupal samples were within the same cluster as N. asiatica adults and formed sister cluster to N. cyanescens. A combination of morphological and molecular methods enabled accurate identification of N. asiatica. This is the first study using DNA barcode to identify N. asiatica and the obtained DNA sequences will be added to the DNA barcode database.

Slow Collisions of Si3+ with Atomic Hydrogen

NASA Astrophysics Data System (ADS)

Joseph, D. C.; Gu, J.-P.; Saha, B. C.; Liebermann, H. P.; Funke, P.; Buenker, R. J.

2010-03-01

Low energy electron capture from hydrogen atom by multi-charged ions continues to be of interest and applications include both magnetically confined fusion and astrophysical plasmas. The charge exchange process reported here, Si^3+ + H -> Si^2+ + H^+ is an important destruction mechanism of Si^3+ in photo-ionized gas. The soft X-ray emission from comets has been explained by charge transfer of solar wind ions, among them Si^3+, with neutrals in the cometary gas vapor. The state selective cross sections are evaluated using the full quantum [1] and semi-classical molecular orbital close coupling (MOCC) [2] methods. Adiabatic potentials and wave functions for a number of low-lying singlet and triplet states of and symmetry are calculated wing the MRD-CI package [3]. Details will be presented at the conference. [4pt] [1] L. B. Zhao, D. C. Joseph, B. C. Saha, H. P. Liebermann, P. Funke and R. J. Buenker, Phys. Rev A, 79, 034701 (1009).[0pt] [2] M. Kimura and N. F. Lane, At. Mol. Opt. Phys 26, 79 (1990).[0pt] [3] R. J. Buenker, ``Current Aspects of Quantum Chemistry 1981, Vol 21, edited by R. Carbo (Elsevier, Amsterdam) p 17.

Comparative analysis of upper gastrointestinal endoscopy, double-contrast upper gastrointestinal barium X-ray radiography, and the titer of serum anti-Helicobacter pylori IgG focusing on the diagnosis of atrophic gastritis.

PubMed

Yamamichi, Nobutake; Hirano, Chigaya; Takahashi, Yu; Minatsuki, Chihiro; Nakayama, Chiemi; Matsuda, Rie; Shimamoto, Takeshi; Takeuchi, Chihiro; Kodashima, Shinya; Ono, Satoshi; Tsuji, Yosuke; Fujishiro, Mitsuhiro; Wada, Ryoichi; Mitsushima, Toru; Koike, Kazuhiko

2016-04-01

Upper gastrointestinal endoscopy (UGI-ES) and double-contrast upper gastrointestinal barium X-ray radiography (UGI-XR) are two major image-based methods to diagnose atrophic gastritis, which is mostly induced by Helicobacter pylori infection. However, there have been few studies directly comparing them. Atrophic gastritis was evaluated using the data of 962 healthy subjects who underwent UGI-ES and UGI-XR within 1 year. Based on UGI-ES and UGI-XR, 602 subjects did not have atrophic gastritis and 254 subjects did have it. Considering UGI-ES-based atrophic gastritis as the standard, sensitivity and specificity of UGI-XR-based atrophic gastritis were 92.0 % (254/276) and 92.8 % (602/649), respectively. The seven-grade Kimura-Takemoto classification of UGI-ES-based atrophic gastritis showed a strong and significant association with the four-grade UGI-XR-based atrophic gastritis. Sensitivity and specificity of serum anti-Helicobacter pylori IgG to detect UGI-ES/UGI-XR-based atrophic gastritis were 89.4 % (227/254) and 99.8 % (601/602), indicating that atrophic gastritis can be overlooked according to serum anti-Helicobacter pylori IgG alone.

Comparison of two models of hemispheric specialization with unilaterally lesioned patients: material-specific impairment vs response-bias distortion.

PubMed

Guimond, Anik; Braun, Claude M J; Daigneault, Sylvie; Farmer, Jean-Pierre

2013-10-01

Validity of two models of hemispheric specialization was compared. The "material-specific impairment" model was radicalized as postulating that left hemisphere (LH) lesions impair processing of verbal material and that right hemisphere (RH) lesions impair processing of visuospatial material, independently of response-bias distortions. The "response-bias distortion" model was radicalized as postulating that LH lesions distort response style toward omissiveness and that RH lesions distort response style toward commissiveness, regardless of material-specific impairments. Participants had comparable left (N=27) or right (N=24) hemisphere cortical lesions having occurred between birth and early adolescence. Four cognitive neuropsychological tests were adjusted to optimize applicability and comparability of the two theoretical models: Rey Complex Figure, Kimura's Recurring Figures, the Story Recall subtest of the Children's Memory Scale, and the California Verbal Learning Test. Both models significantly, independently, and equally distinguished the LH from the RH patients. Both these forms of hemispheric specialization seemed to be implemented very early in life and very rigidly. Intrahemispheric lesion sites, e.g., frontal vs nonfrontal, held no significant relation to the effects described above. © 2013 Elsevier Inc. All rights reserved.

Cell lines derived from the squash bug, Anasa tristis (Coreidae: Hemiptera).

PubMed

Goodman, Cynthia L; Ringbauer, Joseph A; Li, Yao-Fa; Lincoln, Tamra Reall; Stanley, David

2017-05-01

The squash bug, Anasa tristis, is a pest of cucurbits that exerts direct damage on crops and is a vector of plant pathogens. We established cell lines from this insect to serve as tools for basic biology, including virology and immunology, as well as applied studies, such as insecticide development programs. We initiated 15 cell cultures, using nine media or combinations of media. The media yielding the best results were a modification of Kimura's medium and a combination of two commercially available cell culture media (EX-CELL 420 and L15). We designated the two cell lines as BCIRL-AtE-CLG11 and BCIRL-AtE-CLG15. From the AtE-CLG15 line, we isolated two sub-lines, A and B. Of these, the most consistently replicating line was AtE-CLG15A. We determined the doubling time of this line (190 h) and its mean cell diameter (14.5 ± 0.7 μm). We characterized the AtE-CLG15A line using DAF-PCR. The BCIRL-AtE-CLG15A cell line is now available for researchers world-wide.

Absolute Charge Exchange Cross Sections for ^3He^2+ Collisions with ^4He and H_2

NASA Astrophysics Data System (ADS)

Mawhorter, R. J.; Greenwood, J.; Smith, S. J.; Chutjian, A.

2002-05-01

The JPL charge exchange beam-line(J.B. Greenwood, et al., Phys. Rev A 63), 062707 (2001) was modified to increase the forward acceptance angle and enable the measurement of total charge-exchange cross sections for slow, light, highly-charged ion collisions with neutral targets(R. E. Olson and M. Kimura, J. Phys. B 15), 4231 (1982). Data are presented for single charge exchange cross sections for ^3He^2+ nuclei scattered by ^4He and H2 in the energy range 0.33-4.67 keV/amu. For both targets there is good agreement with Kusakabe, et al.(T. Kusakabe, et al., J. Phys. Soc. Japan 59), 1218 (1990). Angular collection is studied by a comparison with differential measurements(D. Bordenave-Montesquieu and R. Dagnac, J. Phys. B 27), 543 (1994), as well as with earlier JPL results(J.B. Greenwood, et al., Ap. J. 533), L175 (2000), ibid. 529, 605 (2000) using heavier projectiles and targets. This work was carried out at JPL/Caltech, and was supported through contract with NASA. RJM thanks the NRC for a Senior Associateship at JPL.

A comparative study of three tissue-cultured Dendrobium species and their wild correspondences by headspace gas chromatography-mass spectrometry combined with chemometric methods.

PubMed

Chen, Nai-Dong; You, Tao; Li, Jun; Bai, Li-Tao; Hao, Jing-Wen; Xu, Xiao-Yuan

2016-10-01

Plant tissue culture technique is widely used in the conservation and utilization of rare and endangered medicinal plants and it is crucial for tissue culture stocks to obtain the ability to produce similar bioactive components as their wild correspondences. In this paper, a headspace gas chromatography-mass spectrometry method combined with chemometric methods was applied to analyze and evaluate the volatile compounds in tissue-cultured and wild Dendrobium huoshanense Cheng and Tang, Dendrobium officinale Kimura et Migo and Dendrobium moniliforme (Linn.) Sw. In total, 63 volatile compounds were separated, with 53 being identified from the three Dendrobium spp. Different provenances of Dendrobiums had characteristic chemicals and showed remarkable quantity discrepancy of common compositions. The similarity evaluation disclosed that the accumulation of volatile compounds in Dendrobium samples might be affected by their provenance. Principal component analysis showed that the first three components explained 85.9% of data variance, demonstrating a good discrimination between samples. Gas chromatography-mass spectrometry techniques, combined with chemometrics, might be an effective strategy for identifying the species and their provenance, especially in the assessment of tissue-cultured Dendrobium quality for use in raw herbal medicines. Copyright © 2016. Published by Elsevier B.V.

Total cross sections for positron scattering from benzene, cyclohexane, and aniline

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zecca, Antonio; Moser, Norberto; Perazzolli, Chiara

2007-08-15

We use a linear transmission technique to measure total cross sections for positron scattering from benzene, cyclohexane, and aniline. In the case of cyclohexane, the energy range of the present study is 0.1-20 eV, while for benzene and aniline it is 0.2-20 eV. With respect to benzene and cyclohexane, comparison is made to the only other existing results we know of [Makochekanwa and co-workers, Phys. Rev. A 68, 032707 (2003); 72, 042705 (2005)]. Agreement with those data is only marginal, being particularly poor at the overlap lower energies. Unlike Kimura et al. [J. Phys. B 37, 1461 (2004)], we findmore » the low-energy dependence of the positron-benzene total cross sections to be qualitatively similar to those found in the electron channel [Gulley et al., J. Phys. B 31, 2735 (1998)]. We believe that the present positron-aniline total cross sections represent the first time such data have been measured. These cross sections are almost identical to those we found for benzene, suggesting that substitution of hydrogen by the amine group on the aromatic ring is largely irrelevant to the scattering process in the energy regimes considered.« less

A light-driven proton pump from Haloterrigena turkmenica: Functional expression in Escherichia coli membrane and coupling with a H{sup +} co-transporter

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kamo, Naoki; Hashiba, Tsuyoshi; Kikukawa, Takashi

2006-03-10

A gene encoding putative retinal protein was cloned from Haloterrigena turkmenica (JCM9743). The deduced amino acid sequence was most closely related to that of deltarhodopsin, which functions as a light-driven H{sup +} pump and was identified in a novel strain Haloterrigena sp. arg-4 (K. Ihara, T. Uemura, I. Katagiri, T. Kitajima-Ihara, Y. Sugiyama, Y. Kimura, Y. Mukohata, Evolution of the archaeal rhodopsins: Evolution rate changes by gene duplication and functional differentiation, J. Mol. Biol. 285 (1999) 163-174. GenBank Accession No. AB009620). Thus, we called the present protein H. turkmenica deltarhodopsin (HtdR) in this report. Differing from the Halobacterium salinarum bacteriorhodopsinmore » (bR), functional expression of HtdR was achieved in Escherichia coli membrane with a high yield of 10-15mg protein/L culture. The photocycle of purified HtdR was similar to that of bR. The photo-induced electrogenic proton pumping activity of HtdR was verified. We co-expressed both HtdR and EmrE, a proton-coupled multi-drug efflux transporter in E. coli, and the cells successfully extruded ethidium, a substrate of EmrE, on illumination.« less

DNA barcoding of freshwater fishes and the development of a quantitative qPCR assay for the species-specific detection and quantification of fish larvae from plankton samples.

PubMed

Loh, W K W; Bond, P; Ashton, K J; Roberts, D T; Tibbetts, I R

2014-08-01

The barcoding of mitochondrial cytochrome c oxidase subunit 1 (coI) gene was amplified and sequenced from 16 species of freshwater fishes found in Lake Wivenhoe (south-eastern Queensland, Australia) to support monitoring of reservoir fish populations, ecosystem function and water health. In this study, 630-650 bp sequences of the coI barcoding gene from 100 specimens representing 15 genera, 13 families and two subclasses of fishes allowed 14 of the 16 species to be identified and differentiated. The mean ± s.e. Kimura 2 parameter divergence within and between species was 0.52 ± 0.10 and 23.8 ± 2.20% respectively, indicating that barcodes can be used to discriminate most of the fish species accurately. The two terapontids, Amniataba percoides and Leiopotherapon unicolor, however, shared coI DNA sequences and could not be differentiated using this gene. A barcoding database was established and a qPCR assay was developed using coI sequences to identify and quantify proportional abundances of fish species in ichthyoplankton samples from Lake Wivenhoe. These methods provide a viable alternative to the time-consuming process of manually enumerating and identifying ichthyoplankton samples. © 2014 The Fisheries Society of the British Isles.

DNA barcoding for identifying synanthropic flesh flies (Diptera, Sarcophagidae) of Colombia.

PubMed

Buenaventura, Eliana; Valverde-Castro, César; Wolff, Marta; Triana-Chavez, Omar; Gómez-Palacio, Andrés

2018-06-01

The first step for a successful use of any insect as indicator in forensic sciences is providing a precise taxonomic identification at species level. Due to morphology-based identification of Sarcophaginae flies (Diptera, Sarcophagidae) is often difficult and requires strong taxonomic expertise, their use as forensic indicators has been limited. Consequently, molecular-based approaches have been accepted as alternative means of identification. Thus, we aimed testing the efficiency of the barcode region of the mitochondrial cytochrome oxidase subunit I (COI) gene for identification of synanthropic flesh flies of several species of the genera Peckia, Oxysarcodexia, Ravinia, and Tricharaea collected in Colombia. The 645-bp fragment of COI was amplified and aligned (215 parsimoniously informative variable sites). We calculated Kimura two-parameter genetic distances and reconstruct a Neighbor-Joining phylogenetic tree. Our Neighbor-Joining tree recovered all species as monophyletic, and confirmed a new species of the genus Ravinia as also indicated by the interspecific genetic divergences and morphological observations. We obtained a 100% of identification success. Thus, the COI barcodes showed efficiency as an alternative mean of identification of species of flesh flies collected on decaying organic matter in Colombia. Copyright © 2018 Elsevier B.V. All rights reserved.

Clustering and Phase Transitions on a Neutral Landscape

NASA Astrophysics Data System (ADS)

Scott, Adam; King, Dawn; Maric, Nevena; Bahar, Sonya

2012-02-01

The problem of speciation and species aggregation on a neutral landscape, subject to random mutational fluctuations rather than selective drive, has been a focus of research since the seminal work of Kimura on genetic drift. These ideas have received increased attention due to the more recent development of a neutral ecological theory by Hubbell. De Aguiar et al. recently demonstrated, in a computational model, that speciation can occur under neutral conditions; this study bears some comparison with more mathematical studies of clustering on neutral landscapes in the context of branching and annihilating random walks. Here, we show that clustering can occur on a neutral landscape where the dimensions specify the simulated organisms' phenotypes. Unlike the De Aguiar et al. model, we simulate sympatric speciation: the organisms cluster phenotypically, but are not spatially separated. Moreover, we find that clustering occurs not only in the case of assortative mating, but also in the case of asexual fission. Clustering is not observed in a control case where organisms can mate randomly. We find that the population size and the number of clusters undergo phase-transition-like behavior as the maximum mutation size is varied.

Chemical properties and antioxidant activity of a water-soluble polysaccharide from Dendrobium officinale.

PubMed

Luo, Qiu-Lian; Tang, Zhuan-Hui; Zhang, Xue-Feng; Zhong, Yong-Hong; Yao, Su-Zhi; Wang, Li-Sheng; Lin, Cui-Wu; Luo, Xuan

2016-08-01

In this report, a water-soluble polysaccharide was obtained from the dried stems of Dendrobium officinale Kimura et Migo by hot-water (70-75°C) extraction and 85% ethanol precipitation, and successively purification by DEAE-cellulose anion-exchange chromatography and gel-permeation chromatography. The D. officinale polysaccharide (DOP) has a molecular weight of 8500Da. Monosaccharide composition analysis reveals that DOP is composed of mannose, glucose, and arabinose with a trace of galacturonic acid in a molar ratio of 6.2:2.3:2.1:0.1. Periodate oxidation-smith degradation and 1D and 2D NMR spectroscopy analysis suggest the predominance of mannose and glucose, and it contains a 2-O-acetylglucomannan and (1→4)-linked-β-d-mannopyranosyl and (1→4)-linked-β-d-glucopyranosyl residues. Atomic force microscope shows that DOP mainly exists as rod-shaped chains, supporting high degrees of polymerization. The antioxidant activities of the polysaccharide in vitro assay indicate that DOP has good scavenging activity of 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical, higher scavenging activity of hydroxyl radical, and metal chelating activities. Copyright © 2016 Elsevier B.V. All rights reserved.

The Genome of Dendrobium officinale Illuminates the Biology of the Important Traditional Chinese Orchid Herb.

PubMed

Yan, Liang; Wang, Xiao; Liu, Hui; Tian, Yang; Lian, Jinmin; Yang, Ruijuan; Hao, Shumei; Wang, Xuanjun; Yang, Shengchao; Li, Qiye; Qi, Shuai; Kui, Ling; Okpekum, Moses; Ma, Xiao; Zhang, Jiajin; Ding, Zhaoli; Zhang, Guojie; Wang, Wen; Dong, Yang; Sheng, Jun

2015-06-01

Dendrobium officinale Kimura et Migo is a traditional Chinese orchid herb that has both ornamental value and a broad range of therapeutic effects. Here, we report the first de novo assembled 1.35 Gb genome sequences for D. officinale by combining the second-generation Illumina Hiseq 2000 and third-generation PacBio sequencing technologies. We found that orchids have a complete inflorescence gene set and have some specific inflorescence genes. We observed gene expansion in gene families related to fungus symbiosis and drought resistance. We analyzed biosynthesis pathways of medicinal components of D. officinale and found extensive duplication of SPS and SuSy genes, which are related to polysaccharide generation, and that the pathway of D. officinale alkaloid synthesis could be extended to generate 16-epivellosimine. The D. officinale genome assembly demonstrates a new approach to deciphering large complex genomes and, as an important orchid species and a traditional Chinese medicine, the D. officinale genome will facilitate future research on the evolution of orchid plants, as well as the study of medicinal components and potential genetic breeding of the dendrobe. Copyright © 2015 The Author. Published by Elsevier Inc. All rights reserved.

Effects of Exogenous Gibberellic Acid3 on Iron and Manganese Plaque Amounts and Iron and Manganese Uptake in Rice

PubMed Central

Guo, Yue; Zhu, Changhua; Gan, Lijun; Ng, Denny; Xia, Kai

2015-01-01

Gibberellins (GA) regulate various components of plant development. Iron and Mn plaque result from oxiding and hydroxiding Fe and Mn, respectively, on the roots of aquatic plant species such as rice (Oryza sativa L.). In this study, we found that exogenous gibberellic acid3 (GA3) spray decreased Fe plaque, but increased Mn plaque, with applications of Kimura B nutrient solution. Similar effects from GA3, leading to reduced Fe plaque and increased Mn plaque, were also found by scanning electron microscopy and energy dispersive X-ray spectrometric microanalysis. Reduced Fe plaque was observed after applying GA3 to the groups containing added Fe2+ (17 and 42 mg•L-1) and an increasing trend was detected in Mn plaques of the Mn2+ (34 and 84 mg•L-1) added treatments. In contrast, an inhibitor of GA3, uniconazole, reversed the effects of GA3. The uptake of Fe or Mn in rice plants was enhanced after GA3 application and Fe or Mn plaque production. Strong synergetic effects of GA3 application on Fe plaque production were detected. However, no synergetic effects on Mn plaque production were detected. PMID:25710173

DNA barcoding for identification of sand fly species (Diptera: Psychodidae) from leishmaniasis-endemic areas of Peru.

PubMed

Nzelu, Chukwunonso O; Cáceres, Abraham G; Arrunátegui-Jiménez, Martín J; Lañas-Rosas, Máximo F; Yañez-Trujillano, Henrry H; Luna-Caipo, Deysi V; Holguín-Mauricci, Carlos E; Katakura, Ken; Hashiguchi, Yoshihisa; Kato, Hirotomo

2015-05-01

Phlebotomine sand flies are the only proven vectors of leishmaniases, a group of human and animal diseases. Accurate knowledge of sand fly species identification is essential in understanding the epidemiology of leishmaniasis and vector control in endemic areas. Classical identification of sand fly species based on morphological characteristics often remains difficult and requires taxonomic expertise. Here, we generated DNA barcodes of the cytochrome c oxidase subunit 1 (COI) gene using 159 adult specimens morphologically identified to be 19 species of sand flies, belonging to 6 subgenera/species groups circulating in Peru, including the vector species. Neighbor-joining (NJ) analysis based on Kimura 2-Parameter genetic distances formed non-overlapping clusters for all species. The levels of intraspecific genetic divergence ranged from 0 to 5.96%, whereas interspecific genetic divergence among different species ranged from 8.39 to 19.08%. The generated COI barcodes could discriminate between all the sand fly taxa. Besides its success in separating known species, we found that DNA barcoding is useful in revealing population differentiation and cryptic diversity, and thus promises to be a valuable tool for epidemiological studies of leishmaniasis. Copyright © 2015 Elsevier B.V. All rights reserved.

Laser surgery and medicine including photodynamic therapy in China today

NASA Astrophysics Data System (ADS)

Li, Junheng

2000-10-01

The development of laser medicine in China is correlated with the development of laser science in China. After the first Chinese laser, ruby laser came into being in 1961, Chinese medical scientists began to do the studies about laser medicine in the middle 1960s. For example, ruby laser was adopted for the retina coagulation experiment in 1965. Since 1970s, through the free choice of utilizing Co2, He-Ne, Nd:YAG argon, ruby lasers, laser surgery and medicine has been widely applied to the treatment for diseases of the eyes, ENT, dermatology, surgery, gynecology, tumors and diseases suitable to physical therapy or acupuncture with satisfactory effects. In June 1977, a nation-wide laser medicine symposium was held at Wuhan, Hubei Province with 200 participants including medical doctors and laser technologies from 23 provinces and municipal towns. Till the end of seventies, utilization of lasers has been extended to Nd glass laser, N laser and tunable dye lasers. The scope covered most of the clinical sections. After Dr. Thomas J. Dougherty developed the PDT for cancers in Roswell Park Memorial Institute in Buffalo in late 1970s and Professor Yoshihiro Hayata successfully applied the PDT in clinical treatment for lung cancer in 1980, Chinese pharmacists successfully produced the Chinese HpD and the first case of PDT, a lower eyelid basal cell carcinoma patient was treated with the Chinese laser equipment in 1981 in Beijing. Its success brought attention establishing a research group supported by the government in 1982. The members of the group consisted the experts on preclinical and clinical research, pharmaceutical chemistry, laser physicists and technologists. A systemic research on PDT was then carried out and obvious result was achieved. The step taken for PDT also accelerated the researchers on other kinds of laser medicine and surgery because the medical doctors had begun to master the knowledge about laser science. The prosperous situation of rapid

Measurements of interfacial thermal contact conductance between pressed alloys at low temperatures

NASA Astrophysics Data System (ADS)

Zheng, Jiang; Li, Yanzhong; Chen, Pengwei; Yin, Geyuan; Luo, Huaihua

2016-12-01

Interfacial thermal contact conductance is the primary factor limiting the heat transfer in many cryogenic engineering applications. This paper presents an experimental apparatus to measure interfacial thermal contact conductance between pressed alloys in a vacuum environment at low temperatures. The measurements of thermal contact conductance between pressed alloys are conducted by using the developed apparatus. The results show that the contact conductance increases with the decrease of surface roughness, the increase of interface temperature and contact pressure. The temperature dependence of thermal conductivity and mechanical properties is analyzed to explain the results. Thermal contact conductance of a pair of stainless steel specimens is obtained in the interface temperature range of 135-245 K and in the contact pressure range of 1-9 MPa. The results are regressed as a power function of temperature and load. Thermal conductance is also obtained between aluminums as well as between stainless steel and aluminum. The load exponents of the regressed relations for different contacts are compared. Existing theoretical models (the Cooper-Mikic-Yovanovich plastic model, the Mikic elastic model and the improved Kimura model) are reviewed and compared with the experimental results. The Cooper-Mikic-Yovanovich model predictions are found to be in good agreement with experimental results, especially with measurements between aluminums.

Rooster comb hyaluronate-protein, a non-covalently linked complex.

PubMed Central

Tsiganos, C P; Vynios, D H; Kalpaxis, D L

1986-01-01

Hyaluronate from rooster comb was isolated by ion-exchange chromatography on DEAE-cellulose from tissue extracts and papain digests. The preparations were labelled with [14C]acetic anhydride and subjected to CsCl-density-gradient centrifugation in 4 M-guanidinium chloride in the presence and absence of 4% ZwittergentTM 3-12. A radioactive protein fraction was separated from the hyaluronate when the zwitterionic detergent was also present. The protein could also be separated from the glycosaminoglycan by chromatography on Sepharose CL-6B eluted with the same solvent mixture. The protein fraction contained three protein bands of Mr 15,000-17,000 as assessed by polyacrylamide-gel electrophoresis in 0.1% SDS, and seemed to lack lysozyme activity. No evidence of other protein or amino acid(s) covalently linked with the hyaluronate was obtained. The hyaluronate-protein complex may be re-formed upon mixing the components, the extent of its formation depending on the conditions used. The results show that, as in chondrosarcoma [Mason, d'Arville, Kimura & Hascall (1982) Biochem. J. 207, 445-457] and teratocarcinoma cells [Prehm (1983) Biochem. J. 211, 191-198] the rooster comb hyaluronate also is not linked covalently to a core protein. PMID:3741374

Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics.

PubMed

Dutheil, Julien; Gaillard, Sylvain; Bazin, Eric; Glémin, Sylvain; Ranwez, Vincent; Galtier, Nicolas; Belkhir, Khalid

2006-04-04

A large number of bioinformatics applications in the fields of bio-sequence analysis, molecular evolution and population genetics typically share input/output methods, data storage requirements and data analysis algorithms. Such common features may be conveniently bundled into re-usable libraries, which enable the rapid development of new methods and robust applications. We present Bio++, a set of Object Oriented libraries written in C++. Available components include classes for data storage and handling (nucleotide/amino-acid/codon sequences, trees, distance matrices, population genetics datasets), various input/output formats, basic sequence manipulation (concatenation, transcription, translation, etc.), phylogenetic analysis (maximum parsimony, markov models, distance methods, likelihood computation and maximization), population genetics/genomics (diversity statistics, neutrality tests, various multi-locus analyses) and various algorithms for numerical calculus. Implementation of methods aims at being both efficient and user-friendly. A special concern was given to the library design to enable easy extension and new methods development. We defined a general hierarchy of classes that allow the developer to implement its own algorithms while remaining compatible with the rest of the libraries. Bio++ source code is distributed free of charge under the CeCILL general public licence from its website http://kimura.univ-montp2.fr/BioPP.

DNA Barcoding of Freshwater Fishes of Indo-Myanmar Biodiversity Hotspot.

PubMed

Barman, Anindya Sundar; Singh, Mamta; Singh, Soibam Khogen; Saha, Himadri; Singh, Yumlembam Jackie; Laishram, Martina; Pandey, Pramod Kumar

2018-06-05

To develop an effective conservation and management strategy, it is required to assess the biodiversity status of an ecosystem, especially when we deal with Indo-Myanmar biodiversity hotspot. Importance of this reaches to an entirely different level as the hotspot represents the area of high endemism which is under continuous threat. Therefore, the need of the present study was conceptualized, dealing with molecular assessment of the fish fauna of Indo-Myanmar region, which covers the Indian states namely, Manipur, Meghalaya, Mizoram, and Nagaland. A total of 363 specimens, representing 109 species were collected and barcoded from the different rivers and their tributaries of the region. The analyses performed in the present study, i.e. Kimura 2-Parameter genetic divergence, Neighbor-Joining, Automated Barcode Gap Discovery and Bayesian Poisson Tree Processes suggest that DNA barcoding is an efficient and reliable tool for species identification. Most of the species were clearly delineated. However, presence of intra-specific and inter-specific genetic distance overlap in few species, revealed the existence of putative cryptic species. A reliable DNA barcode reference library, established in our study provides an adequate knowledge base to the groups of non-taxonomists, researchers, biodiversity managers and policy makers in sketching effective conservation measures for this ecosystem.

Distinguishing the Chinese materia medica Tiepishihu from similar Dendrobium species of the same genus using histological and microscopic method.

PubMed

Yu, Kun-Zi; Yan, Hua; Tai, Hai-Chuan; Zhang, Nan-Ping; Cheng, Xian-Long; Guo, Zeng-Xi; Ma, Shuang-Cheng; Wei, Feng

2017-07-01

The Chinese Materia Medica, Tiepishihu, used as a tonic for over one thousand years, is a well-known precious medicine in China. According to the Chinese Pharmacopoeia, its source is the species Dendrobium officinale Kimura et Migo, which is distinguished from other species in Dendrobium genus. However, these species from the same genus are similar with Tiepishihu and caused confusion in the market. To find a quick and simple method to distinguish Tiepishihu from other similar species, histologic and microscopic methods were combined together to investigate the transverse section of stem of Tiepishihu and other similar species. Phloroglucinol test solution with hydrochloric acid was used to reveal the lignified tissue by staining the transverse section of Tiepishihu and similar species. Results revealed the unique identification characteristics to distinguish Tiepishihu from similar species, which were difficult to distinguish by other methods. The identification characteristics of Tiepishihu include the cells of vascular bundle sheath were stained red, parenchyma cells were not stained red. What's more, other species can be distinguished from each other with microscopic and histological characteristics. These characteristics proved stable and can be easily observed by normal light microscopic examination. This method is rapid, accurate, stable, and inexpensive. © 2017 Wiley Periodicals, Inc.

Magnetic structures and excitations in a multiferroic Y-type hexaferrite BaSrCo2Fe11AlO22

NASA Astrophysics Data System (ADS)

Nakajima, Taro; Tokunaga, Yusuke; Matsuda, Masaaki; Dissanayake, Sachith; Fernandez-Baca, Jaime; Kakurai, Kazuhisa; Taguchi, Yasujiro; Tokura, Yoshinori; Arima, Taka-hisa

2016-11-01

We have investigated magnetic orders and excitations in a Y-type hexaferrite BaSrCo2Fe11AlO22 (BSCoFAO), which was reported to exhibit spin-driven ferroelectricity at room temperature [S. Hirose, K. Haruki, A. Ando, and T. Kimura, Appl. Phys. Lett. 104, 022907 (2014), 10.1063/1.4862432]. By means of magnetization, electric polarization, and neutron-diffraction measurements using single-crystal samples, we establish a H -T magnetic phase diagram for magnetic field perpendicular to the c axis (H⊥c). This system exhibits an alternating longitudinal conical (ALC) magnetic structure in the ground state, and it turns into a non-co-planar commensurate magnetic order with spin-driven ferroelectricity under H⊥c. The field-induced ferroelectric phase remains as a metastable state after removing magnetic field below ˜250 K. This metastability is the key to understanding of magnetic field reversal of the spin-driven electric polarization in this system. Inelastic polarized neutron-scattering measurements in the ALC phase reveal a magnetic excitation at around 7.5 meV, which is attributed to spin components oscillating in a plane perpendicular to the cone axis. This phasonlike excitation is expected to be an electric-field active magnon, i.e., electromagnon excitation, in terms of the magnetostriction mechanism.

Numerical investigation of shape domain effect to its elasticity and surface energy using adaptive finite element method

NASA Astrophysics Data System (ADS)

Alfat, Sayahdin; Kimura, Masato; Firihu, Muhammad Zamrun; Rahmat

2018-05-01

In engineering area, investigation of shape effect in elastic materials was very important. It can lead changing elasticity and surface energy, and also increase of crack propagation in the material. A two-dimensional mathematical model was developed to investigation of elasticity and surface energy in elastic material by Adaptive Finite Element Method. Besides that, behavior of crack propagation has observed for every those materials. The government equations were based on a phase field approach in crack propagation model that developed by Takaishi-Kimura. This research has varied four shape domains where physical properties of materials were same (Young's modulus E = 70 GPa and Poisson's ratio ν = 0.334). Investigation assumptions were; (1) homogeneous and isotropic material, (2) there was not initial cracking at t = 0, (3) initial displacement was zero [u1, u2] = 0) at initial condition (t = 0), and (4) length of time simulation t = 5 with interval Δt = 0.005. Mode I/II or mixed mode crack propagation has been used for the numerical investigation. Results of this studies were very good and accurate to show changing energy and behavior of crack propagation. In the future time, this research can be developed to complex phenomena and domain. Furthermore, shape optimization can be investigation by the model.

Applying ecological models to communities of genetic elements: the case of neutral theory.

PubMed

Linquist, Stefan; Cottenie, Karl; Elliott, Tyler A; Saylor, Brent; Kremer, Stefan C; Gregory, T Ryan

2015-07-01

A promising recent development in molecular biology involves viewing the genome as a mini-ecosystem, where genetic elements are compared to organisms and the surrounding cellular and genomic structures are regarded as the local environment. Here, we critically evaluate the prospects of ecological neutral theory (ENT), a popular model in ecology, as it applies at the genomic level. This assessment requires an overview of the controversy surrounding neutral models in community ecology. In particular, we discuss the limitations of using ENT both as an explanation of community dynamics and as a null hypothesis. We then analyse a case study in which ENT has been applied to genomic data. Our central finding is that genetic elements do not conform to the requirements of ENT once its assumptions and limitations are made explicit. We further compare this genome-level application of ENT to two other, more familiar approaches in genomics that rely on neutral mechanisms: Kimura's molecular neutral theory and Lynch's mutational-hazard model. Interestingly, this comparison reveals that there are two distinct concepts of neutrality associated with these models, which we dub 'fitness neutrality' and 'competitive neutrality'. This distinction helps to clarify the various roles for neutral models in genomics, for example in explaining the evolution of genome size. © 2015 John Wiley & Sons Ltd.

Dendrobium officinale Prevents Early Complications in Streptozotocin-Induced Diabetic Rats

PubMed Central

Hou, Shao-zhen; Liang, Chu-yan; Liu, Hua-zhen; Zhu, Dong-mei; Wu, Ya-yun; Liang, Jian; Zhao, Ya; Guo, Jian-ru; Huang, Song; Lai, Xiao-Ping

2016-01-01

Background. Dendrobium officinale (DO) Kimura et Migo is a precious Chinese herb that is considered beneficial for health due to its antioxidant and antidiabetes properties, and so on. In this research, we try to determine the preventive effect of DO on the early complications of STZ-induced diabetic rats. Methods. Type 1 diabetic rats were produced with a single intraperitoneal injection of STZ (50 mg/kg). DO (1 g/kg/day) was then orally administered for 5 weeks. Blood glucose, TC, TG, BUN, CREA, and GSH-PX levels were determined, and electroretinographic activity and hypoalgesia were investigated. Pathological sections of the eyes, hearts, aortas, kidneys, and livers were analyzed. Results. Treatment with DO significantly attenuated the serum levels of TC, TG, BUN, and CREA, markedly increased the amplitudes of ERG a- and b-waves and Ops, and reduced the hypoalgesia and histopathological changes of vital organs induced by hyperglycemia. The protective effect of DO in diabetic rats may be associated with its antioxidant activity, as evidenced by the marked increase in the serum level of glutathione peroxidase. However, DO had no significant effect on blood glucose levels and bodyweight of diabetic rats. Conclusions. DO supplementation is an effective treatment to prevent STZ-induced diabetic complications. PMID:27034693

Granularity and Laxative Effect of Ultrafine Powder of Dendrobium officinale.

PubMed

Luo, DanDan; Qu, Chao; Zhang, ZhenBiao; Xie, JianHui; Xu, LieQiang; Yang, HongMei; Li, CaiLan; Lin, GuoSheng; Wang, HongFeng; Su, ZiRen

2017-02-01

Constipation is a common disorder that is a significant source of morbidity among people around the world ranging from 2% to 28%. Dendrobium officinale Kimura et Migo is a traditional herbal medicine and health food used for tonicity of the stomach and promotion of body fluid production in China. This study aimed to prepare the ultrafine powder of Dendrobium officinale (UDO) and investigate its laxative effect and potential mechanism in mice with diphenoxylate-induced constipation. Results indicated that the mean diameter (d 50 ) of UDO obtained by ball milling was 6.56 μm. UDO (62.5, 125, and 250 mg/kg, p.o.) could significantly enhance the gastrointestinal transit ratio and promote fecal output. Moreover, UDO treatment resulted in significant increases in the serum levels of acetylcholinesterase (AChE), gastrin (Gas), motilin (MTL), and substance P (SP), and obviously decreased serum contents of somatostatin (SS). Taken together, UDO, which can be easily obtained through milling to a satisfactory particle size, exhibited obvious laxative effect in diphenoxylate-induced constipated mice, and the mechanism might be associated with elevated levels of AChE, Gas, MTL, SP, and reduced production of SS. UDO has the potential for further development into an alternative effective diet therapy for constipation.

DNA barcoding commercially important aquatic invertebrates of Turkey.

PubMed

Keskin, Emre; Atar, Hasan Hüseyin

2013-08-01

DNA barcoding was used in order to identify aquatic invertebrates sampled from fisheries bycatch and discards. A total of 440 unique cytochrome c oxidase sub unit I (COI) barcodes were generated for 22 species from three important phyla (Arthropoda, Cnidaria, and Mollusca). All the species were sequenced and submitted to GenBank and Barcode of Life Database (BOLD) databases using 654 bp-long fragment of mitochondrial COI gene. Two of them (Pontastacus leptodactylus and Rapana bezoar) were first records of the species for the BOLD database and six of them (Carcinus aestuarii, Loligo vulgaris, Melicertus kerathurus, Nephrops norvegicus, Scyllarides latus, and Scyllarus arctus) were first standard (>648 bp) COI barcode records for the GenBank database. COI barcodes were analyzed for nucleotide composition, nucleotide pair frequencies, and Kimura's two-parameter genetic distance. Mean genetic distance among species was found increasing at higher taxonomic levels. Neighbor-joining trees generated were congruent with morphometric-based taxonomic classification. Findings of this study clearly demonstrate that DNA barcodes could be used as an efficient molecular tool in identification of not only target species from fisheries but also bycatch and discard species, and so it could provide us leverage for a better understanding in monitoring and management of fisheries and biodiversity.

RNAmutants: a web server to explore the mutational landscape of RNA secondary structures

PubMed Central

Waldispühl, Jerome; Devadas, Srinivas; Berger, Bonnie; Clote, Peter

2009-01-01

The history and mechanism of molecular evolution in DNA have been greatly elucidated by contributions from genetics, probability theory and bioinformatics—indeed, mathematical developments such as Kimura's neutral theory, Kingman's coalescent theory and efficient software such as BLAST, ClustalW, Phylip, etc., provide the foundation for modern population genetics. In contrast to DNA, the function of most noncoding RNA depends on tertiary structure, experimentally known to be largely determined by secondary structure, for which dynamic programming can efficiently compute the minimum free energy secondary structure. For this reason, understanding the effect of pointwise mutations in RNA secondary structure could reveal fundamental properties of structural RNA molecules and improve our understanding of molecular evolution of RNA. The web server RNAmutants provides several efficient tools to compute the ensemble of low-energy secondary structures for all k-mutants of a given RNA sequence, where k is bounded by a user-specified upper bound. As we have previously shown, these tools can be used to predict putative deleterious mutations and to analyze regulatory sequences from the hepatitis C and human immunodeficiency genomes. Web server is available at http://bioinformatics.bc.edu/clotelab/RNAmutants/, and downloadable binaries at http://rnamutants.csail.mit.edu/. PMID:19531740

[Management of adverse effects with antituberculosis chemotherapy].

PubMed

Tsuyuguchi, Kazunari; Wada, Masako

2011-02-01

Tuberculosis has now become a curable disease with chemotherapy. So it is natural that the present issues in tuberculosis management are focused on how to complete standard chemotherapy. In this context, management of adverse effects constitutes an essential part of antituberculosis chemotherapy, as well as directly observed therapy. In this symposium, discussions were held about three major subjects on this issue. First, hepatotoxicity develops frequently and has sometimes fatal outcome, which makes it the most problematic adverse effect. "Management of hepatotoxicity during antituberculosis chemotherapy" was published by the Japanese Society for Tuberculosis (JST) in 2006. Dr. Shinsho Yoshiba evaluated this recommendation and pointed out that the criteria for discontinuation of drug based on AST, ALT and bilirubin levels is too sensitive and the concept of predicting fulminant hepatic failure (FHF) is lacking. He stressed the importance of monitoring serum prothrombin time for predicting FHF. Next, allergic drug reaction such as fever or skin rash often causes distress, although rarely fatal. As isoniazid (INH) and rifampicin (RFP) are key drugs for the cure, readministration of these drugs is often attempted by desensitization therapy. "Recommendation about desensitization therapy of antituberculosis drugs" was also published by JST in 1997. Dr. Yoshihiro Kobashi reported high success rates of 79 percent for INH and 75 percent for RFP according to this recommendation. He also reported correlated factor with the success, such as the longer period from the discontinuation to the desensitization therapy and lower doses of drugs at starting desensitization. Finally, we sometimes experience transient worsening of radiographical findings and general symptoms during antituberculosis chemotherapy. This is presumed to be due to allergic reaction to dead bacilli without requiring discontinuation of the drug. Differential diagnosis includes drug-induced pneumonia requring

Hiperplasia angiolinfoide com eosinofilia: um caso raro em cavidade oral

PubMed Central

Tenório, Jefferson da Rocha; Gonzaga, Amanda Katarinny Goes; Gonçalves, Patrícia Guerra Peixe; de Oliveira, Denise Hélen Imaculada Pereira; Queiroz, Lélia Maria Guedes

2016-01-01

Resumo A hiperplasia angiolinfoide com eosinofilia (HALE) é considerada uma lesão vascular benigna rara que acomete, principalmente, o tecido cutâneo e subcutâneo da região de cabeça e pescoço, mas incomum na cavidade oral. Sua etiopatogenia permanece indefinida, sendo descrita como proliferação vascular reacional, malformação vascular ou neoplasia. Tem como principal diagnóstico diferencial a doença de Kimura. Este trabalho relata um caso de um paciente do sexo masculino, de 50 anos, que exibia aumento de volume nodular na mucosa do lábio superior, com 3 cm de dimensão e 7 anos de evolução. Após a biópsia excisional, o exame histopatológico mostrou lesão bem encapsulada multilobulada com proliferação de capilares sanguíneos com células endoteliais de aspecto epitelioide, infiltrado inflamatório difuso com linfócitos, plasmócitos, inúmeros eosinófilos e presença de folículos linfoides. A análise imuno-histoquímica revelou positividade para CD34 e Ki-67, o que, juntamente com o exame morfológico, direcionou o diagnóstico para HALE. PMID:29930611

[Discussion on the botanical origin of Isatidis radix and Isatidis folium based on DNA barcoding].

PubMed

Sun, Zhi-Ying; Pang, Xiao-Hui

2013-12-01

This paper aimed to investigate the botanical origins of Isatidis Radix and Isatidis Folium, and clarify the confusion of its classification. The second internal transcribed spacer (ITS2) of ribosomal DNA, the chloroplast matK gene of 22 samples from some major production areas were amplified and sequenced. Sequence assembly and consensus sequence generation were performed using the CodonCode Aligner. Phylogenetic study was performed using MEGA 4.0 software in accordance with the Kimura 2-Parameter (K2P) model, and the phylogenetic tree was constructed using the neighbor-joining methods. The results showed that the length of ITS2 sequence of the botanical origins of Isatidis Radix and Isatidis Folium was 191 bp. The sequence showed that some samples had several SNP sites, and some samples had heterozygosis sites. In the NJ tree, based on ITS2 sequence, the studied samples were separated into two groups, and one of them was gathered with Isatis tinctoria L. The studied samples also were divided into two groups obviously based on the chloroplast matK gene. In conclusion, our results support that the botanical origins of Isatidis Radix and Isatidis Folium are Isatis indigotica Fortune, and Isatis indigotica and Isatis tinctoria are two distinct species. This study doesn't support the opinion about the combination of these two species in Flora of China.

Personalized immune-interception of cancer and the battle of two adaptive systems--when is the time right?

PubMed

Dhodapkar, Madhav V

2013-03-01

A growing body of evidence points to a coevolutionary model of cancer, wherein the cross-talk between tumor cells (or their subclones) and the host determine the malignant potential of individual tumors. Most of this natural history is clinically invisible and includes preneoplastic states. The capacity of the immune system to recognize these incipient lesions provides the basis for targeting them immunologically to arrest the development of preneoplasia toward clinical cancer. Kimura and colleagues provide evidence of immunogenicity of a potential cancer vaccine in patients with a history of advanced colon adenomas. These studies provide proof-of-principle or feasibility of such an approach in the clinic. Here, we discuss emerging opportunities and challenges in harnessing the immune system to "intercept" the precursor or preneoplastic lesions. Both cancer cells as well as the immune system represent independent and complex systems with plasticity and adaptive potential. It is therefore likely that specific aspects of the cross-talk between tumor cells and host may differ between individual tumors and determine the evolution of both tumors and the host response. We try to make the case to consider individualized approaches based on the genetic make-up of tumor cells and properties of the host response. Such strategies may be needed to optimally position the immune system to prevent cancers. ©2013 AACR.

Regulation of photochemical energy transfer accompanied by structural changes in thylakoid membranes of heat-stressed wheat.

PubMed

Marutani, Yoko; Yamauchi, Yasuo; Miyoshi, Akihito; Inoue, Kanako; Ikeda, Ken-ichi; Mizutani, Masaharu; Sugimoto, Yukihiro

2014-12-11

Photosystems of higher plants alleviate heat-induced damage in the presence of light under moderate stressed conditions; however, in the absence of light (i.e., in the dark), the same plants are damaged more easily. (Yamauchi and Kimura, 2011) We demonstrate that regulating photochemical energy transfer in heat-treated wheat at 40 °C with light contributed to heat tolerance of the photosystem. Chlorophyll fluorescence analysis using heat-stressed wheat seedlings in light showed increased non-photochemical quenching (NPQ) of chlorophyll fluorescence, which was due to thermal dissipation that was increased by state 1 to state 2 transition. Transmission electron microscopy revealed structural changes in thylakoid membranes, including unstacking of grana regions under heat stress in light. It was accompanied by the phosphorylation of thylakoid proteins such as D1 and D2 proteins and the light harvesting complex II proteins Lhcb1 and Lhcb2. These results suggest that heat stress at 40 °C in light induces state 1 to state 2 transition for the preferential excitation of photosystem I (PSI) by phosphorylating thylakoid proteins more strongly. Structural changes of thylakoid membrane also assist the remodeling of photosystems and regulation of energy distribution by transition toward state 2 probably contributes to plastoquione oxidation; thus, light-driven electrons flowing through PSI play a protective role against PSII damage under heat stress.

Cytochrome b gene reveals panmixia among Japanese Threadfin Bream, Nemipterus japonicus (Bloch, 1791) populations along the coasts of Peninsular Malaysia and provides evidence of a cryptic species.

PubMed

Lim, Hong-Chiun; Ahmad, Abu Talib; Nuruddin, Ahmad Adnan; Mohd Nor, Siti Azizah

2016-01-01

We evaluated genetic differentiation among ten presumed Japanese threadfin bream, Nemipterus japonicus populations along the coast of Peninsular Malaysia based on the partial sequence of the mitochondrial cytochrome b gene (982 bp). Genetic divergences (Kimura-2 parameter) ranged from 0.5% to 0.8% among nine of the ten populations while these nine populations were 4.4% to 4.6% diverged from the Kuala Besar population located at the Northeast coast. The constructed Neighbour Joining (NJ) phylogenetic trees based on haplotypes showed the Kuala Besar population forming an isolated cluster. The Analysis of Molecular Variance (AMOVA) of the ten populations a priori assigned into four regions, revealed that most of the variation occurred within population with a fairly low but significant level of regional differentiation (FST = 0.07, p < 0.05, FSC = 0.00, p > 0.05 and FCT = 0.07, p < 0.05) attributed to the Kuala Besar population. p Value after Bonferroni correction revealed that only pairwise FST values involving the Kuala Besar population with the other nine populations were significant. Thus, this study revealed that the N. japonicus populations off Peninsular Malaysia were panmictic. However, the Kuala Besar population, although morphologically identical was composed of a genetically discrete taxon from the rest. These findings are important contributions in formulating sustainable fishery management policies for this important fishery in Peninsular Malaysia.

Minor and trace element concentrations in adjacent kamacite and taenite in the Krymka chondrite

NASA Astrophysics Data System (ADS)

Meftah, N.; Mostefaoui, S.; Jambon, A.; Guedda, E. H.; Pont, S.

2016-04-01

We report in situ NanoSIMS siderophile minor and trace element abundances in individual Fe-Ni metal grains in the unequilibrated chondrite Krymka (LL3.2). Associated kamacite and taenite of 10 metal grains in four chondrules and one matrix metal were analyzed for elemental concentrations of Fe, Ni, Co, Cu, Rh, Ir, and Pt. The results show large elemental variations among the metal grains. However, complementary and correlative variations exist between adjacent kamacite-taenite. This is consistent with the unequilibrated character of the chondrite and corroborates an attainment of chemical equilibrium between the metal phases. The calculated equilibrium temperature is 446 ± 9 °C. This is concordant with the range given by Kimura et al. (2008) for the Krymka postaccretion thermal metamorphism. Based on Ni diffusivity in taenite, a slow cooling rate is estimated of the Krymka parent body that does not exceed ~1K Myr-1, which is consistent with cooling rates inferred by other workers for unequilibrated ordinary chondrites. Elemental ionic radii might have played a role in controlling elemental partitioning between kamacite and taenite. The bulk compositions of the Krymka metal grains have nonsolar (mostly subsolar) element/Ni ratios suggesting the Fe-Ni grains could have formed from distinct precursors of nonsolar compositions or had their compositions modified subsequent to chondrule formation events.

Highlighting Astyanax Species Diversity through DNA Barcoding

PubMed Central

Oliveira, Carlos Alexandre Miranda; de Melo, Filipe Augusto Gonçalves; Bertaco, Vinicius de Araújo; de Astarloa, Juan M. Díaz; Rosso, Juan J.; Foresti, Fausto; Oliveira, Claudio

2016-01-01

DNA barcoding has been used extensively to solve taxonomic questions and identify new species. Neotropical fishes are found in a wide variety of shapes and sizes, with a large number of species yet to be described, many of which are very difficult to identify. Characidae is the most species-rich family of the Characiformes, and many of its genera are affected by taxonomic uncertainties, including the widely-distributed, species-rich genus Astyanax. In this study, we present an extensive analysis of Astyanax covering almost its entire area of occurrence, based on DNA barcoding. The use of different approaches (ABGD, GMYC and BIN) to the clustering of the sequences revealed ample consistency in the results obtained by the initial cutoff value of 2% divergence for putative species in the Neighbor-Joining analysis using the Kimura-2-parameter model. The results indicate the existence of five Astyanax lineages. Some groups, such as that composed by the trans-Andean forms, are mostly composed of well-defined species, and in others a number of nominal species are clustered together, hampering the delimitation of species, which in many cases proved impossible. The results confirm the extreme complexity of the systematics of the genus Astyanax and show that DNA barcoding can be an useful tool to address these complexes questions. PMID:27992537

[Exploration of the concept of genetic drift in genetics teaching of undergraduates].

PubMed

Wang, Chun-ming

2016-01-01

Genetic drift is one of the difficulties in teaching genetics due to its randomness and probability which could easily cause conceptual misunderstanding. The “sampling error" in its definition is often misunderstood because of the research method of “sampling", which disturbs the results and causes the random changes in allele frequency. I analyzed and compared the definitions of genetic drift in domestic and international genetic textbooks, and found that the definitions containing “sampling error" are widely adopted but are interpreted correctly in only a few textbooks. Here, the history of research on genetic drift, i.e., the contributions of Wright, Fisher and Kimura, is introduced. Moreover, I particularly describe two representative articles recently published about genetic drift teaching of undergraduates, which point out that misconceptions are inevitable for undergraduates during the studying process and also provide a preliminary solution. Combined with my own teaching practice, I suggest that the definition of genetic drift containing “sampling error" can be adopted with further interpretation, i.e., “sampling error" is random sampling among gametes when generating the next generation of alleles which is equivalent to a random sampling of all gametes participating in mating in gamete pool and has no relationship with artificial sampling in general genetics studies. This article may provide some help in genetics teaching.

DNA barcoding of fishes of Laguna de Bay, Philippines.

PubMed

Aquino, Luis Miguel G; Tango, Jazzlyn M; Canoy, Reynand Jay C; Fontanilla, Ian Kendrich C; Basiao, Zubaida U; Ong, Perry S; Quilang, Jonas P

2011-08-01

Laguna de Bay, the largest lake in the Philippines, is an important part of the country's fisheries industry. It is also home to a number of endemic fishes including Gobiopterus lacustris (Herre 1927) of family Gobiidae, Leiopotherapon plumbeus (Kner 1864) of family Terapontidae, Zenarchopterus philippinus (Peters 1868) of family Hemiramphidae and Arius manillensis Valenciennes 1840 of family Ariidae. Over the years, a steady decline has been observed in the abundance and diversity of native fishes in the lake due to anthropogenic disturbances. In this study, a total of 71 specimens of 18 different species belonging to 18 genera, 16 families, and seven orders were DNA barcoded using the mitochondrial cytochrome c oxidase subunit I (COI) gene. All of the fish species were discriminated by their COI sequences and one endemic species G. lacustris, showing deep genetic divergence, was highlighted for further taxonomic investigation. Average Kimura 2-parameter genetic distances within species, family, and order were 1.33%, 18.91%, and 24.22%, respectively. These values show that COI divergence increases as taxa become less exclusive. All of the COI sequences obtained were grouped together according to their species designation in the Neighbor-joining tree that was constructed. This study demonstrated that DNA barcoding has great potential as a tool for fast and accurate species identification and also for highlighting species that warrant further taxonomic investigation.

Chemical Differentiation of Dendrobium officinale and Dendrobium devonianum by Using HPLC Fingerprints, HPLC-ESI-MS, and HPTLC Analyses

PubMed Central

Ye, Zi; Dai, Jia-Rong; Zhang, Cheng-Gang; Lu, Ye; Wu, Lei-Lei; Gong, Amy G. W.; Wang, Zheng-Tao

2017-01-01

The stems of Dendrobium officinale Kimura et Migo (Dendrobii Officinalis Caulis) have a high medicinal value as a traditional Chinese medicine (TCM). Because of the limited supply, D. officinale is a high priced TCM, and therefore adulterants are commonly found in the herbal market. The dried stems of a closely related Dendrobium species, Dendrobium devonianum Paxt., are commonly used as the substitute; however, there is no effective method to distinguish the two Dendrobium species. Here, a high performance liquid chromatography (HPLC) method was successfully developed and applied to differentiate D. officinale and D. devonianum by comparing the chromatograms according to the characteristic peaks. A HPLC coupled with electrospray ionization multistage mass spectrometry (HPLC-ESI-MS) method was further applied for structural elucidation of 15 flavonoids, 5 phenolic acids, and 1 lignan in D. officinale. Among these flavonoids, 4 flavonoid C-glycosides were firstly reported in D. officinale, and violanthin and isoviolanthin were identified to be specific for D. officinale compared with D. devonianum. Then, two representative components were used as chemical markers. A rapid and reliable high performance thin layer chromatography (HPTLC) method was applied in distinguishing D. officinale from D. devonianum. The results of this work have demonstrated that these developed analytical methods can be used to discriminate D. officinale and D. devonianum effectively and conveniently. PMID:28769988

Structure analysis of a novel heteroxylan from the stem of Dendrobium officinale and anti-angiogenesis activities of its sulfated derivative.

PubMed

Yue, Han; Liu, Yanqiu; Qu, Huanhuan; Ding, Kan

2017-10-01

Dendrobium officinale Kimura et Migo (Tie-Pi-Shi-Hu), a precious folk medicine exhibiting multiple bioactivities, including antitumor, immune-enhancing and so on. Although evidences showed polysaccharide is one of the major bioactive substances from this herb, several of them were homogenous with fine structures elucidated. In this study, we showed a novel homogeneous heteroxylan obtained from alkali-extracted crude polysaccharide. It composed of arabinose, xylose, glucose and 4-O-methylglucuronic acid (4-MGA) as well as trace amount of rhamnose and galactose in a ratio of 8.9:62.7:8.5:12.3:3.9:3.7. We further showed that it contained a backbone of 1,4-linked β-d-xylan, with branches of 1,4-linked α-d-glucose, 1,3-linked α-l-rhamnose, and terminal-linked α-l-arabinose, β-d-galactose, 4-MGA, and β-d-xylose directly or indirectly attached to C-2 position of glycosyl residues on backbone. The sulfated derivative with substitution degree about 0.9 was prepared according to the chlorosulfonic acid (CSA)-pyridine method. Bioactivity tests suggested that the sulfated polysaccharide could significantly disrupt tube formation and inhibit the migration of human microvascular endothelial cells (HMEC-1) at a low concentration (0.29μM) in a dose-dependent way without significant cytotoxity. Copyright © 2017 Elsevier B.V. All rights reserved.

FRET ratiometric probes reveal the chiral-sensitive cysteine-dependent H2S production and regulation in living cells

NASA Astrophysics Data System (ADS)

Wei, Lv; Yi, Long; Song, Fanbo; Wei, Chao; Wang, Bai-Fan; Xi, Zhen

2014-04-01

Hydrogen sulfide (H2S) is an endogenously produced gaseous signalling molecule with multiple biological functions. In order to visualize and quantify the endogenous in situ production of H2S in living cells, here we developed two new sulphide ratiometric probes (SR400 and SR550) based on fluorescence resonance energy transfer (FRET) strategy for live capture of H2S. The FRET-based probes show excellent selectivity toward H2S in a high thiol background under physiological buffer. The probe can be used to in situ visualize cysteine-dependent H2S production in a chiral-sensitive manner in living cells. The ratiometric imaging studies indicated that D-Cys induces more H2S production than that of L-Cys in mitochondria of human embryonic kidney 293 cells (HEK293). The cysteine mimics propargylglycine (PPG) has also been found to inhibit the cysteine-dependent endogenous H2S production in a chiral-sensitive manner in living cells. D-PPG inhibited D-Cys-dependent H2S production more efficiently than L-PPG, while, L-PPG inhibited L-Cys-dependent H2S production more efficiently than D-PPG. Our bioimaging studies support Kimura's discovery of H2S production from D-cysteine in mammalian cells and further highlight the potential of D-cysteine and its derivatives as an alternative strategy for classical H2S-releasing drugs.

DNA barcoding of Clarias gariepinus, Coptodon zillii and Sarotherodon melanotheron from Southwestern Nigeria

PubMed Central

Falade, Mofolusho O.; Opene, Anthony J.; Benson, Otarigho

2016-01-01

DNA barcoding has been adopted as a gold standard rapid, precise and unifying identification system for animal species and provides a database of genetic sequences that can be used as a tool for universal species identification. In this study, we employed mitochondrial genes 16S rRNA (16S) and cytochrome oxidase subunit I (COI) for the identification of some Nigerian freshwater catfish and Tilapia species. Approximately 655 bp were amplified from the 5′ region of the mitochondrial cytochrome C oxidase subunit I (COI) gene whereas 570 bp were amplified for the 16S rRNA gene. Nucleotide divergences among sequences were estimated based on Kimura 2-parameter distances and the genetic relationships were assessed by constructing phylogenetic trees using the neighbour-joining (NJ) and maximum likelihood (ML) methods. Analyses of consensus barcode sequences for each species, and alignment of individual sequences from within a given species revealed highly consistent barcodes (99% similarity on average), which could be compared with deposited sequences in public databases. The nucleotide distance between species belonging to different genera based on COI ranged from 0.17% between Sarotherodon melanotheron and Coptodon zillii to 0.49% between Clarias gariepinus and C. zillii, indicating that S. melanotheron and C. zillii are closely related. Based on the data obtained, the utility of COI gene was confirmed in accurate identification of three fish species from Southwest Nigeria. PMID:27990256

Developing a DNA barcode library for perciform fishes in the South China Sea: Species identification, accuracy and cryptic diversity.

PubMed

Hou, Gang; Chen, Wei-Tao; Lu, Huo-Sheng; Cheng, Fei; Xie, Song-Guang

2018-01-01

DNA barcodes were studied for 1,353 specimens representing 272 morphological species belonging to 149 genera and 55 families of Perciformes from the South China Sea (SCS). The average Kimura 2-parameter (K2P) distances within species, genera and families were 0.31%, 8.71% and 14.52%, respectively. A neighbour-joining (NJ) tree, Bayesian inference (BI) and maximum-likelihood (ML) trees and Automatic Barcode Gap Discovery (ABGD) revealed 260, 253 and 259 single-species-representing clusters, respectively. Barcoding gap analysis (BGA) demonstrated that barcode gaps were present for 178 of 187 species analysed with multiple specimens (95.2%), with the minimum interspecific distance to the nearest neighbour larger than the maximum intraspecific distance. A group of three Thunnus species (T. albacares, T. obesus and T. tonggol), a pair of Gerres species (G. oyena and G. japonicus), a pair of Istiblennius species (I. edentulous and I. lineatus) and a pair of Uranoscopus species (U. oligolepis and U. kaianus) were observed with low interspecific distances and overlaps between intra- and interspecific genetic distances. Three species (Apogon ellioti, Naucrates ductor and Psenopsis anomala) showed deep intraspecific divergences and generated two lineages each, suggesting the possibility of cryptic species. Our results demonstrated that DNA barcodes are highly reliable for delineating species of Perciformes in the SCS. The DNA barcode library established in this study will shed light on further research on the diversity of Perciformes in the SCS. © 2017 John Wiley & Sons Ltd.

Identification of Belgian mosquito species (Diptera: Culicidae) by DNA barcoding.

PubMed

Versteirt, V; Nagy, Z T; Roelants, P; Denis, L; Breman, F C; Damiens, D; Dekoninck, W; Backeljau, T; Coosemans, M; Van Bortel, W

2015-03-01

Since its introduction in 2003, DNA barcoding has proven to be a promising method for the identification of many taxa, including mosquitoes (Diptera: Culicidae). Many mosquito species are potential vectors of pathogens, and correct identification in all life stages is essential for effective mosquito monitoring and control. To use DNA barcoding for species identification, a reliable and comprehensive reference database of verified DNA sequences is required. Hence, DNA sequence diversity of mosquitoes in Belgium was assessed using a 658 bp fragment of the mitochondrial cytochrome oxidase I (COI) gene, and a reference data set was established. Most species appeared as well-supported clusters. Intraspecific Kimura 2-parameter (K2P) distances averaged 0.7%, and the maximum observed K2P distance was 6.2% for Aedes koreicus. A small overlap between intra- and interspecific K2P distances for congeneric sequences was observed. Overall, the identification success using best match and the best close match criteria were high, that is above 98%. No clear genetic division was found between the closely related species Aedes annulipes and Aedes cantans, which can be confused using morphological identification only. The members of the Anopheles maculipennis complex, that is Anopheles maculipennis s.s. and An. messeae, were weakly supported as monophyletic taxa. This study showed that DNA barcoding offers a reliable framework for mosquito species identification in Belgium except for some closely related species. © 2014 John Wiley & Sons Ltd.

Confirmation of Two Sibling Species among Anopheles fluviatilis Mosquitoes in South and Southeastern Iran by Analysis of Cytochrome Oxidase I Gene.

PubMed

Naddaf, Saied Reza; Oshaghi, Mohammad Ali; Vatandoost, Hassan

2012-12-01

Anopheles fluviatilis, one of the major malaria vectors in Iran, is assumed to be a complex of sibling species. The aim of this study was to evaluate Cytochrome oxidase I (COI) gene alongside 28S-D3 as a diagnostic tool for identification of An. fluviatilis sibling species in Iran. DNA sample belonging to 24 An. fluviatilis mosquitoes from different geographical areas in south and southeastern Iran were used for amplification of COI gene followed by sequencing. The 474-475 bp COI sequences obtained in this study were aligned with 59 similar sequences of An. fluviatilis and a sequence of Anopheles minimus, as out group, from GenBank database. The distances between group and individual sequences were calculated and phylogenetic tree for obtained sequences was generated by using Kimura two parameter (K2P) model of neighbor-joining method. Phylogenetic analysis using COI gene grouped members of Fars Province (central Iran) in two distinct clades separate from other Iranian members representing Hormozgan, Kerman, and Sistan va Baluchestan Provinces. The mean distance between Iranian and Indian individuals was 1.66%, whereas the value between Fars Province individuals and the group comprising individuals from other areas of Iran was 2.06%. Presence of 2.06% mean distance between individuals from Fars Province and those from other areas of Iran is indicative of at least two sibling species in An. fluviatilis mosquitoes of Iran. This finding confirms earlier results based on RAPD-PCR and 28S-D3 analysis.

Future change in seasonal march of snow water equivalent due to global climate change

NASA Astrophysics Data System (ADS)

Hara, M.; Kawase, H.; Ma, X.; Wakazuki, Y.; Fujita, M.; Kimura, F.

2012-04-01

Western side of Honshu Island in Japan is one of the heaviest snowfall areas in the world, although the location is relatively lower latitude than other heavy snowfall areas. Snowfall is one of major source for agriculture, industrial, and house-use in Japan. The change in seasonal march of snow water equivalent, e.g., snowmelt season and amount will strongly influence to social-economic activities (ex. Ma et al., 2011). We performed the four numerical experiments including present and future climate simulations and much-snow and less-snow cases using a regional climate model. Pseudo-Global-Warming (PGW) method (Kimura and Kitoh, 2008) is applied for the future climate simulations. NCEP/NCAR reanalysis is used for initial and boundary conditions in present climate simulation and PGW method. MIROC 3.2 medres 2070s output under IPCC SRES A2 scenario and 1990s output under 20c3m scenario used for PGW method. In much-snow cases, Maximum total snow water equivalent over Japan, which is mostly observed in early February, is 49 G ton in the present simulation, the one decreased 26 G ton in the future simulation. The decreasing rate of snow water equivalent due to climate change was 49%. Main cause of the decrease of the total snow water equivalent is strongly affected by the air temperature rise due to global climate change. The difference in present and future precipitation amount is little.

Identification of HIV-1 genitourinary tract compartmentalization by analyzing the env gene sequences in urine.

PubMed

Blasi, Maria; Carpenter, J Harris; Balakumaran, Bala; Cara, Andrea; Gao, Feng; Klotman, Mary E

2015-08-24

HIV-1 persists indefinitely in memory CD4 T cells and other long-lived cellular reservoirs despite antiretroviral therapy. Our group had previously demonstrated that HIV-1 can establish a productive infection in renal epithelial cells and that the kidney represents a separate compartment for HIV-1 replication. Here, to better understand the viruses in this unique site, we genetically characterized and compared the viruses in blood and urine specimens from 24 HIV-1 infected patients with detectable viremia. Blood and urine samples were obtained from 35 HIV-1 positive patients. Single-genome amplification was performed on HIV-1 env RNA and DNA isolated from urine supernatants and urine-derived cell pellets, respectively, as well as from plasma and peripheral blood mononuclear cell from the same individuals. Neighbor-joining trees were constructed under the Kimura 2-parameter model. We amplified and sequenced the full-length HIV-1 envelope (env) gene from 12 of the 24 individuals, indicating that 50% of the viremic HIV-1-positive patients had viral RNA in their urine. Phylogenetic analysis of the env sequences from four individuals with more than 15 urine-derived env sequences showed that the majority of the sequences from urine formed distinct cluster(s) independent of those peripheral blood mononuclear cell and plasma-derived sequences, consistent with viral compartmentalization in the urine. Our results suggest the presence of a distinct HIV compartment in the genitourinary tract.

Identification of HIV-1 Genitourinary Tract Compartmentalization by Analyzing the env Gene Sequences in Urine

PubMed Central

BLASI, Maria; CARPENTER, J. Harris; BALAKUMARAN, Bala; CARA, Andrea; GAO, Feng; KLOTMAN, Mary E.

2015-01-01

Objective HIV-1 persists indefinitely in memory CD4+ T cells and other long-lived cellular reservoirs despite antiretroviral therapy (ART). Our group had previously demonstrated that HIV-1 can establish a productive infection in renal epithelial cells and that the kidney represents a separate compartment for HIV-1 replication. Here, to better understand the viruses in this unique site, we genetically characterized and compared the viruses in blood and urine specimens from twenty-four HIV-1 infected subjects with detectable viremia. Design and Methods Blood and urine samples were obtained from 35 HIV-1 positive subjects. Single-genome amplification was performed on HIV-1 env RNA and DNA isolated from urine supernatants and urine derived cell pellets respectively, as well as from plasma and PBMC from the same individuals. Neighbor-joining trees were constructed under the Kimura 2-parameter mode. Results We amplified and sequenced the full-length HIV-1 envelope (env) gene from twelve of the twenty-four individuals, indicating that fifty percent (50%) of the viremic HIV-1 positive patients had viral RNA in their urine. Phylogenetic analysis of the env sequences from four subjects with more than fifteen urine-derived env sequences showed that the majority of the sequences from urine formed distinct cluster(s) independent of those PBMC and plasma-derived sequences, consistent with viral compartmentalization in the urine. Conclusions Our results suggest the presence of a distinct HIV compartment in the genitourinary tract. PMID:26372275

Activation of caspase-3 is associated with oxidative stress in the hydropic guinea pig cochlea.

PubMed

Labbé, Daniel; Teranishi, Masa-Aki; Hess, Alexander; Bloch, Wilhelm; Michel, Olaf

2005-04-01

The aim of this study was to investigate the involvement of oxidative stress and apoptosis in an animal model of Meniere's disease. Endolymphatic hydrops (ELH) is generally accepted as the decisive histological characteristic of Meniere's disease. Closure of the endolymphatic duct (Kimura's method) was used to induce endolymphatic hydrops in guinea pigs. Sham-operated animals served as controls. After 4 weeks the animals operated showed a significant elevation of the hearing thresholds as measured by audiometric brainstem responses (ABR) pre- and postoperatively. Immediately after the second ABR measurement, the animals were sacrificed for further immunohistological examinations of the inner ear with specific antibodies to active caspase-3 (cas-3) as a marker for apoptosis and antibodies to 8-isoprostane (8-iso) and nitrotyrosine (NT) as indicators of oxidative stress. Compared with the sham-operated controls, hydropic cochleae showed strong immunostaining for both oxidative stress markers in spiral ganglion cells, in the blood-vessels and fibrocytes of the lateral wall, as well as in supporting cells of the organ of Corti. Activation of cas-3 in spiral ganglion cells and the lateral wall was found exclusively in hydropic cochleae. Our findings suggest that oxidative stress is involved in the development of endolymphatic hydrops and may lead to cellular damage which induces apoptosis by activation of cas-3. Apoptotic cell death might contribute to the sensorineural hearing loss found in later stages of Meniere's disease.

Cytochrome C oxidase subunit I barcodes provide an efficient tool for Jinqian Baihua She (Bungarus parvus) authentication

PubMed Central

Chao, Zhi; Liao, Jing; Liang, Zhenbiao; Huang, Suhua; Zhang, Liang; Li, Junde

2014-01-01

Objective: To test the feasibility of DNA barcoding for accurate identification of Jinqian Baihua She and its adulterants. Materials and Methods: Standard cytochrome C oxidase subunit I (COI) gene fragments were sequenced for DNA barcoding of 39 samples from 9 snake species, including Bungarus multicinctus, the officially recognized origin animal by Chinese Pharmacopoeia, and other 8 adulterate species. The aligned sequences, 658 base pairs in length, were analyzed for divergence using the Kimura-2-parameter (K2P) distance model with MEGA5.0. Results: The mean intraspecific K2P distance was 0.0103 and the average interspecific genetic distance was 0.2178 in B. multicinctus, far greater than the minimal interspecific genetic distance of 0.027 recommended for species identification. A neighbor-joining (NJ) tree was constructed, in which each species formed a monophyletic clade with bootstrap supports of 100%. All the data were submitted to Barcode of Life Data system version 3.0 (BOLD, http://www.barcodinglife.org) under the project title “DNA barcoding Bungarus multicinctus and its adulterants”. Ten samples of commercially available crude drugs of JBS were identified using the identification engine provided by BOLD. All the samples were clearly identified at the species level, among which five were found to be the adulterants and identified as Dinodon rufozonatum. Conclusion: DNA barcoding using the standard COI gene fragments provides an effective and accurate means for JBS identification and authentication. PMID:25422545

Characterization of multi-dye pressure-sensitive microbeads

NASA Astrophysics Data System (ADS)

Lacroix, Daniel; Viraye-Chevalier, Teddy; Seiter, Guillaume; Howard, Jonathan; Dabiri, Dana; Khalil, Gamal E.; Xia, Younan; Zhu, Cun

2013-11-01

The response times of pressure-sensitive particles to passing shockwaves were measured to investigate their ability to accurately determine pressure changes in unsteady flows. The particles tested were loaded with novel pressure-sensitive dyes such as Pt (II) meso-tetra(pentafluorophenyl)porphine, Pt(II) octaethylporphine, bis(3,5-difluoro-2-(2-pyridyl)phenyl-(2-carboxypyridyl))iridium III, and iridium(III) bis(4-phenylthieno[3,2-c] pyridinato-N,C2')acetylacetonate. For this work, porous silicon dioxide pressure-sensitive beads (PSBeads) were used. Two synthetic procedures were used to fabricate the particles. In the first, a one-step method loaded dyes during the synthesis of microbeads, in the second a two-step method synthesized the microbeads first, then loaded the dyes. The shock tube facility was used to measure the response times of microbeads to fast pressure jumps. The study involved testing multiple luminophors loaded in microbeads with various size distributions. Response times for the silica-based microbeads ranged between 26 μs and 462 μs (at 90% of the amplitude response), which are much faster than previously reported polystyrene-based microbead response times, which range from 507 μs to 1582 μs (at 90% of the amplitude response) [F. Kimura, M. Rodriguez, J. McCann, B. Carlson, D. Dabiri, G. Khalil, J. B. Callis, Y. Xia, and M. Gouterman, "Development and characterization of fast responding pressure sensitive microspheres," Rev. Sci. Instrum. 79, 074102 (2008)].

CzcR and CzcD, gene products affecting regulation of resistance to cobalt, zinc, and cadmium (czc system) in Alcaligenes eutrophus.

PubMed Central

Nies, D H

1992-01-01

The czcR gene, one of the two control genes responsible for induction of resistance to Co2+, Zn2+, and Cd2+ (czc system) in the Alcaligenes eutrophus plasmid pMOL30, was cloned and characterized. The 1,376-bp sequence upstream of the czcCBAD structural genes encodes a 41.4-kDa protein, the czcR gene product, transcribed in the opposite direction of that of the czcCBAD genes. The putative CzcR polypeptide (355 amino acid residues) contains 11 cysteine and 14 histidine residues which might form metal cation-binding sites. A czcC::lacZ reporter gene translational fusion was constructed, inserted into plasmid pMOL30 in A. eutrophus, and expressed under the control of CzcR. Zn2+, Co2+, and Cd2+, as well as Ni2+, Cu2+, Hg2+, and Mn2+ and even Al3+, served as inducers of beta-galactosidase activity. Besides the CzcR protein, the membrane-bound CzcD protein was essential for induction of czc. The CzcR and CzcD proteins display no sequence similarity to two-component regulatory systems of a sensor and a response activator type; however, CzcD has 34% identity with the ZRC-1 protein, which mediates zinc resistance in Saccharomyces cerevisiae (A. Kamizomo, M. Nishizawa, Y. Teranishi, K. Murata, and A. Kimura, Mol. Gen. Genet. 219:161-167, 1989). Images PMID:1459958

Evolution dynamics of a model for gene duplication under adaptive conflict

NASA Astrophysics Data System (ADS)

Ancliff, Mark; Park, Jeong-Man

2014-06-01

We present and solve the dynamics of a model for gene duplication showing escape from adaptive conflict. We use a Crow-Kimura quasispecies model of evolution where the fitness landscape is a function of Hamming distances from two reference sequences, which are assumed to optimize two different gene functions, to describe the dynamics of a mixed population of individuals with single and double copies of a pleiotropic gene. The evolution equations are solved through a spin coherent state path integral, and we find two phases: one is an escape from an adaptive conflict phase, where each copy of a duplicated gene evolves toward subfunctionalization, and the other is a duplication loss of function phase, where one copy maintains its pleiotropic form and the other copy undergoes neutral mutation. The phase is determined by a competition between the fitness benefits of subfunctionalization and the greater mutational load associated with maintaining two gene copies. In the escape phase, we find a dynamics of an initial population of single gene sequences only which escape adaptive conflict through gene duplication and find that there are two time regimes: until a time t* single gene sequences dominate, and after t* double gene sequences outgrow single gene sequences. The time t* is identified as the time necessary for subfunctionalization to evolve and spread throughout the double gene sequences, and we show that there is an optimum mutation rate which minimizes this time scale.

Cytochrome c oxidase subunit 1 barcode data of fish of the Nayband National Park in the Persian Gulf and analysis using meta-data flag several cryptic species.

PubMed

Asgharian, Hosseinali; Sahafi, Homayoun Hosseinzadeh; Ardalan, Aria Ashja; Shekarriz, Shahrokh; Elahi, Elahe

2011-05-01

We provide cytochrome c oxidase subunit 1 (COI) barcode sequences of fishes of the Nayband National Park, Persian Gulf, Iran. Industrial activities, ecological considerations and goals of The Fish Barcode of Life campaign make it crucial that fish species residing in the park be identified. To the best of our knowledge, this is the first report of barcoding data on fishes of the Persian Gulf. We examined 187 individuals representing 76 species, 56 genera and 32 families. The data flagged potentially cryptic species of Gerres filamentosus and Plectorhinchus schotaf. 16S rDNA data on these species are provided. Exclusion of these two potential cryptic species resulted in a mean COI intraspecific distance of 0.18%, and a mean inter- to intraspecific divergence ratio of 66.7. There was no overlap between maximum Kimura 2-parameter distances among conspecifics (1.66%) and minimum distance among congeneric species (6.19%). Barcodes shared among species were not observed. Neighbour-joining analysis showed that most species formed cohesive sequence units with little variation. Finally, the comparison of 16 selected species from this study with meta-data of conspecifics from Australia, India, China and South Africa revealed high interregion divergences and potential existence of six cryptic species. Pairwise interregional comparisons were more informative than global divergence assessments with regard to detection of cryptic variation. Our analysis exemplifies optimal use of the expanding barcode data now becoming available. © 2011 Blackwell Publishing Ltd.

The algebra of the general Markov model on phylogenetic trees and networks.

PubMed

Sumner, J G; Holland, B R; Jarvis, P D

2012-04-01

It is known that the Kimura 3ST model of sequence evolution on phylogenetic trees can be extended quite naturally to arbitrary split systems. However, this extension relies heavily on mathematical peculiarities of the associated Hadamard transformation, and providing an analogous augmentation of the general Markov model has thus far been elusive. In this paper, we rectify this shortcoming by showing how to extend the general Markov model on trees to include incompatible edges; and even further to more general network models. This is achieved by exploring the algebra of the generators of the continuous-time Markov chain together with the “splitting” operator that generates the branching process on phylogenetic trees. For simplicity, we proceed by discussing the two state case and then show that our results are easily extended to more states with little complication. Intriguingly, upon restriction of the two state general Markov model to the parameter space of the binary symmetric model, our extension is indistinguishable from the Hadamard approach only on trees; as soon as any incompatible splits are introduced the two approaches give rise to differing probability distributions with disparate structure. Through exploration of a simple example, we give an argument that our extension to more general networks has desirable properties that the previous approaches do not share. In particular, our construction allows for convergent evolution of previously divergent lineages; a property that is of significant interest for biological applications.

DNA barcoding gap: reliable species identification over morphological and geographical scales.

PubMed

Čandek, Klemen; Kuntner, Matjaž

2015-03-01

The philosophical basis and utility of DNA barcoding have been a subject of numerous debates. While most literature embraces it, some studies continue to question its use in dipterans, butterflies and marine gastropods. Here, we explore the utility of DNA barcoding in identifying spider species that vary in taxonomic affiliation, morphological diagnosibility and geographic distribution. Our first test searched for a 'barcoding gap' by comparing intra- and interspecific means, medians and overlap in more than 75,000 computed Kimura 2-parameter (K2P) genetic distances in three families. Our second test compared K2P distances of congeneric species with high vs. low morphological distinctness in 20 genera of 11 families. Our third test explored the effect of enlarging geographical sampling area at a continental scale on genetic variability in DNA barcodes within 20 species of nine families. Our results generally point towards a high utility of DNA barcodes in identifying spider species. However, the size of the barcoding gap strongly depends on taxonomic groups and practices. It is becoming critical to define the barcoding gap statistically more consistently and to document its variation over taxonomic scales. Our results support models of independent patterns of morphological and molecular evolution by showing that DNA barcodes are effective in species identification regardless of their morphological diagnosibility. We also show that DNA barcodes represent an effective tool for identifying spider species over geographic scales, yet their variation contains useful biogeographic information. © 2014 John Wiley & Sons Ltd.

β-Hydroxybutyrate modulates N-type calcium channels in rat sympathetic neurons by acting as an agonist for the G-protein-coupled receptor FFA3.

PubMed

Won, Yu-Jin; Lu, Van B; Puhl, Henry L; Ikeda, Stephen R

2013-12-04

Free fatty acids receptor 3 (FFA3, GPR41) and 2 (FFA2, GPR43), for which the short-chain fatty acids (SCFAs) acetate and propionate are agonist, have emerged as important G-protein-coupled receptors influenced by diet and gut flora composition. A recent study (Kimura et al., 2011) demonstrated functional expression of FFA3 in the rodent sympathetic nervous system (SNS) providing a potential link between nutritional status and autonomic function. However, little is known of the source of endogenous ligands, signaling pathways, or effectors in sympathetic neurons. In this study, we found that FFA3 and FFA2 are unevenly expressed in the rat SNS with higher transcript levels in prevertebral (e.g., celiac-superior mesenteric and major pelvic) versus paravertebral (e.g., superior cervical and stellate) ganglia. FFA3, whether heterologously or natively expressed, coupled via PTX-sensitive G-proteins to produce voltage-dependent inhibition of N-type Ca(2+) channels (Cav2.2) in sympathetic neurons. In addition to acetate and propionate, we show that β-hydroxybutyrate (BHB), a metabolite produced during ketogenic conditions, is also an FFA3 agonist. This contrasts with previous interpretations of BHB as an antagonist at FFA3. Together, these results indicate that endogenous BHB levels, especially when elevated under certain conditions, such as starvation, diabetic ketoacidosis, and ketogenic diets, play a potentially important role in regulating the activity of the SNS through FFA3.

Integrative taxonomy supports new candidate fish species in a poorly studied neotropical region: the Jequitinhonha River Basin.

PubMed

Pugedo, Marina Lages; de Andrade Neto, Francisco Ricardo; Pessali, Tiago Casarim; Birindelli, José Luís Olivan; Carvalho, Daniel Cardoso

2016-06-01

Molecular identification through DNA barcoding has been proposed as a way to standardize a global biodiversity identification system using a partial sequence of the mitochondrial COI gene. We applied an integrative approach using DNA barcoding and traditional morphology-based bioassessment to identify fish from a neotropical region possessing low taxonomic knowledge: the Jequitinhonha River Basin (Southeastern Brazil). The Jequitinhonha River Basin (JRB) has a high rate of endemism and is considered an area of high priority for fish conservation, with estimates indicating the presence of around 110 native and non-indigenous species. DNA barcodes were obtained from 260 individuals belonging to 52 species distributed among 35 genera, 21 families and 6 orders, including threatened and rare species such as Rhamdia jequitinhonha and Steindachneridion amblyurum. The mean Kimura two-parameter genetic distances within species, genera and families were: 0.44, 12.16 and 20.58 %, respectively. Mean intraspecific genetic variation ranged from 0 to 11.43 %, and high values (>2 %) were recovered for five species. Species with a deep intraspecific distance, possibly flagging overlooked taxa, were detected within the genus Pimelodella. Fifteen species, only identified to the genus level, had unique BINs, with a nearest neighbor distance over 2 % and therefore, potential new candidate species supported by DNA barcoding. The integrative taxonomy approach using DNA barcoding and traditional taxonomy may be a remedy to taxonomy impediment, accelerating species identification by flagging potential new candidate species and to adequately conserve the megadiverse neotropical ichthyofauna.

Downscaling of snow depth and river discharge in Japan by the Pseudo-Global-Warming Method

NASA Astrophysics Data System (ADS)

Kimura, F.; Ma, X.; Hara, M.; Advanced Atmosphere-Ocean-Land Modeling Program

2010-12-01

in the 2070s is investigated. Assuming the reference present climate period of 1990s, the monthly mean discharge for the 2070s is projected to increase by approximately 43% in January and 55% in February, but to decrease by approximately 38% in April and 32% in May. The flood peak in the hydrograph will shift to approximately one month earlier, i.e., from April in the 1990s to March in the 2070s. Furthermore, the 10-year average of snowfall amount is projected to be approximately 49.5% lower in the 2070s than that in the 1990s. Acknowledgment: This work was supported by the Global Environment Research Fund (S-5-3) of the Ministry of the Environment, Japan. References 1. Ma, X., T. Yoshikane, M. Hara, Y. Wakazuki, H. G Takahashi, and F. Kimura, 2010: Hydrological response to future climate change in the Agano River basin, Japan, Hydrological Research Letters, 4, 25-29 2. Hara,M., T.Yoshikane, H.Kawase and F.Kimura 2008:Impact of the Estimation of Global Warming on Snow Depth in Japan by the Pseudo-Global-Warming Method. Hydrological Research Letters 2 61-64.

PREFACE: The 16th International Symposium on Boron, Borides and Related Materials (ISBB 2008)

NASA Astrophysics Data System (ADS)

Tanaka, Takaho

2009-07-01

supported by Tokyo University of Science, Suwa and foundations including, the Kajima Foundation, Foundation for Promotion of Material Science and Technology of Japan and Nippon Sheet Glass Foundation for Materials Science and Engineering, as well as companies including JFE Steel Corporation, Shincron Co, Ltd, Toyo Kohan Co, Ltd, Fukuda Metal Foil and Powder Co, Ltd, Japan New Metals Co, Ltd, H C Starck Ltd and Fritsch Japan Co, Ltd. Editors Chair Takaho Tanaka (National Institute for Materials Science, Japan) Vice chairs Koun Shirai (Osaka University, Japan) Kaoru Kimura (The University of Tokyo, Japan) Ken-ichi Takagi (Tokyo City University, Japan) Touetsu Shishido (Tohoku University, Japan) Shigeru Okada (Kokushikan University) Hideaki Itoh (Nagoya University,Japan) Katsumitsu Nakamura (Nihon University, Japan) Organizing committee of ISBB 2008 K Takagi Chairman (Tokyo City University) T Tanaka Program Committee Chairman (National Institute for Materials Science) K Kimura Secretary (The University of Tokyo) J Akimitsu (Aoyama University)K Shirai (Osaka University) H Itoh (Nagoya University)T Shishido (Tohoku University) K Nakamura (Nihon University)K Soga (Tokyo University of Science) K Nishiyama (Tokyo University of Science, Suwa)M Takeda (Nagaoka University of Technology) S Okada (Kokushikan University)Y Yamazaki (Toyo Kohan Co, Ltd) International Scientific Committee 0f ISBB (2008-2011) K Takagi Chairman (Japan) B Albert (Germany) J-F Halet (France) M Takeda (Japan) M Antadze (Georgia) H Hillebrecht (Germany) T Tanaka (Japan) J Bauer (France) W Jung (Germany) R Telle (Germany) I Boustani (Germany) K Kimura (Japan) M Trenary (USA) D Emin (USA) T Mori (Japan) O Tsagareishvili (Georgia) M Engler (Germany) P D Ownby (USA) H Werheit (Germany) N Frage (Israel) P Rogl (Austria) G Will (Germany) Yu Grin (Germany) S Shalamberidze (Georgia) O Yucel (Turkey) V N Gurin (Russia) N Shitsevalova (Ukraine) G Zhang (China)

The genetic architecture of local adaptation and reproductive isolation in sympatry within the Mimulus guttatus species complex.

PubMed

Ferris, Kathleen G; Barnett, Laryssa L; Blackman, Benjamin K; Willis, John H

2017-01-01

The genetic architecture of local adaptation has been of central interest to evolutionary biologists since the modern synthesis. In addition to classic theory on the effect size of adaptive mutations by Fisher, Kimura and Orr, recent theory addresses the genetic architecture of local adaptation in the face of ongoing gene flow. This theory predicts that with substantial gene flow between populations local adaptation should proceed primarily through mutations of large effect or tightly linked clusters of smaller effect loci. In this study, we investigate the genetic architecture of divergence in flowering time, mating system-related traits, and leaf shape between Mimulus laciniatus and a sympatric population of its close relative M. guttatus. These three traits are probably involved in M. laciniatus' adaptation to a dry, exposed granite outcrop environment. Flowering time and mating system differences are also reproductive isolating barriers making them 'magic traits'. Phenotypic hybrids in this population provide evidence of recent gene flow. Using next-generation sequencing, we generate dense SNP markers across the genome and map quantitative trait loci (QTLs) involved in flowering time, flower size and leaf shape. We find that interspecific divergence in all three traits is due to few QTL of large effect including a highly pleiotropic QTL on chromosome 8. This QTL region contains the pleiotropic candidate gene TCP4 and is involved in ecologically important phenotypes in other Mimulus species. Our results are consistent with theory, indicating that local adaptation and reproductive isolation with gene flow should be due to few loci with large and pleiotropic effects. © 2016 John Wiley & Sons Ltd.

[Phylogeny and divergence time estimation of Schizothoracinae fishes in Xinjiang].

PubMed

Ayelhan, Haysa; Guo, Yan; Meng, Wei; Yang, Tianyan; Ma, Yanwu

2014-10-01

Based on combined data of mitochondrial COI, ND4 and 16S RNA genes, molecular phylogeny of 4 genera, 10 species or subspecies of Schizothoracinae fishes distributed in Xinjiang were analyzed. The molecular clock was calibrated by divergence time of Cyprininae and geological segregation event between the upper Yellow River and Qinghai Lake. Divergence time of Schizothoracinae fishes was calculated, and its relationship with the major geological events and the climate changes in surrounding areas of Tarim Basin was discussed. The results showed that genus Aspiorhynchus did not form an independent clade, but clustered with Schizothorax biddulphi and S. irregularis. Kimura 2-parameter model was used to calculate the genetic distance of COI gene, the genetic distance between genus Aspiorhynchus and Schizothorax did not reach genus level, and Aspiorhynchus laticeps might be a specialized species of genus Schizothorax. Cluster analysis showed a different result with morphological classification method, and it did not support the subgenus division of Schizothorax fishes. Divergence of two groups of primitive Schizothoracinae (8.18Ma) and divergence of Gymnodiptychus dybowskii and Diptychus maculates (7.67Ma) occurred in late Miocene, which might be related with the separation of Kunlun Mountain and north Tianshan Mountain River system that was caused by the uplift of Qinghai-Tibet Plateau and Tianshan Mountain, and the aridification of Tarim Basin. The terrain of Tarim Basin that was affected by Quaternary Himalayan movement was high in west but low in east, as a result, Lop Nor became the center of surrounding mountain rivers in Tarim Basin, which shaped the distribution pattern of genus Schizothorax.

Variance to mean ratio, R(t), for poisson processes on phylogenetic trees.

PubMed

Goldman, N

1994-09-01

The ratio of expected variance to mean, R(t), of numbers of DNA base substitutions for contemporary sequences related by a "star" phylogeny is widely seen as a measure of the adherence of the sequences' evolution to a Poisson process with a molecular clock, as predicted by the "neutral theory" of molecular evolution under certain conditions. A number of estimators of R(t) have been proposed, all predicted to have mean 1 and distributions based on the chi 2. Various genes have previously been analyzed and found to have values of R(t) far in excess of 1, calling into question important aspects of the neutral theory. In this paper, I use Monte Carlo simulation to show that the previously suggested means and distributions of estimators of R(t) are highly inaccurate. The analysis is applied to star phylogenies and to general phylogenetic trees, and well-known gene sequences are reanalyzed. For star phylogenies the results show that Kimura's estimators ("The Neutral Theory of Molecular Evolution," Cambridge Univ. Press, Cambridge, 1983) are unsatisfactory for statistical testing of R(t), but confirm the accuracy of Bulmer's correction factor (Genetics 123: 615-619, 1989). For all three nonstar phylogenies studied, attained values of all three estimators of R(t), although larger than 1, are within their true confidence limits under simple Poisson process models. This shows that lineage effects can be responsible for high estimates of R(t), restoring some limited confidence in the molecular clock and showing that the distinction between lineage and molecular clock effects is vital.(ABSTRACT TRUNCATED AT 250 WORDS)

Babesia lengau associated with cerebral and haemolytic babesiosis in two domestic cats.

PubMed

Bosman, Anna-Mari; Oosthuizen, Marinda C; Venter, Estelle H; Steyl, Johan C A; Gous, Tertius A; Penzhorn, Barend L

2013-05-01

Although reported sporadically from various countries, feline babesiosis appears to be a significant clinical entity only in South Africa, where Babesia felis is usually incriminated as the causative agent. Babesia lengau, recently described from asymptomatic cheetahs, has now possibly been incriminated as the causative agent in two severe clinical cases in domestic cats. Both cats were euthanised in extremis. While typical feline babesiosis in South Africa is an afebrile disease with a chronic manifestation, there was acute onset of severe clinical signs in both cats and their body temperatures were above the normal range when they were presented for treatment. Haemolytic anaemia was confirmed in one case. To our knowledge, this is the first report of cerebral babesiosis in cats.On reverse line blot 18S rDNA PCR products obtained from both cats showed positive hybridization profiles with the B. lengau species-specific probe. The two partial parasite 18S rRNA gene sequences obtained, showed high sequence similarity (99.9%) to B. lengau. In a representative tree constructed by the neighbor-joining method using the two-parameter model of Kimura the two obtained partial 18S rDNA sequences and that of B. lengau formed a monophyletic group with B. conradae and sequences previously isolated from humans and wildlife in the western USA. All clinical cases of feline babesiosis in South Africa are not necessarily caused by B. felis. Other piroplasms, e.g. B. lengau, may be incriminated in clinical cases, especially those occurring outside the known endemic area.

Contrasting effects of geographical separation on the genetic population structure of sympatric species of mites in avocado orchards.

PubMed

Guzman-Valencia, S; Santillán-Galicia, M T; Guzmán-Franco, A W; González-Hernández, H; Carrillo-Benítez, M G; Suárez-Espinoza, J

2014-10-01

Oligonychus punicae and Oligonychus perseae (Acari: Tetranychidae) are the most important mite species affecting avocado orchards in Mexico. Here we used nucleotide sequence data from segments of the nuclear ribosomal internal transcribed spacers (ITS1 and ITS2) and mitochondrial cytochrome oxidase subunit I (COI) genes to assess the phylogenetic relationships between both sympatric mite species and, using only ITS sequence data, examine genetic variation and population structure in both species, to test the hypothesis that, although both species co-occur, their genetic population structures are different in both Michoacan state (main producer) and Mexico state. Phylogenetic analysis showed a clear separation between both species using ITS and COI sequence information. Haplotype network analysis done on 24 samples of O. punicae revealed low genetic diversity with only three haplotypes found but a significant geographical population structure confirmed by analysis of molecular variance (AMOVA) and Kimura-2-parameter (K2P) analyses. In addition, a Mantel test revealed that geographical isolation was a factor responsible for the genetic differentiation. In contrast, analyses of 22 samples of O. perseae revealed high genetic diversity with 15 haplotypes found but no geographical structure confirmed by the AMOVA, K2P and Mantel test analyses. We have suggested that geographical separation is one of the most important factors driving genetic variation, but that it affected each species differently. The role of the ecology of these species on our results, and the importance of our findings in the development of monitoring and control strategies are discussed.

Evaluation of DNA barcoding and identification of new haplomorphs in Canadian deerflies and horseflies.

PubMed

Cywinska, A; Hannan, M A; Kevan, P G; Roughley, R E; Iranpour, M; Hunter, F F

2010-12-01

This paper reports the first tests of the suitability of the standardized mitochondrial cytochrome c oxidase subunit I (COI) barcoding system for the identification of Canadian deerflies and horseflies. Two additional mitochondrial molecular markers were used to determine whether unambiguous species recognition in tabanids can be achieved. Our 332 Canadian tabanid samples yielded 650 sequences from five genera and 42 species. Standard COI barcodes demonstrated a strong A + T bias (mean 68.1%), especially at third codon positions (mean 93.0%). Our preliminary test of this system showed that the standard COI barcode worked well for Canadian Tabanidae: the target DNA can be easily recovered from small amounts of insect tissue and aligned for all tabanid taxa. Each tabanid species possessed distinctive sets of COI haplotypes which discriminated well among species. Average conspecific Kimura two-parameter (K2P) divergence (0.49%) was 12 times lower than the average divergence within species. Both the neighbour-joining and the Bayesian methods produced trees with identical monophyletic species groups. Two species, Chrysops dawsoni Philip and Chrysops montanus Osten Sacken (Diptera: Tabanidae), showed relatively deep intraspecific sequence divergences (∼ 10 times the average) for all three mitochondrial gene regions analysed. We suggest provisional differentiation of Ch. montanus into two haplotypes, namely, Ch. montanus haplomorph 1 and Ch. montanus haplomorph 2, both defined by their molecular sequences and by newly discovered differences in structural features near their ocelli. © 2010 Brock University. Medical and Veterinary Entomology © 2010 The Royal Entomological Society.

DNA barcodes for the fishes of the Narmada, one of India's longest rivers.

PubMed

Khedkar, Gulab Dattarao; Jamdade, Rahul; Naik, Suresh; David, Lior; Haymer, David

2014-01-01

This study describes the species diversity of fishes of the Narmada River in India. A total of 820 fish specimens were collected from 17 sampling locations across the whole river basin. Fish were taxonomically classified into one of 90 possible species based on morphological characters, and then DNA barcoding was employed using COI gene sequences as a supplemental identification method. A total of 314 different COI sequences were generated, and specimens were confirmed to belong to 85 species representing 63 genera, 34 families and 10 orders. Findings of this study include the identification of five putative cryptic or sibling species and 43 species not previously known from the Narmada River basin. Five species are endemic to India and three are introduced species that had not been previously reported to occur in the Narmada River. Conversely, 43 species previously reported to occur in the Narmada were not found. Genetic diversity and distance values were generated for all of the species within genera, families and orders using Kimura's 2 parameter distance model followed by the construction of a Neighbor Joining tree. High resolution clusters generated in NJ trees aided the groupings of species corresponding to their genera and families which are in confirmation to the values generated by Automatic Barcode Gap Discovery bioinformatics platform. This aided to decide a threshold value for the discrimination of species boundary from the Narmada River. This study provides an important validation of the use of DNA barcode sequences for monitoring species diversity and changes within complex ecosystems such as the Narmada River.

The Epidemiological Importance of Bats in the Transmission of Rabies to Dogs and Cats in the State of São Paulo, Brazil, Between 2005 and 2014.

PubMed

Castilho, J G; de Souza, D N; Oliveira, R N; Carnieli, P; Batista, H B C R; Pereira, P M C; Achkar, S M; Macedo, C I

2017-09-01

In Brazil, rabies control in dogs and cats was pioneered by the state of São Paulo with the adoption of the Pan American Health Organization recommendations for prophylaxis and control, which led to a reduction in rabies cases from 1994 onwards. As a result of these measures, the rabies virus (RABV) genetic lineage associated with dogs has not been found in the state since 1998, and all the cases in domestic animals reported since then have been caused by bat-associated lineages of RABV. In the light of this, this study sought to investigate rabies cases in dogs and cats in the state of São Paulo between 2005 and 2014 and identify the associated transmission cycles by characterizing the RABV lineages responsible for these cases. Nine samples from dogs (n = 5) and from cats (n = 4) were collected between 2005 and 2014. The tenth animal, a rabid cat, was analysed by a different laboratory. The N gene nucleotide sequences obtained were analysed with the neighbor-joining algorithm and Kimura 2-parameter model using the MEGA 6 program. Phylogenetic analysis revealed that the genetic lineages identified in all the samples were those circulating in Brazilian bats. The findings of this study demonstrate that bats play an important role in the transmission of rabies to domestic animals in São Paulo state and that emphasis should be placed on the implementation of public policies to support surveillance of chiropterans for rabies. © 2016 Blackwell Verlag GmbH.

DNA Barcode for Identifying Folium Artemisiae Argyi from Counterfeits.

PubMed

Mei, Quanxi; Chen, Xiaolu; Xiang, Li; Liu, Yue; Su, Yanyan; Gao, Yuqiao; Dai, Weibo; Dong, Pengpeng; Chen, Shilin

2016-01-01

Folium Artemisiae Argyi is an important herb in traditional Chinese medicine. It is commonly used in moxibustion, medicine, etc. However, identifying Artemisia argyi is difficult because this herb exhibits similar morphological characteristics to closely related species and counterfeits. To verify the applicability of DNA barcoding, ITS2 and psbA-trnH were used to identify A. argyi from 15 closely related species and counterfeits. Results indicated that total DNA was easily extracted from all the samples and that both ITS2 and psbA-trnH fragments can be easily amplified. ITS2 was a more ideal barcode than psbA-trnH and ITS2+psbA-trnH to identify A. argyi from closely related species and counterfeits on the basis of sequence character, genetic distance, and tree methods. The sequence length was 225 bp for the 56 ITS2 sequences of A. argyi, and no variable site was detected. For the ITS2 sequences, A. capillaris, A. anomala, A. annua, A. igniaria, A. maximowicziana, A. princeps, Dendranthema vestitum, and D. indicum had single nucleotide polymorphisms (SNPs). The intraspecific Kimura 2-Parameter distance was zero, which is lower than the minimum interspecific distance (0.005). A. argyi, the closely related species, and counterfeits, except for Artemisia maximowicziana and Artemisia sieversiana, were separated into pairs of divergent clusters by using the neighbor joining, maximum parsimony, and maximum likelihood tree methods. Thus, the ITS2 sequence was an ideal barcode to identify A. argyi from closely related species and counterfeits to ensure the safe use of this plant.

Simulation of 'stationary' SAP and SEP phenomena by 2-dimensional potential field modelling.

PubMed

Cunningham, K; Halliday, A M; Jones, S J

1986-11-01

In order to model the distribution of potentials in the hand due to antidromic SAP propagation and in the body due to afferent conduction of the median nerve volley, 2-dimensional matrices of the appropriate shape were constructed, each containing a 'generator' consisting of up to 3 'source' and 3 'sink' points. The value of the field potential at other sites was calculated using a finite difference method. It was shown that the potential gradient is virtually zero in matrix zones which are separated from the region containing the generator by a constriction in the boundary of the conductor. Points on the far side of the constriction remain virtually equipotential, at a level determined by the potential at the junction. This is naturally influenced by the proximity of the generator, so that as the generator approaches the constriction a potential difference will develop between points on the far side, irrespective of their distance from the junction, and other remote parts of the matrix. In the context of human SAPs and SEPs, such factors may be of paramount importance in the generation of so-called 'stationary' or 'far-field' potentials. With additional postulates concerning the manner in which the SAP is attenuated by the termination of axons as it propagates through the hand, and the course taken by the median nerve volley between the arm and neck, it was possible to model the majority of stationary SAP phenomena described by Kimura et al. (1984), and also the distribution and latency of the P9 SEP component following median nerve stimulation.

Iterative Calibration: A Novel Approach for Calibrating the Molecular Clock Using Complex Geological Events.

PubMed

Loeza-Quintana, Tzitziki; Adamowicz, Sarah J

2018-02-01

During the past 50 years, the molecular clock has become one of the main tools for providing a time scale for the history of life. In the era of robust molecular evolutionary analysis, clock calibration is still one of the most basic steps needing attention. When fossil records are limited, well-dated geological events are the main resource for calibration. However, biogeographic calibrations have often been used in a simplistic manner, for example assuming simultaneous vicariant divergence of multiple sister lineages. Here, we propose a novel iterative calibration approach to define the most appropriate calibration date by seeking congruence between the dates assigned to multiple allopatric divergences and the geological history. Exploring patterns of molecular divergence in 16 trans-Bering sister clades of echinoderms, we demonstrate that the iterative calibration is predominantly advantageous when using complex geological or climatological events-such as the opening/reclosure of the Bering Strait-providing a powerful tool for clock dating that can be applied to other biogeographic calibration systems and further taxa. Using Bayesian analysis, we observed that evolutionary rate variability in the COI-5P gene is generally distributed in a clock-like fashion for Northern echinoderms. The results reveal a large range of genetic divergences, consistent with multiple pulses of trans-Bering migrations. A resulting rate of 2.8% pairwise Kimura-2-parameter sequence divergence per million years is suggested for the COI-5P gene in Northern echinoderms. Given that molecular rates may vary across latitudes and taxa, this study provides a new context for dating the evolutionary history of Arctic marine life.

Phylogenetic status of brown trout Salmo trutta populations in five rivers from the southern Caspian Sea and two inland lake basins, Iran: a morphogenetic approach.

PubMed

Hashemzadeh Segherloo, I; Farahmand, H; Abdoli, A; Bernatchez, L; Primmer, C R; Swatdipong, A; Karami, M; Khalili, B

2012-10-01

Interrelationships, origin and phylogenetic affinities of brown trout Salmo trutta populations from the southern Caspian Sea basin, Orumieh and Namak Lake basins in Iran were analysed from complete mtDNA control region sequences, 12 microsatellite loci and morphological characters. Among 129 specimens from six populations, seven haplotypes were observed. Based on mtDNA haplotype data, the Orumieh and southern Caspian populations did not differ significantly, but the Namak basin-Karaj population presented a unique haplotype closely related to the haplotypes of the other populations (0·1% Kimura two-parameter, K2P divergence). All Iranian haplotypes clustered as a distinct group within the Danube phylogenetic grouping, with an average K2P distance of 0·41% relative to other Danubian haplotypes. The Karaj haplotype in the Namak basin was related to a haplotype (Da26) formerly identified in the Tigris basin in Turkey, to a Salmo trutta oxianus haplotype from the Aral Sea basin, and to haplotype Da1a with two mutational steps, as well as to other Iranian haplotypes with one to two mutational steps, which may indicate a centre of origin in the Caspian basin. In contrast to results of the mtDNA analysis, more pronounced differentiation was observed among the populations studied in the morphological and microsatellite DNA data, except for the two populations from the Orumieh basin, which were similar, possibly due to anthropogenic causes. © 2012 The Authors. Journal of Fish Biology © 2012 The Fisheries Society of the British Isles.

[Integration of pharmacokinetics and pharmacodynamics based on the in vivo analysis of drug-receptor binding].

PubMed

Yamada, Shizuo

2015-01-01

  As I was deeply interested in the effects of drugs on the human body, I chose pharmacology as the subject of special study when I became a 4th year student at Shizuoka College of Pharmacy. I studied abroad as a postdoctoral fellow for two years, from 1978, under the tutelage of Professor Henry I. Yamamura (pharmacology) in the College of Medicine at the University of Arizona, USA. He taught me a variety of valuable skills such as the radioreceptor binding assay, which represented the most advanced technology developed in the US at that time. After returning home, I engaged in clarifying receptor abnormalities in pathological conditions, as well as in drug action mechanisms, by making the best use of this radioreceptor binding assay. In 1989, following the founding of the University of Shizuoka, I was invited by Professor Ryohei Kimura to join the Department of Pharmacokinetics. This switch in discipline provided a good opportunity for me to broaden my perspectives in pharmaceutical sciences. I worked on evaluating drug-receptor binding in vivo as a combined index for pharmacokinetics and pharmacological effect manifestation, with the aim of bridging pharmacology and pharmacokinetics. In fact, by focusing on data from in vivo receptor binding, it became possible to clearly rationalize the important consideration of drug dose-concentration-action relationships, and to study quantitative and kinetic analyses of relationships among pharmacokinetics, receptor binding and pharmacological effects. Based on this concept, I was able to demonstrate the utility of dynamic analyses of drug-receptor binding in drug discovery, drug fostering, and the proper use of pharmacokinetics with regard to many drugs.

DNA Barcoding the Medusozoa using mtCOI

NASA Astrophysics Data System (ADS)

Ortman, Brian D.; Bucklin, Ann; Pagès, Francesc; Youngbluth, Marsh

2010-12-01

The Medusozoa are a clade within the Cnidaria comprising the classes Hydrozoa, Scyphozoa, and Cubozoa. Identification of medusozoan species is challenging, even for taxonomic experts, due to their fragile forms and complex, morphologically-distinct life history stages. In this study 231 sequences for a portion of the mitochondrial Cytochrome Oxidase I (mtCOI) gene were obtained from 95 species of Medusozoans including; 84 hydrozoans (61 siphonophores, eight anthomedusae, four leptomedusae, seven trachymedusae, and four narcomedusae), 10 scyphozoans (three coronatae, four semaeostomae, two rhizostomae, and one stauromedusae), and one cubozoan. This region of mtCOI has been used as a DNA barcode (i.e., a molecular character for species recognition and discrimination) for a diverse array of taxa, including some Cnidaria. Kimura 2-parameter (K2P) genetic distances between sequence variants within species ranged from 0 to 0.057 (mean 0.013). Within the 13 genera for which multiple species were available, K2P distance between congeneric species ranged from 0.056 to 0.381. A cluster diagram generated by Neighbor Joining (NJ) using K2P distances reliably clustered all barcodes of the same species with ≥99% bootstrap support, ensuring accurate identification of species. Intra- and inter-specific variation of the mtCOI gene for the Medusozoa are appropriate for this gene to be used as a DNA barcode for species-level identification, but not for phylogenetic analysis or taxonomic classification of unknown sequences at higher taxonomic levels. This study provides a set of molecular tools that can be used to address questions of speciation, biodiversity, life-history, and population boundaries in the Medusozoa.

DNA barcoding of Cuban freshwater fishes: evidence for cryptic species and taxonomic conflicts.

PubMed

Lara, Ariagna; Ponce de León, José Luis; Rodríguez, Rodet; Casane, Didier; Côté, Guillaume; Bernatchez, Louis; García-Machado, Erik

2010-05-01

Despite ongoing efforts to protect species and ecosystems in Cuba, habitat degradation, overuse and introduction of alien species have posed serious challenges to native freshwater fish species. In spite of the accumulated knowledge on the systematics of this freshwater ichthyofauna, recent results suggested that we are far from having a complete picture of the Cuban freshwater fish diversity. It is estimated that 40% of freshwater Cuban fish are endemic; however, this number may be even higher. Partial sequences (652 bp) of the mitochondrial gene COI (cytochrome c oxidase subunit I) were used to barcode 126 individuals, representing 27 taxonomically recognized species in 17 genera and 10 families. Analysis was based on Kimura 2-parameter genetic distances, and for four genera a character-based analysis (population aggregation analysis) was also used. The mean conspecific, congeneric and confamiliar genetic distances were 0.6%, 9.1% and 20.2% respectively. Molecular species identification was in concordance with current taxonomical classification in 96.4% of cases, and based on the neighbour-joining trees, in all but one instance, members of a given genera clustered within the same clade. Within the genus Gambusia, genetic divergence analysis suggests that there may be at least four cryptic species. In contrast, low genetic divergence and a lack of diagnostic sites suggest that Rivulus insulaepinorum may be conspecific with Rivulus cylindraceus. Distance and character-based analysis were completely concordant, suggesting that they complement species identification. Overall, the results evidenced the usefulness of the DNA barcodes for cataloguing Cuban freshwater fish species and for identifying those groups that deserve further taxonomic attention. © 2009 Blackwell Publishing Ltd.

A Cryptic Species of the Tylonycteris pachypus Complex (Chiroptera: Vespertilionidae) and Its Population Genetic Structure in Southern China and nearby Regions

PubMed Central

HUANG, Chujing; YU, Wenhua; XU, Zhongxian; QIU, Yuanxiong; CHEN, Miao; QIU, Bing; MOTOKAWA, Masaharu; HARADA, Masashi; LI, Yuchun; WU, Yi

2014-01-01

Three distinct bamboo bat species (Tylonycteris) are known to inhabit tropical and subtropical areas of Asia, i.e., T. pachypus, T. robustula, and T. pygmaeus. This study performed karyotypic examinations of 4 specimens from southern Chinese T. p. fulvidus populations and one specimen from Thai T. p. fulvidus population, which detected distinct karyotypes (2n=30) compared with previous karyotypic descriptions of T. p. pachypus (2n=46) and T. robustula (2n=32) from Malaysia. This finding suggested a cryptic Tylonycteris species within T. pachypus complex in China and Thailand. Morphometric studies indicated the difficulty in distinguishing the cryptic species and T. p. pachypus from Indonesia apart from the external measurements, which might be the reason for their historical misidentification. Based on 623 bp mtDNA COI segments, a phylogeographic examination including T. pachypus individuals from China and nearby regions, i.e., Vietnam, Laos, and Cambodia, was conducted to examine the population genetic structure. Genealogical and phylogeographical results indicated that at least two diverged lineages existed in these regions (average 3.4 % of Kimura 2-parameter distances) and their population structure did not match the geographic pattern. These results suggested that at least two historical colonizations have occurred by the cryptic species. Furthermore, through integration of traditional and geometric morphological results, morphological differences on zygomatic arches, toothrows and bullae were detected between two lineages in China. Given the similarity of vegetation and climate of Guangdong and Guangxi regions, we suggested that such differences might be derived from their historical adaptation or distinct evolutionary history rather than the differences of habitats they occurred currently. PMID:24550688

Incremental dynamical downscaling for probabilistic analysis based on multiple GCM projections

NASA Astrophysics Data System (ADS)

Wakazuki, Y.

2015-12-01

A dynamical downscaling method for probabilistic regional scale climate change projections was developed to cover an uncertainty of multiple general circulation model (GCM) climate simulations. The climatological increments (future minus present climate states) estimated by GCM simulation results were statistically analyzed using the singular vector decomposition. Both positive and negative perturbations from the ensemble mean with the magnitudes of their standard deviations were extracted and were added to the ensemble mean of the climatological increments. The analyzed multiple modal increments were utilized to create multiple modal lateral boundary conditions for the future climate regional climate model (RCM) simulations by adding to an objective analysis data. This data handling is regarded to be an advanced method of the pseudo-global-warming (PGW) method previously developed by Kimura and Kitoh (2007). The incremental handling for GCM simulations realized approximated probabilistic climate change projections with the smaller number of RCM simulations. Three values of a climatological variable simulated by RCMs for a mode were used to estimate the response to the perturbation of the mode. For the probabilistic analysis, climatological variables of RCMs were assumed to show linear response to the multiple modal perturbations, although the non-linearity was seen for local scale rainfall. Probability of temperature was able to be estimated within two modes perturbation simulations, where the number of RCM simulations for the future climate is five. On the other hand, local scale rainfalls needed four modes simulations, where the number of the RCM simulations is nine. The probabilistic method is expected to be used for regional scale climate change impact assessment in the future.

Future Change of Snow Water Equivalent over Japan

NASA Astrophysics Data System (ADS)

Hara, M.; Kawase, H.; Kimura, F.; Fujita, M.; Ma, X.

2012-12-01

Western side of Honshu Island and Hokkaido Island in Japan are ones of the heaviest snowfall areas in the world. Although a heavy snowfall often brings disaster, snow is one of the major sources for agriculture, industrial, and house-use in Japan. Even during the winter, the monthly mean of the surface air temperature often exceeds 0 C in large parts of the heavy snow areas along the Sea of Japan. Thus, snow cover may be seriously reduced in these areas as a result of the global warming, which is caused by an increase in greenhouse gases. The change in seasonal march of snow water equivalent, e.g., snowmelt season and amount will strongly influence to social-economic activities. We performed a series of numerical experiments including present and future climate simulations and much-snow and less-snow cases using a regional climate model. Pseudo-Global-Warming (PGW) method (Kimura and Kitoh, 2008) is applied for the future climate simulations. MIROC 3.2 medres 2070s output under IPCC SRES A2 scenario and 1990s output under 20c3m scenario used for PGW method. The precipitation, snow depth, and surface air temperature of the hindcast simulations show good agreement with the AMeDAS station data. In much-snow cases, The decreasing rate of maximum total snow water equivalent over Japan due to climate change was 49%. Main cause of the decrease of the total snow water equivalent is the air temperature rise due to global climate change. The difference in the precipitation amount between the present and the future simulations is small.

Napoleon Bonaparte and the fate of an Amazonian rat: new data on the taxonomy of Mesomys hispidus (Rodentia: Echimyidae).

PubMed

Orlando, Ludovic; Mauffrey, Jean-François; Cuisin, Jacques; Patton, James L; Hänni, Catherine; Catzeflis, François

2003-04-01

The spiny rat Mesomys hispidus is one of many South American rodents that lack adequate taxonomic definition. The few sampled populations of this broadly distributed trans-Amazonian arboreal rat have come from widely separated regions and are typically highly divergent. The holotype was described in 1817 by A.-G. Desmarest, after Napoleon's army brought it to Paris following the plunder of Lisbon in 1808; however, the locality of origin has remained unknown. Here we examine the taxonomic status of this species by direct comparison of 50 extant individuals with the holotype at the morphometric and genetic levels, the latter based on 331 bp of the mitochondrial cytochrome b gene retrieved from a small skin fragment of the holotype with ancient DNA technology. Extensive sequence divergence is present among samples of M. hispidus collected from throughout its range, from French Guiana across Amazonia to Bolivia and Peru, with at least seven mitochondrial clades recognized (average divergence of 7.7% Kimura 2-parameter distance). Sequence from the holotype is, however, only weakly divergent from those of recent samples from French Guiana. Moreover, the holotype clusters with greater that 99% posterior probability with samples from this part of Amazonia in a discriminant analysis based on 22 cranial and dental measurements. Thus, we suggest that the holotype was originally obtained in eastern Amazonia north of the Amazon River, most likely in the Brazilian state of Amapá. Despite the high level of sequence diversity and marked morphological differences in size across the range of M. hispidus, we continue to regard this assemblage as a single species until additional samples and analyses suggest otherwise. Copyright 2002 Elsevier Science (USA)

Efficacy of the Kyoto Classification of Gastritis in Identifying Patients at High Risk for Gastric Cancer.

PubMed

Sugimoto, Mitsushige; Ban, Hiromitsu; Ichikawa, Hitomi; Sahara, Shu; Otsuka, Taketo; Inatomi, Osamu; Bamba, Shigeki; Furuta, Takahisa; Andoh, Akira

2017-01-01

Objective The Kyoto gastritis classification categorizes the endoscopic characteristics of Helicobacter pylori (H. pylori) infection-associated gastritis and identifies patterns associated with a high risk of gastric cancer. We investigated its efficacy, comparing scores in patients with H. pylori-associated gastritis and with gastric cancer. Methods A total of 1,200 patients with H. pylori-positive gastritis alone (n=932), early-stage H. pylori-positive gastric cancer (n=189), and successfully treated H. pylori-negative cancer (n=79) were endoscopically graded according to the Kyoto gastritis classification for atrophy, intestinal metaplasia, fold hypertrophy, nodularity, and diffuse redness. Results The prevalence of O-II/O-III-type atrophy according to the Kimura-Takemoto classification in early-stage H. pylori-positive gastric cancer and successfully treated H. pylori-negative cancer groups was 45.1%, which was significantly higher than in subjects with gastritis alone (12.7%, p<0.001). Kyoto gastritis scores of atrophy and intestinal metaplasia in the H. pylori-positive cancer group were significantly higher than in subjects with gastritis alone (all p<0.001). No significant differences were noted in the rates of gastric fold hypertrophy or diffuse redness between the two groups. In a multivariate analysis, the risks for H. pylori-positive gastric cancer increased with intestinal metaplasia (odds ratio: 4.453, 95% confidence interval: 3.332-5.950, <0.001) and male sex (1.737, 1.102-2.739, p=0.017). Conclusion Making an appropriate diagnosis and detecting patients at high risk is crucial for achieving total eradication of gastric cancer. The scores of intestinal metaplasia and atrophy of the scoring system in the Kyoto gastritis classification may thus be useful for detecting these patients.

Genetic variability in E6, E7, and L1 genes of human papillomavirus genotype 52 from Southwest China.

PubMed

Zhang, Yiwen; Cao, Man; Wang, Mengting; Ding, Xianping; Jing, Yaling; Chen, Zuyi; Ma, Tengjiao; Chen, Honghan

2016-07-01

Human papillomavirus (HPV) is the major causative agent of cervical cancer, which accounts for the second highest cancer burden in women worldwide. HPV-52, the prevalent subtype in Asia, especially in southwest China, was analyzed in this study. To analyze polymorphisms, intratypic variants, and genetic variability in the E6-E7 (n=26) and L1 (n=53) genes of HPV-52, these genes were sequenced and the sequences were submitted to GenBank. Phylogenetic trees were constructed using the neighbor-joining and Kimura 2-parameters methods, followed by analysis of the diversity of secondary structure. Finally, we estimated the selection pressures acting on the E6-E7 and L1 genes. Fifty-one novel variants of HPV-52 L1, and two novel variants of HPV-52 E6-E7 were identified in this study. Thirty single nucleotide changes were observed in HPV-52 E6-E7 sequences with 19/30 non-synonymous mutations and 11/30 synonymous mutations (five in the alpha helix and five in the beta sheet). Fifty-five single nucleotide changes were observed in HPV-52 L1 sequences with 17/55 non-synonymous mutations (seven in the alpha helix and fourteen in the beta sheet) and 38/55 synonymous mutations. Selective pressure analysis predicted that most of these mutations reflect positive selection. Identifying new variants in HPV-52 may inform the rational design of new vaccines specifically for women in southwest China. Knowledge of genetic variation in HPV may be useful as an epidemiologic correlate of cervical cancer risk, or may even provide critical information for developing diagnostic probes. Copyright © 2016 Elsevier B.V. All rights reserved.

Hydrogen Sulfide Treatment Promotes Glucose Uptake by Increasing Insulin Receptor Sensitivity and Ameliorates Kidney Lesions in Type 2 Diabetes

PubMed Central

Xue, Rong; Hao, Dan-Dan; Sun, Ji-Ping; Li, Wen-Wen; Zhao, Man-Man; Li, Xing-Hui; Chen, Ying; Zhu, Jian-Hua; Ding, Ying-Jiong; Liu, Jun

2013-01-01

Abstract Aims: To examine if hydrogen sulfide (H2S) can promote glucose uptake and provide amelioration in type 2 diabetes. Results: Treatment with sodium hydrosulfide (NaHS, an H2S donor) increased glucose uptake in both myotubes and adipocytes. The H2S gas solution showed similar effects. The NaHS effects were blocked by an siRNA-mediated knockdown of the insulin receptor (IR). NaHS also increased phosphorylation of the IR, PI3K, and Akt. In Goto-Kakizaki (GK) diabetic rats, chronic NaHS treatment (30 μmol·kg−1·day−1) decreased fasting blood glucose, increased insulin sensitivity, and increased glucose tolerance with increased phosphorylation of PI3K and Akt in muscles. Similar insulin-sensitizing effects of NaHS treatment were also observed in Wistar rats. Moreover, glucose uptake was reduced in the cells with siRNA-mediated knockdown of the H2S-generating enzyme cystathionine γ-lyase in the presence or absence of exogenous H2S. Moreover, chronic NaHS treatment reduced oxygen species and the number of crescentic glomeruli in the kidney of GK rats. Innovation and Conclusion: This study provides the first piece of evidence for the insulin-sensitizing effect of NaHS/H2S in the both in vitro and in vivo models of insulin resistance. Rebound Track: This work was rejected during a standard peer review and rescued by the Rebound Peer Review (Antoxid Redox Signal 16: 293–296, 2012) with the following serving as open reviewers: Jin-Song Bian, Samuel Dudley, Hideo Kimura, and Xian Wang. Antioxid. Redox Signal. 19, 5–23. PMID:23293908

Selective phylogenetic analysis targeting 16S rRNA genes of hyperthermophilic archaea in the deep-subsurface hot biosphere.

PubMed

Kimura, Hiroyuki; Ishibashi, Jun-Ichiro; Masuda, Harue; Kato, Kenji; Hanada, Satoshi

2007-04-01

International drilling projects for the study of microbial communities in the deep-subsurface hot biosphere have been expanded. Core samples obtained by deep drilling are commonly contaminated with mesophilic microorganisms in the drilling fluid, making it difficult to examine the microbial community by 16S rRNA gene clone library analysis. To eliminate mesophilic organism contamination, we previously developed a new method (selective phylogenetic analysis [SePA]) based on the strong correlation between the guanine-plus-cytosine (G+C) contents of the 16S rRNA genes and the optimal growth temperatures of prokaryotes, and we verified the method's effectiveness (H. Kimura, M. Sugihara, K. Kato, and S. Hanada, Appl. Environ. Microbiol. 72:21-27, 2006). In the present study we ascertained SePA's ability to eliminate contamination by archaeal rRNA genes, using deep-sea hydrothermal fluid (117 degrees C) and surface seawater (29.9 degrees C) as substitutes for deep-subsurface geothermal samples and drilling fluid, respectively. Archaeal 16S rRNA gene fragments, PCR amplified from the surface seawater, were denatured at 82 degrees C and completely digested with exonuclease I (Exo I), while gene fragments from the deep-sea hydrothermal fluid remained intact after denaturation at 84 degrees C because of their high G+C contents. An examination using mixtures of DNAs from the two environmental samples showed that denaturation at 84 degrees C and digestion with Exo I completely eliminated archaeal 16S rRNA genes from the surface seawater. Our method was quite useful for culture-independent community analysis of hyperthermophilic archaea in core samples recovered from deep-subsurface geothermal environments.

Molecular Identification of Sibling Species of Sclerodermus (Hymenoptera: Bethylidae) That Parasitize Buprestid and Cerambycid Beetles by Using Partial Sequences of Mitochondrial DNA Cytochrome Oxidase Subunit 1 and 28S Ribosomal RNA Gene

PubMed Central

Jiang, Yuan; Yang, Zhongqi; Wang, Xiaoyi; Hou, Yuxia

2015-01-01

The species belonging to Sclerodermus (Hymenoptera: Bethylidae) are currently the most important insect natural enemies of wood borer pests, mainly buprestid and cerambycid beetles, in China. However, some sibling species of this genus are very difficult to distinguish because of their similar morphological features. To address this issue, we conducted phylogenetic and genetic analyses of cytochrome oxidase subunit I (COI) and 28S RNA gene sequences from eight species of Sclerodermus reared from different wood borer pests. The eight sibling species were as follows: S. guani Xiao et Wu, S. sichuanensis Xiao, S. pupariae Yang et Yao, and Sclerodermus spp. (Nos. 1–5). A 594-bp fragment of COI and 750-bp fragment of 28S were subsequently sequenced. For COI, the G-C content was found to be low in all the species, averaging to about 30.0%. Sequence divergences (Kimura-2-parameter distances) between congeneric species averaged to 4.5%, and intraspecific divergences averaged to about 0.09%. Further, the maximum sequence divergences between congeneric species and Sclerodermus sp. (No. 5) averaged to about 16.5%. All 136 samples analyzed were included in six reciprocally monophyletic clades in the COI neighbor-joining (NJ) tree. The NJ tree inferred from the 28S rRNA sequence yielded almost identical results, but the samples from S. guani, S. sichuanensis, S. pupariae, and Sclerodermus spp. (Nos. 1–4) clustered together and only Sclerodermus sp. (No. 5) clustered separately. Our findings indicate that the standard barcode region of COI can be efficiently used to distinguish morphologically similar Sclerodermus species. Further, we speculate that Sclerodermus sp. (No. 5) might be a new species of Sclerodermus. PMID:25782000

List of participants at SIDE IV meeting, Tokyo, 27 November--1 December 2000

NASA Astrophysics Data System (ADS)

2001-12-01

Mark J Ablowitz, Vsevolod Adler, Mark Alber, Said Belmehdi, Marco Boiti, Claude Brezinski, R Bullough, Y M Chiang, Theodore Chihara, Peter A Clarkson, Robert Conte, Adam Doliwa, Vladimir Dorodnitsyn, Mitsuaki Eguchi, Claire Gilson, Basil Grammaticos, Valeri Gromak, Rod Halburd, Koji Hasegawa, Jarmo Hietarinta, Ryogo Hirota, Xing Biao Hu, M Idzumi, J Inoguchi, Hiroya Ishikara, Mourad Ismail, Shin Isojima, Kenichi Ito, Yoshiaki Itoh, Masashi Iwasaki, Klara Janglajew, Michio Jimbo, Nalini Joshi, Kenji Kajiwara, Saburo Kakei, Masaru Kamata, Satoshi Kamei, Rinat Kashaev, Shingo Kawai, Taeko Kimijima, K Kimura, Anatol Kirillov, Koichi Kondo, Boris Konopelchenko, Martin Kruskal, Atsuo Kuniba, Wataru Kunishima, Franklin Lambert, Serguei Leble, Decio Levi, Shigeru Maeda, Manuel Manas, Ken-Ichi Maruno, Tetsu Masuda, J Matsukidaira, Atsushi Matsumiya, Shigeki Matsutani, Yukitaka Minesaki, Mikio Murata, Micheline Musette, Atsushi Nagai, Katsuya Nakagawa, Atsushi Nakamula, Akira Nakamura, Yoshimasa Nakamura, Frank Nijhoff, J J C Nimmo, Katsuhiro Nishinari, Michitomo Nishizawa, A Nobe, Masatoshi Noumi, Yaeko Ohsaki, Yasuhiro Ohta, Kazuo Okamoto, Alexandre Orlov, Naoki Osada, Flora Pempinelli, Spiro Pyrlis, Reinout Quispel, Orlando Ragnisco, Alfred Ramani, Jean-Pierre Ramis, Andreas Ruffing, Simon Ruijsenaars, Satoru Saito, Noriko Saitoh, Hidetaka Sakai, Paulo Santini, Narimasa Sasa, Ryu Sasaki, Yoshikatsu Sasaki, Junkichi Satsuma, Sergei Sergeev, Nobuhiko Shinzawa, Evgueni Sklyanin, Juris Suris, Norio Suzuki, Yukiko Tagami, Katsuaki Takahashi, Daisuke Takahashi, Tomoyuki Takenawa, Yoshiro Takeyama, K M Tamizhmani, T Tamizhmani, Kouichi Toda, Morikatsu Toda, Tetsuji Tokihiro, Takayuki Tsuchida, Yohei Tsuchiya, Teruhisa Tsuda, Satoru Tsujimoto, Walter Van Assche, Claude Viallet, Luc Vinet, Shinsuke Watanabe, Yoshihida Watanabe, Ralph Willox, Pavel Winternitz, Yasuhiko Yamada, Yuji Yamada, Jin Yoneda, Haruo Yoshida, Katsuhiko Yoshida, Daisuke Yoshihara, Fumitaka Yura, J

Characterization of Clostridium Baratii Type F Strains Responsible for an Outbreak of Botulism Linked to Beef Meat Consumption in France.

PubMed

Mazuet, Christelle; Legeay, Christine; Sautereau, Jean; Bouchier, Christiane; Criscuolo, Alexis; Bouvet, Philippe; Trehard, Hélène; Jourdan Da Silva, Nathalie; Popoff, Michel

2017-02-01

A second botulism outbreak due to Clostridium baratii occurred in France in August 2015 and included three patients who had their meal in a restaurant the same day. We report the characterization of C. baratii isolates including whole genome sequencing (WGS). Four C. baratii isolates collected in August 2015 from the outbreak 2 were analysed for toxin production and typing as well as for genetic characterization. WGS was done using using the NEBNext Ultra DNA Library Prep kit for Illumina (New England Biolabs) and sequenced on MiSeq machine (Illumina) in paired-end reads of 250 bases. The phylogenetic tree was generated based on the UPGMA method with genetic distances computed by using the Kimura two-parameter model. Evolutionary analyses were conducted in Bionumerics (V.6.6 Applied Maths). Three C. baratii isolates for patient's stools and one isolate from meat produced botulinum neurotoxin (BoNT) type F and retained a bont/F7 gene in OrfX cluster. All isolates were identical according to the WGS. However, phylogeny of the core genome showed that the four C. baratii strains were distantly related to that of the previous C. baratii outbreak in France in 2014 and from the other C. baratii strains reported in databanks. The fact that the strains isolated from the patients and meat samples were genetically identical supports that the meat used for the Bolognese sauce was responsible for this second botulism outbreak in France. These isolates were unrelated to that from the first C. baratii outbreak in France in 2014 indicating a distinct source of contamination. WGS provided robust determination of genetic relatedness and information regarding BoNT typing and toxin gene locus genomic localization.

Discrimination and similarity evaluation of tissue-cultured and wild Dendrobium species using Fourier transform infrared spectroscopy

NASA Astrophysics Data System (ADS)

Chen, Nai-dong; Chen, Han; Li, Jun; Sang, Mang-mang; Ding, Shen; Yu, Hao

2015-04-01

The FTIR method was applied to evaluate the similarity of tissue-cultured and wild Dendrobium huoshanense C.Z. Tang et S.J. Cheng, Dendrobium officinale Kimura et Migo and Dendrobium moniliforme (Linn.) Sw and discriminate different Dendrobium species, especially D. huoshanense and its main goldbrick Dendrobium henanense J.L. Lu et L.X. Gao. Despite the general pattern of the IR spectra, different intensities, shapes and peak positions were found in the IR spectra of these samples, especially in the range of 1800-600 cm-1, which could be used to discriminate them. The methanol, aqueous extracting procedure and the second derivative transformation obviously enlarged the tiny spectral differences among these samples. The similarity evaluation based on the IR spectra and the second derivative IR spectrum revealed that the similarity of the methanol extracts between tissue-cultured and wild Dendrobiums might be lower than that between different Dendrobium species. The similarities of the powders and aqueous extracts between tissue-cultured and wild Dendrobiums were higher than those between different Dendrobium species. The further principal component analysis showed that the first three components explained 99.7%, 87.7% and 85.1% of data variance for powder, methanol extract and aqueous extract, respectively, demonstrating a good discrimination between samples. Our research suggested that the variations of secondary metabolites between different origins of the investigated Dendrobiums might be higher than what we had supposed. Tissue culture techniques were widely used in the conversation of rare and endangered medicinal amedica, however, our study suggested that the chemical constituents of tissue-cultured plants might be quite different from their wild correspondences.

DNA barcoding commercially important fish species of Turkey.

PubMed

Keskın, Emre; Atar, Hasan H

2013-09-01

DNA barcoding was used in the identification of 89 commercially important freshwater and marine fish species found in Turkish ichthyofauna. A total of 1765 DNA barcodes using a 654-bp-long fragment of the mitochondrial cytochrome c oxidase subunit I gene were generated for 89 commercially important freshwater and marine fish species found in Turkish ichthyofauna. These species belong to 70 genera, 40 families and 19 orders from class Actinopterygii, and all were associated with a distinct DNA barcode. Nine and 12 of the COI barcode clusters represent the first species records submitted to the BOLD and GenBank databases, respectively. All COI barcodes (except sequences of first species records) were matched with reference sequences of expected species, according to morphological identification. Average nucleotide frequencies of the data set were calculated as T = 29.7%, C = 28.2%, A = 23.6% and G = 18.6%. Average pairwise genetic distance among individuals were estimated as 0.32%, 9.62%, 17,90% and 22.40% for conspecific, congeneric, confamilial and within order, respectively. Kimura 2-parameter genetic distance values were found to increase with taxonomic level. For most of the species analysed in our data set, there is a barcoding gap, and an overlap in the barcoding gap exists for only two genera. Neighbour-joining trees were drawn based on DNA barcodes and all the specimens clustered in agreement with their taxonomic classification at species level. Results of this study supported DNA barcoding as an efficient molecular tool for a better monitoring, conservation and management of fisheries. © 2013 John Wiley & Sons Ltd.

Deciduous Trees and the Application of Universal DNA Barcodes: A Case Study on the Circumpolar Fraxinus

PubMed Central

Cruaud, Corinne; Bousquet, Jean; Frascaria-Lacoste, Nathalie

2012-01-01

The utility of DNA barcoding for identifying representative specimens of the circumpolar tree genus Fraxinus (56 species) was investigated. We examined the genetic variability of several loci suggested in chloroplast DNA barcode protocols such as matK, rpoB, rpoC1 and trnH-psbA in a large worldwide sample of Fraxinus species. The chloroplast intergenic spacer rpl32-trnL was further assessed in search for a potentially variable and useful locus. The results of the study suggest that the proposed cpDNA loci, alone or in combination, cannot fully discriminate among species because of the generally low rates of substitution in the chloroplast genome of Fraxinus. The intergenic spacer trnH-psbA was the best performing locus, but genetic distance-based discrimination was moderately successful and only resulted in the separation of the samples at the subgenus level. Use of the BLAST approach was better than the neighbor-joining tree reconstruction method with pairwise Kimura's two-parameter rates of substitution, but allowed for the correct identification of only less than half of the species sampled. Such rates are substantially lower than the success rate required for a standardised barcoding approach. Consequently, the current cpDNA barcodes are inadequate to fully discriminate Fraxinus species. Given that a low rate of substitution is common among the plastid genomes of trees, the use of the plant cpDNA “universal” barcode may not be suitable for the safe identification of tree species below a generic or sectional level. Supplementary barcoding loci of the nuclear genome and alternative solutions are proposed and discussed. PMID:22479532

Anti-atopic dermatitis effects and the mechanism of lactic acid bacteria isolated from Mongolian fermented milk.

PubMed

Hayashi, Atsushi; Kimura, Makoto; Nakamura, Yusaku; Yasui, Hisako

2009-05-01

We investigated the anti-allergic effects of one strain (T120) of a lactic acid bacteria (LAB) isolated from Mongolian fermented milk using atopic dermatitis (AD) model mice (NC/Nga mice). Strain T120 has already been identified as Enterococcus faecium and shown to induce strong production of IL-12 (Kimura et al. 2006). In in vitro studies, strain T120 suppressed total IgE production and induced IL-12 and IFN-gamma production by splenocytes of NC/Nga mice. The additional examination of various neutralization antibodies was performed to elucidate in detail the mechanism of depressed IgE production by strain T120. As a result, it became clear that IL-12 induced by strain T120 increased production of IFN-gamma and total IgE production was mainly controlled by the IFN-gamma. In order to define the cells which produce IL-12 powerfully by this strain, antigen-presenting cells (APCs) such as macrophages and dendritic cells (DCs) were removed from the splenocytes, and the reactivity of these cells to the strain was examined. Induction of IL-12 and IFN-gamma by strain T120 became significantly very low by removal of APCs from splenocytes. Therefore, it was clear that strain T120 acted on APCs and induced production of IL-12. Further, this strain enhanced the production of IL-10 by splenocytes. In in vivo studies, intraperitoneal injection of strain T120 inhibited serum IgE elevation and atopic dermatitis symptoms in NC/Nga mice. These results suggest that an anti-allergic effect of strain T120 depends on the increased production of IL-12 by APCs activated by the strain and following the increased production of IFN-gamma. Further, activation of regulatory T cells by strain T120 may inhibit atopic disease.

DNA barcoding of Arctic Ocean holozooplankton for species identification and recognition

NASA Astrophysics Data System (ADS)

Bucklin, Ann; Hopcroft, Russell R.; Kosobokova, Ksenia N.; Nigro, Lisa M.; Ortman, Brian D.; Jennings, Robert M.; Sweetman, Christopher J.

2010-01-01

Zooplankton species diversity and distribution are important measures of environmental change in the Arctic Ocean, and may serve as 'rapid-responders' of climate-induced changes in this fragile ecosystem. The scarcity of taxonomists hampers detailed and up-to-date monitoring of these patterns for the rarer and more problematic species. DNA barcodes (short DNA sequences for species recognition and discovery) provide an alternative approach to accurate identification of known species, and can speed routine analysis of zooplankton samples. During 2004-2008, zooplankton samples were collected during cruises to the central Arctic Ocean and Chukchi Sea. A ˜700 base-pair region of the mitochondrial cytochrome oxidase I (mtCOI) gene was amplified and sequenced for 82 identified specimens of 41 species, including cnidarians (six hydrozoans, one scyphozoan), arthropod crustaceans (five amphipods, 24 copepods, one decapod, and one euphausiid); two chaetognaths; and one nemertean. Phylogenetic analysis used the Neighbor-Joining algorithm with Kimura-2-Parameter (K-2-P) distances, with 1000-fold bootstrapping. K-2-P genetic distances between individuals of the same species ranged from 0.0 to 0.2; genetic distances between species ranged widely from 0.1 to 0.7. The mtCOI gene tree showed monophyly (at 100% bootstrap value) for each of the 26 species for which more than one individual was analyzed. Of seven genera for which more than one species was analyzed, four were shown to be monophyletic; three genera were not resolved. At higher taxonomic levels, only the crustacean order Copepoda was resolved, with bootstrap value of 83%. The mtCOI barcodes accurately discriminated and identified known species of 10 taxonomic groups of Arctic Ocean holozooplankton. A comprehensive DNA barcode database for the estimated 300 described species of Arctic holozooplankton will allow rapid assessment of species diversity and distribution in this climate-vulnerable ocean ecosystem.

Detection of the first G6P[14] human rotavirus strain in an infant with diarrhoea in Ghana.

PubMed

Damanka, Susan; Lartey, Belinda; Agbemabiese, Chantal; Dennis, Francis E; Adiku, Theophilus; Nyarko, Kofi; Ofori, Michael; Armah, George E

2016-11-10

Rotaviruses with G6P[14] specificity are mostly isolated in cattle and have been established as a rare cause of gastroenteritis in humans. This study reports the first detection of G6P[14] rotavirus strain in Ghana from the stool of an infant during a hospital-based rotavirus surveillance study in 2010. Viral RNA was extracted and rotavirus VP7 and VP4 genes amplified by one step RT-PCR using gene-specific primers. The DNA was purified, sequenced and genotypes determined using BLAST and RotaC v2.0. Phylogenetic tree was constructed using maximum likelihood method in MEGA v6.06 software and statistically supported by bootstrapping with 1000 replicates. Phylogenetic distances were calculated using the Kimura-2 parameter model. The study strain, GHA-M0084/2010 was characterised as G6P[14]. The VP7 gene of the Ghanaian strain clustered in G6 lineage-III together with artiodactyl and human rotavirus (HRV) strains. It exhibited the highest nucleotide (88.1 %) and amino acid (86.9 %) sequence identity with Belgian HRV strain, B10925. The VP8* fragment of the VP4 gene was closely related to HRV strains detected in France, Italy, Spain and Belgium. It exhibited the strongest nucleotide sequence identity (87.9 %) with HRV strains, PA169 and PR/1300 (Italy) and the strongest amino acid sequence identity (89.3 %) with HRV strain R2775/FRA/07 (France). The study reports the first detection of G6P[14] HRV strain in an infant in Ghana. The detection of G6P[14], an unusual strain pre-vaccine introduction in Ghana, suggests a potential compromise of vaccine effectiveness and indicates the necessity for continuous surveillance in the post vaccine era.

Jupiter's X-ray Auroral Pulsations and Spectra During Juno Perijove 7

NASA Astrophysics Data System (ADS)

Dunn, W.; Branduardi-Raymont, G.; Ray, L. C.; Jackman, C. M.; Kraft, R.; Gladstone, R.; Yao, Z.; Rae, J.; Gray, R.; Elsner, R.; Grodent, D. C.; Nichols, J. D.; Ford, P. G.; Ness, J. U.; Kammer, J.; Rodriguez, P.

2017-12-01

Jupiter's X-ray aurora is concentrated into a bright and dynamic hot spot that is produced by precipitating 10 MeV ions [Gladstone et al. 2002; Elsner et al. 2005; Branduardi-Raymont et al. 2007]. These highly energetic emissions exhibit pulsations over timescales of 10s of minutes and change morphology, intensity and precipitating particle populations from observation to observation and pole to pole [e.g. Dunn et al. 2016; in-press]. The acceleration process/es that allow Jupiter to produce these high-energy ion charge exchange emissions are not well understood, but are concentrated in the most poleward regions of the aurora, where field lines map to the outer magnetosphere and possibly beyond [Vogt et al. 2015; Kimura et al. 2016]. On July 11th 2017, NASA's Juno spacecraft conducted its 7th perijove flyby of Jupiter and is predicted to have flown directly through field lines that map to the Northern and Southern X-ray hot spots. During this unique flight, the XMM-Newton observatory conducted 40 hours of continuous time-tagged X-ray observations. We present the results from these X-ray observations, showing that Jupiter's X-ray aurora varies significantly from one planetary rotation to the next and that the spectral signatures, indicative of the precipitating ion and electron populations producing the emission, also vary. We measure the Doppler broadening of the spectral lines to calculate the ion energies at the point when they impact the ionosphere, in order that these might be compared with in-situ data to constrain Jovian auroral acceleration processes. Finally, we compare X-ray signatures from the last decade of observations with UV polar emissions at similar times to further enrich multi-wavelength connections and deepen our understanding of how Jupiter is able to generate its highly energetic polar auroral precipitations.

Efficacy of the Kyoto Classification of Gastritis in Identifying Patients at High Risk for Gastric Cancer

PubMed Central

Sugimoto, Mitsushige; Ban, Hiromitsu; Ichikawa, Hitomi; Sahara, Shu; Otsuka, Taketo; Inatomi, Osamu; Bamba, Shigeki; Furuta, Takahisa; Andoh, Akira

2017-01-01

Objective The Kyoto gastritis classification categorizes the endoscopic characteristics of Helicobacter pylori (H. pylori) infection-associated gastritis and identifies patterns associated with a high risk of gastric cancer. We investigated its efficacy, comparing scores in patients with H. pylori-associated gastritis and with gastric cancer. Methods A total of 1,200 patients with H. pylori-positive gastritis alone (n=932), early-stage H. pylori-positive gastric cancer (n=189), and successfully treated H. pylori-negative cancer (n=79) were endoscopically graded according to the Kyoto gastritis classification for atrophy, intestinal metaplasia, fold hypertrophy, nodularity, and diffuse redness. Results The prevalence of O-II/O-III-type atrophy according to the Kimura-Takemoto classification in early-stage H. pylori-positive gastric cancer and successfully treated H. pylori-negative cancer groups was 45.1%, which was significantly higher than in subjects with gastritis alone (12.7%, p<0.001). Kyoto gastritis scores of atrophy and intestinal metaplasia in the H. pylori-positive cancer group were significantly higher than in subjects with gastritis alone (all p<0.001). No significant differences were noted in the rates of gastric fold hypertrophy or diffuse redness between the two groups. In a multivariate analysis, the risks for H. pylori-positive gastric cancer increased with intestinal metaplasia (odds ratio: 4.453, 95% confidence interval: 3.332-5.950, <0.001) and male sex (1.737, 1.102-2.739, p=0.017). Conclusion Making an appropriate diagnosis and detecting patients at high risk is crucial for achieving total eradication of gastric cancer. The scores of intestinal metaplasia and atrophy of the scoring system in the Kyoto gastritis classification may thus be useful for detecting these patients. PMID:28321054

Optical calibration of a new two-way optical component network analyzer

NASA Astrophysics Data System (ADS)

Tsao, Shyh-Lin; Ko, Chih-Han; Liou, Tai-Chi

2003-12-01

High-speed fiber communications show promising results recently [1,2]. Using of lightwave technology for measuring S parameters with optical component becoming important. For this purpose to develop a two-way network analyzer has been reported [3]. In this paper, we report the calibration method of a new two-way lightwave component analyze for applying in fiber optical signal processing elements. The background error and circulator wavelength response are all calibrated. We have designed a new probe for two-way optical component network analyzer. The probe is composed of frequency division multiplexer(FDM), electrical circulator, optical transmitter, optical receiver, and an optical circulator. We design 2-D grating structures as frequency division. The PCB we adopted is Kinstan GD1530 160 whose relative dielectric constantɛ= 4.3, length= 120 mm, and height= 1.8 mm. Two dimensional non-metal covered array square pads are designed on FR4 Glass-Epoxy board for FDM. The FDM can be achieved by the two dimensional non-metalized covered array square pads. Finally we use a single fiber ring resonator filter as our test samples. Comparing the numerical and experimental results, test the device we made. References [1] D. D. Curtis and E. E. Ames,"Optical Test Set for Microwave Fiber-Optic Network Analysis," IEEE Transactions on Microwave Theory and Techniques. , vol. 38, NO.5, pp. 552-559, 1990. [2] J. A. C. Bingham,"Multicarrier modulation for data transmission: an idea whose time has come," IEEE Commun. Magazine., pp. 5 -14, 1990. [3] M. Nakazawa, K. Suzuki, and Y. Kimura, " 3.2-5 Gbps 100km error-free soliton transmission with erbium amplifiers and repenters," IEEE Photonics Tech Lett.,vol.2,pp.216-219,1990.

Lacanobia oleracea nucleopolyhedrovirus (LaolNPV): A new European species of alphabaculovirus with a narrow host range

PubMed Central

Erlandson, Martin A.; Frayssinet, Marie; Williams, Trevor; Theilmann, David A.; Volkoff, Anne-Nathalie; Caballero, Primitivo

2017-01-01

During an insect sampling program in alfalfa crops near Montpellier, France in 2011, Lacanobia oleracea larvae were collected that died due to nucleopolyhedrovirus infection (LaolNPV). This virus was subjected to molecular and biological characterization. The virus was a multiple nucleocapsid NPV that showed similar restriction profiles to Mamestra configurata NPV-A (MacoNPV-A) but with significant differences. Polypeptide analysis demonstrated similar proteins in occlusion bodies and occlusion derived virions, to those observed in NPVs from Mamestra spp. Terminal sequencing revealed that the genome organization shared similarity with that of MacoNPV-A. The most homologous virus was MacoNPV-A 90/2 isolate (95.63% identity and 96.47% similarity), followed by MacoNPV-A 90/4 strain (95.37% and 96.26%), MacoNPV-B (89.21% and 93.53%) and M. brassicae MNPV (89.42% and 93.74%). Phylogenetic analysis performed with lef-8, lef-9, polh and a concatenated set of genes showed that LaolNPV and the Mamestra spp. NPVs clustered together with HaMNPV, but with a closer genetic distance to MacoNPV-A strains. The Kimura 2-parameter (K-2-P) distances of the complete genes were greater than 0.05 between LaolNPV and the MbMNPV/MacoNPV-B/HaMNPV complex, which indicates that LaolNPV is a distinct species. K-2-P distances were in the range 0.015–0.050 for comparisons of LaolNPV with MacoNPV-A strains, such that additional biological characteristics should be evaluated to determine species status. While MacoNPV-A was pathogenic to seven lepidopteran species tested, LaolNPV was only pathogenic to Chrysodeixis chalcites. Given these findings, Lacanobia oleracea nucleopolyhedrovirus should be considered as a new species in the Alphabaculovirus genus. PMID:28426736

Simulations of coupled, Antarctic ice-ocean evolution using POP2x and BISICLES (Invited)

NASA Astrophysics Data System (ADS)

Price, S. F.; Asay-Davis, X.; Martin, D. F.; Maltrud, M. E.; Hoffman, M. J.

2013-12-01

We present initial results from Antarctic, ice-ocean coupled simulations using large-scale ocean circulation and land ice evolution models. The ocean model, POP2x is a modified version of POP, a fully eddying, global-scale ocean model (Smith and Gent, 2002). POP2x allows for circulation beneath ice shelf cavities using the method of partial top cells (Losch, 2008). Boundary layer physics, which control fresh water and salt exchange at the ice-ocean interface, are implemented following Holland and Jenkins (1999), Jenkins (1999), and Jenkins et al. (2010). Standalone POP2x output compares well with standard ice-ocean test cases (e.g., ISOMIP; Losch, 2008; Kimura et al., 2013) and with results from other idealized ice-ocean coupling test cases (e.g., Goldberg et al., 2012). The land ice model, BISICLES (Cornford et al., 2012), includes a 1st-order accurate momentum balance (L1L2) and uses block structured, adaptive-mesh refinement to more accurately model regions of dynamic complexity, such as ice streams, outlet glaciers, and grounding lines. For idealized test cases focused on marine-ice sheet dynamics, BISICLES output compares very favorably relative to simulations based on the full, nonlinear Stokes momentum balance (MISMIP-3d; Pattyn et al., 2013). Here, we present large-scale (southern ocean) simulations using POP2x with fixed ice shelf geometries, which are used to obtain and validate modeled submarine melt rates against observations. These melt rates are, in turn, used to force evolution of the BISICLES model. An offline-coupling scheme, which we compare with the ice-ocean coupling work of Goldberg et al. (2012), is then used to sequentially update the sub-shelf cavity geometry seen by POP2x.

Major variation of paleo-maximum temperature and consolidation state within post Miocene forearc basin, central Japan

NASA Astrophysics Data System (ADS)

Kamiya, N.; Yamamoto, Y.; Takemura, T.

2015-12-01

Since forearc-basin evolve associated with development of the accretionary prisms, their geologic structures have clues to understanding the tectonic processes associated with plate subduction. We found a major difference in paleo-geothermal structure and consolidation states between the unconformity in the forearc basin in the Boso Peninsula, central Japan. The geology of the Boso Peninsula, central Japan is divided into three parts; Early Miocene and Late Miocene accretionary prisms in the southern part, the Hayama-Mineoka tectonic belt mainly composed of ophiolite in the middle part, and post-Middle Miocene forearc basin in the northern part. Sediments in the forearc basin are composed of 15-3Ma Miura Group and 3-0.6Ma Kazusa Group. Boundary of the two groups is the Kurotaki Unconformity formed about 3Ma, when convergent direction of the Philippine Sea Plate has been changed (Takahashi, 2006). Vitrinite reflectance (Ro) analyses were conducted and revealed that major variation of paleo-maximum temperature between the Miura and Kazusa groups. The maximum paleo-temperature in the Miura Group is estimated as 70-95˚C, whereas in the lower part of the Kazusa Group is less than 10-35˚C. Given 20˚C/km (Sakai et al, 2011) paleo-geothermal gradient, approximately 2000 m uplifting/erosion of the Miura Group is expected when the unconformity formed. To verify the amount of this uplifting/erosion, we are performing consolidation test of mudstone. [Reference] Takahashi, M., 2006, Tectonic Development of the Japanese Islands Controlled by Philippine Sea Plate Motion, Journal of Geography, 115, 116-123. Sakai R., Munakata M., Kimura H., Ichikawa Y., and Nakamura M., 2011, Study on Validation Method of Regional Groundwater Flow Model : Case Study for Boso Peninsula, JAEA-research 2010(66), 1-20, 1-2.

Molecular characterization and phylogenetic relationship of wild type 1 poliovirus strains circulating across Pakistan and Afghanistan bordering areas during 2010-2012.

PubMed

Shaukat, Shahzad; Angez, Mehar; Alam, Muhammad Masroor; Sharif, Salmaan; Khurshid, Adnan; Malik, Farzana; Rehman, Lubna; Zaidi, Syed Sohail Zahoor

2014-01-01

Pakistan and Afghanistan share a long uncontrolled border with extensive population movement on both sides. Wild poliovirus transmission has never been interrupted in this block due to war against terrorism, poor public health infrastructure, misconceptions about polio vaccines and inadequate immunization activities. All these issues complicate the eradication operations and reinforce the complexity of wiping out poliomyelitis from this region. This study illustrates the origins and routes of cross-border wild poliovirus type 1 (WPV1) transmission during 2010-2012 between Pakistan and Afghanistan. Sequence analyses were conducted based on complete VP1 capsid protein sequences for WPV1 study strains to determine the origin of poliovirus genetic lineages and their evolutionary relationships. Phylogenetic tree was constructed from VP1 gene sequences applying Maximum Likelihood method using Kimura 2- parameter model in MEGA program v 5.0. A total of 72 (14.3%) out of 502 wild-type 1 polioviruses were found circulating in border areas of both countries during 2010-2012. Molecular phylogenetic analysis classified these strains in to two sub-genotypes with four clusters and 18 lineages. Genetic data confirmed that the most of WPV1 lineages (12; 66.6%) were transmitted from Pakistan to Afghanistan. However, the genetic diversity was significantly reduced during 2012 as most of the lineages were completely eliminated. In conclusion, Pakistan-Afghanistan block has emerged as a single poliovirus reservoir sharing the multiple poliovirus lineages due to uncontrolled movement of people across the borders between two countries. If it is neglected, it can jeopardize the extensive global efforts done so-far to eradicate the poliovirus infection. Our data will be helpful to devise the preventive strategies for effective control of wild poliovirus transmission in this region.

Markov Chain-Like Quantum Biological Modeling of Mutations, Aging, and Evolution.

PubMed

Djordjevic, Ivan B

2015-08-24

Recent evidence suggests that quantum mechanics is relevant in photosynthesis, magnetoreception, enzymatic catalytic reactions, olfactory reception, photoreception, genetics, electron-transfer in proteins, and evolution; to mention few. In our recent paper published in Life, we have derived the operator-sum representation of a biological channel based on codon basekets, and determined the quantum channel model suitable for study of the quantum biological channel capacity. However, this model is essentially memoryless and it is not able to properly model the propagation of mutation errors in time, the process of aging, and evolution of genetic information through generations. To solve for these problems, we propose novel quantum mechanical models to accurately describe the process of creation spontaneous, induced, and adaptive mutations and their propagation in time. Different biological channel models with memory, proposed in this paper, include: (i) Markovian classical model, (ii) Markovian-like quantum model, and (iii) hybrid quantum-classical model. We then apply these models in a study of aging and evolution of quantum biological channel capacity through generations. We also discuss key differences of these models with respect to a multilevel symmetric channel-based Markovian model and a Kimura model-based Markovian process. These models are quite general and applicable to many open problems in biology, not only biological channel capacity, which is the main focus of the paper. We will show that the famous quantum Master equation approach, commonly used to describe different biological processes, is just the first-order approximation of the proposed quantum Markov chain-like model, when the observation interval tends to zero. One of the important implications of this model is that the aging phenotype becomes determined by different underlying transition probabilities in both programmed and random (damage) Markov chain-like models of aging, which are mutually

Markov Chain-Like Quantum Biological Modeling of Mutations, Aging, and Evolution

PubMed Central

Djordjevic, Ivan B.

2015-01-01

Recent evidence suggests that quantum mechanics is relevant in photosynthesis, magnetoreception, enzymatic catalytic reactions, olfactory reception, photoreception, genetics, electron-transfer in proteins, and evolution; to mention few. In our recent paper published in Life, we have derived the operator-sum representation of a biological channel based on codon basekets, and determined the quantum channel model suitable for study of the quantum biological channel capacity. However, this model is essentially memoryless and it is not able to properly model the propagation of mutation errors in time, the process of aging, and evolution of genetic information through generations. To solve for these problems, we propose novel quantum mechanical models to accurately describe the process of creation spontaneous, induced, and adaptive mutations and their propagation in time. Different biological channel models with memory, proposed in this paper, include: (i) Markovian classical model, (ii) Markovian-like quantum model, and (iii) hybrid quantum-classical model. We then apply these models in a study of aging and evolution of quantum biological channel capacity through generations. We also discuss key differences of these models with respect to a multilevel symmetric channel-based Markovian model and a Kimura model-based Markovian process. These models are quite general and applicable to many open problems in biology, not only biological channel capacity, which is the main focus of the paper. We will show that the famous quantum Master equation approach, commonly used to describe different biological processes, is just the first-order approximation of the proposed quantum Markov chain-like model, when the observation interval tends to zero. One of the important implications of this model is that the aging phenotype becomes determined by different underlying transition probabilities in both programmed and random (damage) Markov chain-like models of aging, which are mutually

Phylogeny and polymorphism in the long control regions E6, E7, and L1 of HPV Type 56 in women from southwest China

PubMed Central

Jing, Yaling; Wang, Tao; Chen, Zuyi; Ding, Xianping; Xu, Jianju; Mu, Xuemei; Cao, Man; Chen, Honghan

2018-01-01

Globally, human papillomavirus (HPV)-56 accounts for a small proportion of all high-risk HPV types; however, HPV-56 is detected at a higher rate in Asia, particularly in southwest China. The present study analyzed polymorphisms, intratypic variants, and genetic variability in the long control regions (LCR), E6, E7, and L1 of HPV-56 (n=75). The LCRs, E6, E7 and L1 were sequenced using a polymerase chain reaction and the sequences were submitted to GenBank. Maximum-likelihood trees were constructed using Kimura's two-parameter model, followed by secondary structure analysis and protein damaging prediction. Additionally, in order to assess the effect of variations in the LCR on putative binding sites for cellular proteins, MATCH server was used. Finally, the selection pressures of the E6-E7 and L1 genes were estimated. A total of 18 point substitutions, a 42-bp deletion and a 19-bp deletion of LCR were identified. Some of those mutations are embedded in the putative binding sites for transcription factors. 18 single nucleotide changes occurred in the E6-E7 sequence, 11/18 were non-synonymous substitutions and 7/18 were synonymous mutations. A total 24 single nucleotide changes were identified in the L1 sequence, 6/24 being non-synonymous mutations and 18/24 synonymous mutations. Selective pressure analysis predicted that the majority of mutations of HPV-56 E6, E7 and L1 were of positive selection. The phylogenetic tree demonstrated that the isolates distributed in two lineages. Data on the prevalence and genetic variation of HPV-56 types in southwest China may aid future studies on viral molecular mechanisms and contribute to future investigations of diagnostic probes and therapeutic vaccines. PMID:29568922

DNA barcoding Australia's fish species

PubMed Central

Ward, Robert D; Zemlak, Tyler S; Innes, Bronwyn H; Last, Peter R; Hebert, Paul D.N

2005-01-01

Two hundred and seven species of fish, mostly Australian marine fish, were sequenced (barcoded) for a 655 bp region of the mitochondrial cytochrome oxidase subunit I gene (cox1). Most species were represented by multiple specimens, and 754 sequences were generated. The GC content of the 143 species of teleosts was higher than the 61 species of sharks and rays (47.1% versus 42.2%), largely due to a higher GC content of codon position 3 in the former (41.1% versus 29.9%). Rays had higher GC than sharks (44.7% versus 41.0%), again largely due to higher GC in the 3rd codon position in the former (36.3% versus 26.8%). Average within-species, genus, family, order and class Kimura two parameter (K2P) distances were 0.39%, 9.93%, 15.46%, 22.18% and 23.27%, respectively. All species could be differentiated by their cox1 sequence, although single individuals of each of two species had haplotypes characteristic of a congener. Although DNA barcoding aims to develop species identification systems, some phylogenetic signal was apparent in the data. In the neighbour-joining tree for all 754 sequences, four major clusters were apparent: chimaerids, rays, sharks and teleosts. Species within genera invariably clustered, and generally so did genera within families. Three taxonomic groups—dogfishes of the genus Squalus, flatheads of the family Platycephalidae, and tunas of the genus Thunnus—were examined more closely. The clades revealed after bootstrapping generally corresponded well with expectations. Individuals from operational taxonomic units designated as Squalus species B through F formed individual clades, supporting morphological evidence for each of these being separate species. We conclude that cox1 sequencing, or ‘barcoding’, can be used to identify fish species. PMID:16214743

The Ashra Project

NASA Astrophysics Data System (ADS)

Sasaki, M.; Aita, Y.; Aoki, T.; Asaoka, Y.; Browder, T.; Chonan, T.; Dye, S.; Eguchi, M.; Fox, R.; Guillian, G.; Hamilton, J.; Kimura, T.; Kohta, N.; Kuze, H.; Learned, J.; Masuda, M.; Matsuno, S.; Morimoto, Y.; Noda, K.; Ogawa, S.; Okumura, A.; Olsen, S.; Shibuya, H.; Shinomiya, K.; Sugiyama, N.; Yamaguchi, Y.; Yasuda, M.; Varner, G.; Watanabe, Y.; Watanabe, Y.

Ashra (All-sky Survey High Resolution Air-shower detector) is a project to build an unconventional optical telescope complex that images very wide field of view, covering 80% of the sky, yet with the angle pixel resolution of 1.2 arcsin, sensitive to the blue to UV light with the use of image intensifier and CMOS technology. The project primarily aims to observe Cherenkov and fluorescence lights from the lateral and longitudinal developments of very-high energy cosmic rays in the atmosphere. It can also be used to monitor optical transients in the wide field of sky. In 2004 we built prototype telescopes to verify and develop techniques at Haleakala in Hawaii, needed for the development of the full-scale telescopes. Construction of the main detector station has begun at Mauna Loa on the Hawaii Island in the summer of 2005. The pilot observation data have been taken. We will present the project status, and expected scientific impacts on the observational objectives such as optical transients, unidentified TeV gamma- ray and PeV neutrino sources, and the propagation of EeV cosmic rays. The Ashra Collaboration: (a) ICRR, Univ. Tokyo (b) Univ. Hawaii Manoa (c) Univ. Hawaii Hilo (d)Ibaraki Univ. (e) Toho Univ. (f) Chiba Univ. (g) Tokyo Inst. Tech. (h) Nagoya Univ. Y. Aita.^a, T. Aoki^a, Y. Asaoka^a, T. Browder^b, T. Chonan^a, S. Dye^b, M. Eguchi^a, R. Fox^c, G. Guillian^b, J. Hamilton^c, T. Kimura^d, N. Kohta^e, H. Kuze^f, J. Learned^b, M. Masuda^g, S. Matsuno^b, Y. Morimoto^e, K. Noda^a, S. Ogawa^e, A. Okumura^a, S. Olsen^b, M. Sasaki^a, H. Shibuya^e, K. Shinomiya^f, N. Sugiyama^h, Y. Yamaguchi^f, M. Yasuda^g, G. Varner^b, Y. Watanabe^g, Y. Watanabe^e

A Tale of Two Forcings: Present-Day Coupled Antarctic Ice-sheet/Southern Ocean dynamics using the POPSICLES model.

NASA Astrophysics Data System (ADS)

Martin, Daniel; Asay-Davis, Xylar; Cornford, Stephen; Price, Stephen; Ng, Esmond; Collins, William

2015-04-01

We present POPSICLES simulation results covering the full Antarctic Ice Sheet and the Southern Ocean spanning the period 1990 to 2010 resulting from two different choices of climate forcing: a 'normal-year' climatology and the CORE v. 2 interannual forcing data (Large and Yeager 2008). Simulations are performed at 0.1o (~5 km) ocean resolution and adaptive ice sheet resolution as fine as 500 m. We compare time-averaged melt rates below a number of major ice shelves with those reported by Rignot et al. (2013) as well as other recent studies. We also present seasonal variability and decadal melting trends from several Antarctic regions, along with the response of the ice shelves and consequent dynamics of the grounded ice sheet. POPSICLES couples the POP2x ocean model, a modified version of the Parallel Ocean Program (Smith and Gent, 2002), and the BISICLES ice-sheet model (Cornford et al., 2012). POP2x includes sub-ice-shelf circulation using partial top cells (Losch, 2008) and boundary layer physics following Holland and Jenkins (1999), Jenkins (2001), and Jenkins et al. (2010). Standalone POP2x output compares well with standard ice-ocean test cases (e.g., ISOMIP; Losch, 2008) and other continental-scale simulations and melt-rate observations (Kimura et al., 2013; Rignot et al., 2013). BISICLES makes use of adaptive mesh refinement and a 1st-order accurate momentum balance similar to the L1L2 model of Schoof and Hindmarsh (2009) to accurately model regions of dynamic complexity, such as ice streams, outlet glaciers, and grounding lines. Results of BISICLES simulations have compared favorably to comparable simulations with a Stokes momentum balance in both idealized tests (MISMIP-3d; Pattyn et al., 2013) and realistic configurations (Favier et al. 2014).

High-resolution coupled ice sheet-ocean modeling using the POPSICLES model

NASA Astrophysics Data System (ADS)

Ng, E. G.; Martin, D. F.; Asay-Davis, X.; Price, S. F.; Collins, W.

2014-12-01

It is expected that a primary driver of future change of the Antarctic ice sheet will be changes in submarine melting driven by incursions of warm ocean water into sub-ice shelf cavities. Correctly modeling this response on a continental scale will require high-resolution modeling of the coupled ice-ocean system. We describe the computational and modeling challenges in our simulations of the full Southern Ocean coupled to a continental-scale Antarctic ice sheet model at unprecedented spatial resolutions (0.1 degree for the ocean model and adaptive mesh refinement down to 500m in the ice sheet model). The POPSICLES model couples the POP2x ocean model, a modified version of the Parallel Ocean Program (Smith and Gent, 2002), with the BISICLES ice-sheet model (Cornford et al., 2012) using a synchronous offline-coupling scheme. Part of the PISCEES SciDAC project and built on the Chombo framework, BISICLES makes use of adaptive mesh refinement to fully resolve dynamically-important regions like grounding lines and employs a momentum balance similar to the vertically-integrated formulation of Schoof and Hindmarsh (2009). Results of BISICLES simulations have compared favorably to comparable simulations with a Stokes momentum balance in both idealized tests like MISMIP3D (Pattyn et al., 2013) and realistic configurations (Favier et al. 2014). POP2x includes sub-ice-shelf circulation using partial top cells (Losch, 2008) and boundary layer physics following Holland and Jenkins (1999), Jenkins (2001), and Jenkins et al. (2010). Standalone POP2x output compares well with standard ice-ocean test cases (e.g., ISOMIP; Losch, 2008) and other continental-scale simulations and melt-rate observations (Kimura et al., 2013; Rignot et al., 2013). For the POPSICLES Antarctic-Southern Ocean simulations, ice sheet and ocean models communicate at one-month coupling intervals.

Testosterone Deficiency Causes Endothelial Dysfunction via Elevation of Asymmetric Dimethylarginine and Oxidative Stress in Castrated Rats.

PubMed

Kataoka, Tomoya; Hotta, Yuji; Maeda, Yasuhiro; Kimura, Kazunori

2017-12-01

damage to the corpus cavernosum, resulting in erectile dysfunction. Kataoka T, Hotta Y, Maeda Y, Kimura K. Testosterone Deficiency Causes Endothelial Dysfunction via Elevation of Asymmetric Dimethylarginine and Oxidative Stress in Castrated Rats. J Sex Med 2017;14:1540-1548. Copyright © 2017 International Society for Sexual Medicine. Published by Elsevier Inc. All rights reserved.

Fungal infections of the eye--laboratory diagnosis and treatment.

PubMed

Nayak, N

2008-03-01

Infections of the eye give rise to severe ocular morbidity and blindness include keratitis, orbital cellulites, endophthalmitis and dacryocystitis. Corneal blindness, in developing countries is predominantly associated with infections. In India, nearly 30-35% of all culture positive infectious keratitis are caused fungi. Laboratory diagnosis mainly depends upon proper collection and transport of clinical specimens. In fungal keratitis, corneal scraping is the ideal sample, but occasionally corneal biopsy or anterior chamber aspirate may also be needed. Corneal scraping is usually by Kimura spatula, under a slit lamp examination, after anaesthetizing the cornea with topical anaesthetic like 0.4% proparcaine. Corneal biopsy is done by a minor trephining and AC aspirate using a sterile tuberculin syringe. In case of endophthalmitis, 150-200 ìl of aqueous humour is collected. Vitreous fluid (500-1000 ìl), however, is collected by pars plana vitrectomy onto sterile tuberculin syringe, the needle is then fixed to a sterile rubber bung after expelling air from the syringe. The collected sample is immediately transported to the laboratory. Swabs from the regurgitating lacrimnal sacs and wound aspirate/swabs are the ideal specimens for dacryocystitis and orbital cellulites, respectively. These samples are cultured onto SDA slants following standard procedures. The main draw back of culture is its long incubation time (5 to 14 days), though it is indispensable from the view point of the specificity. Direct examination (KOH wet mount, Gram's, Giemsa or calcofluor fluorescent staining methods) of the specimen, however, is quick and immensely helpful for ophthalmologist. The newer rapid methods, such as molecular techniques are also available and the management of patients can be according to the results obtained. With the advent of novel antifungal agents such as newer azoles and cell wall acting antifungals like echinocandins, the clinician has the wider option of selecting

Molecular taxonomy of the two Leishmania vectors Lutzomyia umbratilis and Lutzomyia anduzei (Diptera: Psychodidae) from the Brazilian Amazon

PubMed Central

2013-01-01

Background Lutzomyia umbratilis (a probable species complex) is the main vector of Leishmania guyanensis in the northern region of Brazil. Lutzomyia anduzei has been implicated as a secondary vector of this parasite. These species are closely related and exhibit high morphological similarity in the adult stage; therefore, they have been wrongly identified, both in the past and in the present. This shows the need for employing integrated taxonomy. Methods With the aim of gathering information on the molecular taxonomy and evolutionary relationships of these two vectors, 118 sequences of 663 base pairs (barcode region of the mitochondrial DNA cytochrome oxidase I – COI) were generated from 72 L. umbratilis and 46 L. anduzei individuals captured, respectively, in six and five localities of the Brazilian Amazon. The efficiency of the barcode region to differentiate the L. umbratilis lineages I and II was also evaluated. The data were analyzed using the pairwise genetic distances matrix and the Neighbor-Joining (NJ) tree, both based on the Kimura Two Parameter (K2P) evolutionary model. Results The analyses resulted in 67 haplotypes: 32 for L. umbratilis and 35 for L. anduzei. The mean intra-specific genetic distance was 0.008 (0.002 to 0.010 for L. umbratilis; 0.008 to 0.014 for L. anduzei), whereas the mean interspecific genetic distance was 0.044 (0.041 to 0.046), supporting the barcoding gap. Between the L. umbratilis lineages I and II, it was 0.009 to 0.010. The NJ tree analysis strongly supported monophyletic clades for both L. umbratilis and L. anduzei, whereas the L. umbratilis lineages I and II formed two poorly supported monophyletic subclades. Conclusions The barcode region clearly separated the two species and may therefore constitute a valuable tool in the identification of the sand fly vectors of Leishmania in endemic leishmaniasis areas. However, the barcode region had not enough power to separate the two lineages of L. umbratilis, likely reflecting

Molecular taxonomy of the two Leishmania vectors Lutzomyia umbratilis and Lutzomyia anduzei (Diptera: Psychodidae) from the Brazilian Amazon.

PubMed

Scarpassa, Vera Margarete; Alencar, Ronildo Baiatone

2013-09-11

Lutzomyia umbratilis (a probable species complex) is the main vector of Leishmania guyanensis in the northern region of Brazil. Lutzomyia anduzei has been implicated as a secondary vector of this parasite. These species are closely related and exhibit high morphological similarity in the adult stage; therefore, they have been wrongly identified, both in the past and in the present. This shows the need for employing integrated taxonomy. With the aim of gathering information on the molecular taxonomy and evolutionary relationships of these two vectors, 118 sequences of 663 base pairs (barcode region of the mitochondrial DNA cytochrome oxidase I - COI) were generated from 72 L. umbratilis and 46 L. anduzei individuals captured, respectively, in six and five localities of the Brazilian Amazon. The efficiency of the barcode region to differentiate the L. umbratilis lineages I and II was also evaluated. The data were analyzed using the pairwise genetic distances matrix and the Neighbor-Joining (NJ) tree, both based on the Kimura Two Parameter (K2P) evolutionary model. The analyses resulted in 67 haplotypes: 32 for L. umbratilis and 35 for L. anduzei. The mean intra-specific genetic distance was 0.008 (0.002 to 0.010 for L. umbratilis; 0.008 to 0.014 for L. anduzei), whereas the mean interspecific genetic distance was 0.044 (0.041 to 0.046), supporting the barcoding gap. Between the L. umbratilis lineages I and II, it was 0.009 to 0.010. The NJ tree analysis strongly supported monophyletic clades for both L. umbratilis and L. anduzei, whereas the L. umbratilis lineages I and II formed two poorly supported monophyletic subclades. The barcode region clearly separated the two species and may therefore constitute a valuable tool in the identification of the sand fly vectors of Leishmania in endemic leishmaniasis areas. However, the barcode region had not enough power to separate the two lineages of L. umbratilis, likely reflecting incipient species that have not yet reached

Geochemical Character of the Aono Volcanic Group in SW Japan Arc: Implications for Genetic Relationship between Slab Melting and EM Isotopic Signature

NASA Astrophysics Data System (ADS)

Shimoda, G.; Shinjoe, H.; Kogiso, T.; Ishizuka, O.; Yamashita, K.; Yoshitake, M.; Itoh, J.; Ogasawara, M.

2016-12-01

The SW Japan arc is characterized by active subduction of a relatively young (15-26 Ma) segment of the Philippine Sea plate, Shikoku basin, beneath the Eurasian plate and is known for the occurrence of adakites on the quaternary volcanic front. As adakite is typically generated in subduction zones, where high geothermal gradients can be attained in the slab, the adakite magmas are considered to be produced by slab melting. From this perspective, adakites are considered to be modern geochemical analogues of the tonalite-trondhjemite-granodiorite (TTG) suite that can be a major constituent of early continental crust. It has been inferred that recycling of continental crustal material back into the mantle could be a possible origin of enriched mantle reservoirs, such as EM1 and EM2. In order to reveal the role of slab melting on the production of EM isotopic signature, we have conducted a detailed major/trace element and Pb-Nd-Sr isotopic study of 17 adakites from Aono volcanic group in the western end of Honshu Island. The isotopic compositions of the Aono volcanic rocks clearly form a mixing line between the Shikoku back arc basin basalts and local sediments from the Nankai Trough. In addition, the isotopic compositions of Aono adakites have depleted isotopic composition showing some overlap with subducted Shikoku basin basalts. This may imply that the chemical composition of Aono adakites could be mainly derived from Shikoku basin basalts as pointed out by recent work (Kimura et al., 2014). Accordingly, the effect of crustal contamination or sediment melting could be relatively small. On the basis of this assumption, the chemical composition of Aono adakites are used to estimate the chemical fractionation during slab melting. In this presentation, we will present new results of isotopic and trace element analyses of adakites from Aono volcanic group in the SW Japan and discuss role of slab melting in the production of EM reservoirs.

DNA barcoding to identify species of phlebotomine sand fly (Diptera: Psychodidae) in the mixed leishmaniasis focus of the Colombian Caribbean.

PubMed

Romero-Ricardo, Luis; Lastre-Meza, Natalia; Pérez-Doria, Alveiro; Bejarano, Eduar E

2016-07-01

Identification of the species of phlebotomine sand flies present in each focus of leishmaniasis is necessary to incriminate vectors and implement vector control strategies. Although the cytochrome oxidase I (COI) gene has been proposed as a barcode for the identification of animal species, less than 20% of New World phlebotomines have been characterized to date. In this study DNA barcoding was used to identify phlebotomine species of the mixed leishmaniasis focus in the Colombian Caribbean by means of three evolutionary models: Kimura's two parameter (K2P) nucleotide substitution model, that of (Tamura and Nei, 1993) (TN93) and proportional sequence divergence (p-distances). A 681bp sequence of the COI gene was obtained from 66 individuals belonging to 19 species of the genus Lutzomyia (Lu. abonnenci, Lu. atroclavata, Lu. bicolor, Lu. carpenteri, Lu. cayennensis cayennensis, Lu. dubitans, Lu. evansi, Lu. gomezi, Lu. gorbitzi, Lu. longipalpis, Lu. micropyga, Lu. migonei, Lu. panamensis, Lu. (Psathyromyia) sp., Lu. rangeliana, Lu. serrana, Lu. shannoni, Lu. trinidadensis and Lu. venezuelensis) and one of Brumptomyia (B. mesai). The genetic divergence values for TN93 among individuals of the same species fluctuated up to 3.2% (vs. 2.9% for K2P and 2.8% for p-distances), while the values between species ranged from 8.8-43.7% (vs. 6.8-19.6% for K2P and 6.6-17.4% for p-distances). A dendrogram constructed by means of the Neighbor-Joining method grouped phlebotomines into 20 clusters according to species, with bootstrap values of up to 100% in those with more than one individual. However, loss of the phylogenetic signal of the gene COI was observed at the supraspecific level as a consequence of substitutional saturation. In conclusion, irrespective of the evolutionary model selected, all phlebotomines were correctly assigned to species, showing 100% concordance with morphological identification. Copyright © 2016 Elsevier B.V. All rights reserved.

A “Rosetta Stone” for metazoan zooplankton: DNA barcode analysis of species diversity of the Sargasso Sea (Northwest Atlantic Ocean)

NASA Astrophysics Data System (ADS)

Bucklin, Ann; Ortman, Brian D.; Jennings, Robert M.; Nigro, Lisa M.; Sweetman, Christopher J.; Copley, Nancy J.; Sutton, Tracey; Wiebe, Peter H.

2010-12-01

Species diversity of the metazoan holozooplankton assemblage of the Sargasso Sea, Northwest Atlantic Ocean, was examined through coordinated morphological taxonomic identification of species and DNA sequencing of a ˜650 base-pair region of mitochondrial cytochrome oxidase I (mtCOI) as a DNA barcode (i.e., short sequence for species recognition and discrimination). Zooplankton collections were made from the surface to 5,000 meters during April, 2006 on the R/V R.H. Brown. Samples were examined by a ship-board team of morphological taxonomists; DNA barcoding was carried out in both ship-board and land-based DNA sequencing laboratories. DNA barcodes were determined for a total of 297 individuals of 175 holozooplankton species in four phyla, including: Cnidaria (Hydromedusae, 4 species; Siphonophora, 47); Arthropoda (Amphipoda, 10; Copepoda, 34; Decapoda, 9; Euphausiacea, 10; Mysidacea, 1; Ostracoda, 27); and Mollusca (Cephalopoda, 8; Heteropoda, 6; Pteropoda, 15); and Chaetognatha (4). Thirty species of fish (Teleostei) were also barcoded. For all seven zooplankton groups for which sufficient data were available, Kimura-2-Parameter genetic distances were significantly lower between individuals of the same species (mean=0.0114; S.D. 0.0117) than between individuals of different species within the same group (mean=0.3166; S.D. 0.0378). This difference, known as the barcode gap, ensures that mtCOI sequences are reliable characters for species identification for the oceanic holozooplankton assemblage. In addition, DNA barcodes allow recognition of new or undescribed species, reveal cryptic species within known taxa, and inform phylogeographic and population genetic studies of geographic variation. The growing database of "gold standard" DNA barcodes serves as a Rosetta Stone for marine zooplankton, providing the key for decoding species diversity by linking species names, morphology, and DNA sequence variation. In light of the pivotal position of zooplankton in ocean

Chandra observations of Jupiter's X-ray Aurora during Juno upstream and apojove intervals

NASA Astrophysics Data System (ADS)

Dunn, W.; Jackman, C. M.; Kraft, R.; Gladstone, R.; Branduardi-Raymont, G.; Knigge, C.; Altamirano, D.; Elsner, R.; Kammer, J.

2017-12-01

The Chandra space telescope has recently conducted a number of campaigns to observe Jupiter's X-ray aurora. The first set of campaigns took place in summer 2016 while the Juno spacecraft was upstream of the planet sampling the solar wind. The second set of campaigns took place in February, June and August 2017 at times when the Juno spacecraft was at apojove. These campaigns were planned following the Juno orbit correction to capitalise on the opportunity to image the X-ray emission while Juno was orbiting close to the expected position of the magnetopause. Previous work has suggested that the auroral X-ray emissions map close to the magnetopause boundary [e.g. Vogt et al., 2015; Kimura et al., 2016; Dunn et al., 2016] and thus in situ spacecraft coverage in this region combined with remote observation of the X-rays afford the chance to constrain the drivers of these energetic emissions and determine if they originate on open or closed field lines. We aim to examine possible drivers of X-ray emission including reconnection and the Kelvin-Helmholtz instability and to explore the role of the solar wind in controlling the emissions. We report on these upstream and apojove campaigns including intensities and periodicities of auroral X-ray emissions. This new era of jovian X-ray astronomy means we have more data than ever before, long observing windows (up to 72 ks for this Chandra set), and successive observations relatively closely spaced in time. These features combine to allow us to pursue novel methods for examining periodicities in the X-ray emission. Our work will explore significance testing of emerging periodicities, and the search for coherence in X-ray pulsing over weeks and months, seeking to understand the robustness and regularity of previously reported hot spot X-ray emissions. The periods that emerge from our analysis will be compared against those which emerge from radio and UV wavelengths.

Identification, Discrimination, and Discovery of Species of Marine Planktonic Ostracods Using DNA Barcodes.

PubMed

Nigro, Lisa M; Angel, Martin V; Blachowiak-Samolyk, Katarzyna; Hopcroft, Russell R; Bucklin, Ann

2016-01-01

The Ostracoda (Crustacea; Class Ostracoda) is a diverse, frequently abundant, and ecologically important component of the marine zooplankton assemblage. There are more than 200 described species of marine planktonic ostracods, many of which (especially conspecific species) can be identified only by microscopic examination and dissection of fragile morphological characters. Given the complexity of species identification and increasing lack of expert taxonomists, DNA barcodes (short DNA sequences for species discrimination and identification) are particularly useful and necessary. Results are reported from analysis of 210 specimens of 78 species of marine planktonic ostracods, including two novel species, and 51 species for which barcodes have not been previously published. Specimens were collected during 2006 to 2008 from the Atlantic, Indian, and Southern Oceans, Greenland Sea and Gulf of Alaska. Samples were collected from surface to 5,000 m using various collection devices. DNA sequence variation was analyzed for a 598 base-pair region of the mitochondrial cytochrome oxidase subunit I (COI) gene. Kimura-2-Parameter (K2P) genetic distances within described species (mean = 0.010 ± 0.017 SD) were significantly smaller than between species (0.260 + 0.080), excluding eight taxa hypothesized to comprise cryptic species due to morphological variation (especially different size forms) and/or collection from different geographic regions. These taxa showed similar K2P distance values within (0.014 + 0.026) and between (0.221 ± 0.068) species. All K2P distances > 0.1 resulted from comparisons between identified or cryptic species, with no overlap between intra- and interspecific genetic distances. A Neighbor Joining tree resolved nearly all described species analyzed, with multiple sequences forming monophyletic clusters with high bootstrap values (typically 99%). Based on taxonomically and geographically extensive sampling and analysis (albeit with small sample sizes

Identification, Discrimination, and Discovery of Species of Marine Planktonic Ostracods Using DNA Barcodes

PubMed Central

2016-01-01

The Ostracoda (Crustacea; Class Ostracoda) is a diverse, frequently abundant, and ecologically important component of the marine zooplankton assemblage. There are more than 200 described species of marine planktonic ostracods, many of which (especially conspecific species) can be identified only by microscopic examination and dissection of fragile morphological characters. Given the complexity of species identification and increasing lack of expert taxonomists, DNA barcodes (short DNA sequences for species discrimination and identification) are particularly useful and necessary. Results are reported from analysis of 210 specimens of 78 species of marine planktonic ostracods, including two novel species, and 51 species for which barcodes have not been previously published. Specimens were collected during 2006 to 2008 from the Atlantic, Indian, and Southern Oceans, Greenland Sea and Gulf of Alaska. Samples were collected from surface to 5,000 m using various collection devices. DNA sequence variation was analyzed for a 598 base-pair region of the mitochondrial cytochrome oxidase subunit I (COI) gene. Kimura-2-Parameter (K2P) genetic distances within described species (mean = 0.010 ± 0.017 SD) were significantly smaller than between species (0.260 + 0.080), excluding eight taxa hypothesized to comprise cryptic species due to morphological variation (especially different size forms) and/or collection from different geographic regions. These taxa showed similar K2P distance values within (0.014 + 0.026) and between (0.221 ± 0.068) species. All K2P distances > 0.1 resulted from comparisons between identified or cryptic species, with no overlap between intra- and interspecific genetic distances. A Neighbor Joining tree resolved nearly all described species analyzed, with multiple sequences forming monophyletic clusters with high bootstrap values (typically 99%). Based on taxonomically and geographically extensive sampling and analysis (albeit with small sample sizes

An Asiatic Chironomid in Brazil: morphology, DNA barcode and bionomics

PubMed Central

Amora, Gizelle; Hamada, Neusa; Fusari, Lívia Maria; Andrade-Souza, Vanderly

2015-01-01

Abstract In most freshwater ecosystems, aquatic insects are dominant in terms of diversity; however, there is a disproportionately low number of records of alien species when compared to other freshwater organisms. The Chironomidae is one aquatic insect family that includes some examples of alien species around the world. During a study on aquatic insects in Amazonas state (Brazil), we collected specimens of Chironomidae that are similar, at the morphological level, to Chironomus kiiensis Tokunaga and Chironomus striatipennis Kieffer, both with distributions restricted to Asia. The objectives of this study were to provide morphological information on this Chironomus population, to investigate its identity using DNA barcoding and, to provide bionomic information about this species. Chironomus DNA barcode data were obtained from GenBank and Barcode of Life Data Systems (BOLD) and, together with our data, were analyzed using the neighbor-joining method with 1000 bootstrap replicates and the genetic distances were estimated using the Kimura-2-parameter. At the morphological level, the Brazilian population cannot be distinguished either from Chironomus striatipennis or Chironomus kiiensis, configuring a species complex but, at the molecular level our studied population is placed in a clade together with Chironomus striatipennis, from South Korea. Bionomic characteristics of the Brazilian Chironomus population differ from the ones of Chironomus kiiensis from Japan, the only species in this species complex with bionomic information available. The Brazilian Chironomus population has a smaller size, the double of the number of eggs and inhabits oligotrophic water, in artificial container. In the molecular analysis, populations of Chironomus striatipennis and Chironomus kiiensis are placed in a clade, formed by two groups: Group A (which includes populations from both named species, from different Asiatic regions and our Brazilian population) and Group B (with populations of

Toroidal Alfven Waves in Advanced Tokamaks

NASA Astrophysics Data System (ADS)

Berk, Herbert L.

2003-10-01

In burning plasma experiments, alpha particles have speeds that readily resonate with shear Alfven waves. It is essential to understand this Alfven wave spectrum for toroidal plasma confinement. Most interest has focused on the Toroidal Alfven Eigenmode (TAE), and a method of analysis has been developed to understand the structure of this mode at a flux surface with a given magnetic shear. However, this model fails when the shear is too low or reversed. In this case a new method of analysis is required, which must incorporate novel fluid-like effects from the energetic particles [1] and also include effects that are second order in the inverse toroidal aspect ratio. With this new method [2] we can obtain spectral features that agree with experimental results. In particular, this theory gives an explanation for the so-called Cascade modes that have been observed in JT-60 [3], JET [4], and TFTR [5]. For these Cascade modes, slow upward frequency sweeping is observed, beginning from frequencies below the TAE range but then often blending into the TAE range of frequencies. The theoretical understanding of the Cascades modes has evolved to the point where these modes can be used as a diagnostic "signature" [6] to experimentally optimize the formation of thermal barriers in reversed-shear operation when the minimum q value is an integer. [1] H. L. Berk et al., Phys. Rev. Lett. 87, 185 (2002). [2] B. N. Breizman et al., submitted to Phys. Plasmas (2003). [3] H. Kimura et al., Nucl. Fusion 38, 1303 (1998). [4] S. Sharapov et al., Phys. Lett. A 289, 127 (2001); S. Sharapov, Phys. Plasmas 9, 2027 (2002). [5] R. Nazikian, H. L. Berk, et al., Bull. Am. Phys. Soc. 47, 327 (2002). [6] E. Joffrin et al., Plasma Phys. Contr. Fusion 44, 1739 (2002); E. Joffrin et al., in Proc. 2002 IAEA Fusion Energy Conference, submitted to Nucl. Fusion.

SYBR Green-based Real-Time PCR targeting kinetoplast DNA can be used to discriminate between the main etiologic agents of Brazilian cutaneous and visceral leishmaniases

PubMed Central

2012-01-01

Background Leishmaniases control has been hampered by the unavailability of rapid detection methods and the lack of suitable therapeutic and prophylactic measures. Accurate diagnosis, which can distinguish between Leishmania isolates, is essential for conducting appropriate prognosis, therapy and epidemiology. Molecular methods are currently being employed to detect Leishmania infection and categorize the parasites up to genus, complex or species level. Real-time PCR offers several advantages over traditional PCR, including faster processing time, higher sensitivity and decreased contamination risk. Results A SYBR Green real-time PCR targeting the conserved region of kinetoplast DNA minicircles was able to differentiate between Leishmania subgenera. A panel of reference strains representing subgenera Leishmania and Viannia was evaluated by the derivative dissociation curve analyses of the amplified fragment. Distinct values for the average melting temperature were observed, being 78.95°C ± 0.01 and 77.36°C ± 0.02 for Leishmania and Viannia, respectively (p < 0.05). Using the Neighbor-Joining method and Kimura 2-parameters, the alignment of 12 sequences from the amplified conserved minicircles segment grouped together L. (V.) braziliensis and L. (V.) shawii with a bootstrap value of 100%; while for L. (L.) infantum and L. (L.) amazonensis, two groups were formed with bootstrap values of 100% and 62%, respectively. The lower dissociation temperature observed for the subgenus Viannia amplicons could be due to a lower proportion of guanine/cytosine sites (43.6%) when compared to species from subgenus Leishmania (average of 48.4%). The method was validated with 30 clinical specimens from visceral or cutaneous leishmaniases patients living in Brazil and also with DNA samples from naturally infected Lutzomyia spp. captured in two Brazilian localities. Conclusions For all tested samples, a characteristic amplicon melting profile was evidenced for each Leishmania

[Phylogenetic analysis of CO I gene of Oncomelania snails from project of afforestation for schistosomiasis control in marshland endemic regions].

PubMed

Xu, Yu-Mei; Zhang, Shi-Qing; Zhu, Chuan-Gang

2012-04-01

To investigate the genetic difference of cytochrome oxidase I (CO I ) of Oncomelania snails from the project of afforestation for schistosomiasis control in marshland regions, so as to explore the effects of different ecological environments. The snails were collected from 3 different areas, Anqing, Tongling, Wuwei, i.e. the upstream, midstream and downstream regions along the Yangtz River in Anhui Province. Genomic DNA was extracted from the snails, and CO I gene fragments were amplified by PCR, then purified and sequenced. The sequences were edited by using Blast. The CO I genes of O. h. minima and Biomphalaria glabrata were used as the reference of exogenous gene. The genetic distances of the various regions were calculated by the Kimura method and phylogenetic trees were constructed with UPGMA and the NJ method of MEGA (3.1) software. The amplified CO I gene of the snail was a fragment about 700 bp including 2 primers in length. There were little genetic diversity among the different areas, the identities were higher than or equal to 98%. The genetic distances indicated that the distance between the projects of afforestation and woodland in Anqing was 0.003, while Tongling was 0.019, Wuwei was 0.007. The distances among the three projects of afforestation were 0.003-0.012. The two phylogenetic trees were constructed by the methods of UPGMA and NJ respectively, which took on very similar topo-structure in which isolates of Biomphalaria glabrata located in one clade and all the others in the other one. In the other one clade, O. H. minima located in one clade. There was little genetic diversity among Anqing, Tongling, Wuwei clusters. The afforestations of Anqing and Wuwei clustered into one group, while the woodlands of Anqing and Wuwei appeared as another group. There is a little genetic diversity of the snail cytochrome oxidase I (CO I ) in different ecological environments among the upstream, midstream and downstream regions along the Yangtz River in Anhui

Ocean FEST (Families Exploring Science Together)

NASA Astrophysics Data System (ADS)

Bruno, B. C.; Wiener, C. S.

2009-12-01

Ocean FEST (Families Exploring Science Together) exposes families to cutting-edge ocean science research and technology in a fun, engaging way. Research has shown that family involvement in science education adds significant value to the experience. Our overarching goal is to attract underrepresented students (including Native Hawaiians, Pacific Islanders and girls) to geoscience careers. A second goal is to communicate to diverse audiences that geoscience is directly relevant and applicable to their lives, and critical in solving challenges related to global climate change. Ocean FEST engages elementary school students, parents, teachers, and administrators in family science nights based on a proven model developed by Art and Rene Kimura of the Hawaii Space Grant Consortium. Our content focuses on the role of the oceans in climate change, and is based on the transformative research of the NSF Center for Microbial Oceanography: Research and Education (C-MORE) and the Hawaii Institute of Marine Biology (HIMB). Through Ocean FEST, underrepresented students and their parents and teachers learn about new knowledge being generated at Hawaii’s world-renowned ocean research institutes. In the process, they learn about fundamental geoscience concepts and career opportunities. This project is aligned with C-MORE’s goal of increasing the number of underrepresented students pursuing careers in the ocean and earth sciences, and related disciplines. Following a successful round of pilot events at elementary schools on Oahu, funding was obtained through NSF Opportunities for Enhancing Diversity in the Geosciences to implement a three-year program at minority-serving elementary schools in Hawaii. Deliverables include 20 Ocean FEST events per year (each preceded by teacher professional development training), a standards-based program that will be disseminated locally and nationally, three workshops to train educators in program delivery, and an Ocean FEST science kit. In

Probability of fixation under weak selection: a branching process unifying approach.

PubMed

Lambert, Amaury

2006-06-01

We link two-allele population models by Haldane and Fisher with Kimura's diffusion approximations of the Wright-Fisher model, by considering continuous-state branching (CB) processes which are either independent (model I) or conditioned to have constant sum (model II). Recent works by the author allow us to further include logistic density-dependence (model III), which is ubiquitous in ecology. In all models, each allele (mutant or resident) is then characterized by a triple demographic trait: intrinsic growth rate r, reproduction variance sigma and competition sensitivity c. Generally, the fixation probability u of the mutant depends on its initial proportion p, the total initial population size z, and the six demographic traits. Under weak selection, we can linearize u in all models thanks to the same master formula u = p + p(1 - p)[g(r)s(r) + g(sigma)s(sigma) + g(c)s(c)] + o(s(r),s(sigma),s(c), where s(r) = r' - r, s(sigma) = sigma-sigma' and s(c) = c - c' are selection coefficients, and g(r), g(sigma), g(c) are invasibility coefficients (' refers to the mutant traits), which are positive and do not depend on p. In particular, increased reproduction variance is always deleterious. We prove that in all three models g(sigma) = 1/sigma and g(r) = z/sigma for small initial population sizes z. In model II, g(r) = z/sigma for all z, and we display invasion isoclines of the 'mean vs variance' type. A slight departure from the isocline is shown to be more beneficial to alleles with low sigma than with high r. In model III, g(c) increases with z like ln(z)/c, and g(r)(z) converges to a finite limit L > K/sigma, where K = r/c is the carrying capacity. For r > 0 the growth invasibility is above z/sigma when z < K, and below z/sigma when z > K, showing that classical models I and II underestimate the fixation probabilities in growing populations, and overestimate them in declining populations.

Evolutionary advantage via common action of recombination and neutrality

NASA Astrophysics Data System (ADS)

Saakian, David B.; Hu, Chin-Kun

2013-11-01

We investigate evolution models with recombination and neutrality. We consider the Crow-Kimura (parallel) mutation-selection model with the neutral fitness landscape, in which there is a central peak with high fitness A, and some of 1-point mutants have the same high fitness A, while the fitness of other sequences is 0. We find that the effect of recombination and neutrality depends on the concrete version of both neutrality and recombination. We consider three versions of neutrality: (a) all the nearest neighbor sequences of the peak sequence have the same high fitness A; (b) all the l-point mutations in a piece of genome of length l≥1 are neutral; (c) the neutral sequences are randomly distributed among the nearest neighbors of the peak sequences. We also consider three versions of recombination: (I) the simple horizontal gene transfer (HGT) of one nucleotide; (II) the exchange of a piece of genome of length l, HGT-l; (III) two-point crossover recombination (2CR). For the case of (a), the 2CR gives a rather strong contribution to the mean fitness, much stronger than that of HGT for a large genome length L. For the random distribution of neutral sequences there is a critical degree of neutrality νc, and for μ<μc and (μc-μ) is not large, the 2CR suppresses the mean fitness while HGT increases it; for ν much larger than νc, the 2CR and HGT-l increase the mean fitness larger than that of the HGT. We also consider the recombination in the case of smooth fitness landscapes. The recombination gives some advantage in the evolutionary dynamics, where recombination distinguishes clearly the mean-field-like evolutionary factors from the fluctuation-like ones. By contrast, mutations affect the mean-field-like and fluctuation-like factors similarly. Consequently, recombination can accelerate the non-mean-field (fluctuation) type dynamics without considerably affecting the mean-field-like factors.

E6 and E7 Gene Polymorphisms in Human Papillomavirus Types-58 and 33 Identified in Southwest China

PubMed Central

Wen, Qiang; Wang, Tao; Mu, Xuemei; Chenzhang, Yuwei; Cao, Man

2017-01-01

Cancer of the cervix is associated with infection by certain types of human papillomavirus (HPV). The gene variants differ in immune responses and oncogenic potential. The E6 and E7 proteins encoded by high-risk HPV play a key role in cellular transformation. HPV-33 and HPV-58 types are highly prevalent among Chinese women. To study the gene intratypic variations, polymorphisms and positive selections of HPV-33 and HPV-58 E6/E7 in southwest China, HPV-33 (E6, E7: n = 216) and HPV-58 (E6, E7: n = 405) E6 and E7 genes were sequenced and compared to others submitted to GenBank. Phylogenetic trees were constructed by Maximum-likelihood and the Kimura 2-parameters methods by MEGA 6 (Molecular Evolutionary Genetics Analysis version 6.0). The diversity of secondary structure was analyzed by PSIPred software. The selection pressures acting on the E6/E7 genes were estimated by PAML 4.8 (Phylogenetic Analyses by Maximun Likelihood version4.8) software. The positive sites of HPV-33 and HPV-58 E6/E7 were contrasted by ClustalX 2.1. Among 216 HPV-33 E6 sequences, 8 single nucleotide mutations were observed with 6/8 non-synonymous and 2/8 synonymous mutations. The 216 HPV-33 E7 sequences showed 3 single nucleotide mutations that were non-synonymous. The 405 HPV-58 E6 sequences revealed 8 single nucleotide mutations with 4/8 non-synonymous and 4/8 synonymous mutations. Among 405 HPV-58 E7 sequences, 13 single nucleotide mutations were observed with 10/13 non-synonymous mutations and 3/13 synonymous mutations. The selective pressure analysis showed that all HPV-33 and 4/6 HPV-58 E6/E7 major non-synonymous mutations were sites of positive selection. All variations were observed in sites belonging to major histocompatibility complex and/or B-cell predicted epitopes. K93N and R145 (I/N) were observed in both HPV-33 and HPV-58 E6. PMID:28141822

Simulations of Antarctic ice shelves and the Southern Ocean in the POP2x ocean model coupled with the BISICLES ice-sheet model

NASA Astrophysics Data System (ADS)

Asay-Davis, Xylar; Martin, Daniel; Price, Stephen; Maltrud, Mathew

2014-05-01

We present initial results from Antarctic, ice-ocean coupled simulations using large-scale ocean circulation and ice-sheet evolution models. This presentation focuses on the ocean model, POP2x, which is a modified version of POP, a fully eddying, global-scale ocean model (Smith and Gent, 2002). POP2x allows for circulation beneath ice shelf cavities using the method of partial top cells (Losch, 2008). Boundary layer physics, which control fresh water and salt exchange at the ice-ocean interface, are implemented following Holland and Jenkins (1999), Jenkins (2001), and Jenkins et al. (2010). Standalone POP2x output compares well with standard ice-ocean test cases (e.g., ISOMIP; Losch, 2008) and other continental-scale simulations and melt-rate observations (Kimura et al., 2013; Rignot et al., 2013) and with results from other idealized ice-ocean coupling test cases (e.g., Goldberg et al., 2012). A companion presentation, 'Fully resolved whole-continent Antarctica simulations using the BISICLES AMR ice sheet model coupled with the POP2x Ocean Model', concentrates more on the ice-sheet model, BISICLES (Cornford et al., 2012), which includes a 1st-order accurate momentum balance (L1L2) and uses block structured, adaptive-mesh refinement to more accurately model regions of dynamic complexity, such as ice streams, outlet glaciers, and grounding lines. For idealized test cases focused on marine-ice sheet dynamics, BISICLES output compares very favorably relative to simulations based on the full, nonlinear Stokes momentum balance (MISMIP-3d; Pattyn et al., 2013). Here, we present large-scale (Southern Ocean) simulations using POP2x at 0.1 degree resolution with fixed ice shelf geometries, which are used to obtain and validate modeled submarine melt rates against observations. These melt rates are, in turn, used to force evolution of the BISICLES model. An offline-coupling scheme, which we compare with the ice-ocean coupling work of Goldberg et al. (2012), is then used to

Response of the Antarctic ice sheet to ocean forcing using the POPSICLES coupled ice sheet-ocean model

NASA Astrophysics Data System (ADS)

Martin, D. F.; Asay-Davis, X.; Price, S. F.; Cornford, S. L.; Maltrud, M. E.; Ng, E. G.; Collins, W.

2014-12-01

We present the response of the continental Antarctic ice sheet to sub-shelf-melt forcing derived from POPSICLES simulation results covering the full Antarctic Ice Sheet and the Southern Ocean spanning the period 1990 to 2010. Simulations are performed at 0.1 degree (~5 km) ocean resolution and ice sheet resolution as fine as 500 m using adaptive mesh refinement. A comparison of fully-coupled and comparable standalone ice-sheet model results demonstrates the importance of two-way coupling between the ice sheet and the ocean. The POPSICLES model couples the POP2x ocean model, a modified version of the Parallel Ocean Program (Smith and Gent, 2002), and the BISICLES ice-sheet model (Cornford et al., 2012). BISICLES makes use of adaptive mesh refinement to fully resolve dynamically-important regions like grounding lines and employs a momentum balance similar to the vertically-integrated formulation of Schoof and Hindmarsh (2009). Results of BISICLES simulations have compared favorably to comparable simulations with a Stokes momentum balance in both idealized tests like MISMIP3D (Pattyn et al., 2013) and realistic configurations (Favier et al. 2014). POP2x includes sub-ice-shelf circulation using partial top cells (Losch, 2008) and boundary layer physics following Holland and Jenkins (1999), Jenkins (2001), and Jenkins et al. (2010). Standalone POP2x output compares well with standard ice-ocean test cases (e.g., ISOMIP; Losch, 2008) and other continental-scale simulations and melt-rate observations (Kimura et al., 2013; Rignot et al., 2013). A companion presentation, "Present-day circum-Antarctic simulations using the POPSICLES coupled land ice-ocean model" in session C027 describes the ocean-model perspective of this work, while we focus on the response of the ice sheet and on details of the model. The figure shows the BISICLES-computed vertically-integrated ice velocity field about 1 month into a 20-year coupled Antarctic run. Groundling lines are shown in green.

The Feigin Tetrahedron

NASA Astrophysics Data System (ADS)

Rupel, Dylan

2015-03-01

The first goal of this note is to extend the well-known Feigin homomorphisms taking quantum groups to quantum polynomial algebras. More precisely, we define generalized Feigin homomorphisms from a quantum shuffle algebra to quantum polynomial algebras which extend the classical Feigin homomorphisms along the embedding of the quantum group into said quantum shuffle algebra. In a recent work of Berenstein and the author, analogous extensions of Feigin homomorphisms from the dual Hall-Ringel algebra of a valued quiver to quantum polynomial algebras were defined. To relate these constructions, we establish a homomorphism, dubbed the quantum shuffle character, from the dual Hall-Ringel algebra to the quantum shuffle algebra which relates the generalized Feigin homomorphisms. These constructions can be compactly described by a commuting tetrahedron of maps beginning with the quantum group and terminating in a quantum polynomial algebra. The second goal in this project is to better understand the dual canonical basis conjecture for skew-symmetrizable quantum cluster algebras. In the symmetrizable types it is known that dual canonical basis elements need not have positive multiplicative structure constants, while this is still suspected to hold for skew-symmetrizable quantum cluster algebras. We propose an alternate conjecture for the symmetrizable types: the cluster monomials should correspond to irreducible characters of a KLR algebra. Indeed, the main conjecture of this note would establish this ''KLR conjecture'' for acyclic skew-symmetrizable quantum cluster algebras: that is, we conjecture that the images of rigid representations under the quantum shuffle character give irreducible characters for KLR algebras. We sketch a proof in the symmetric case giving an alternative to the proof of Kimura-Qin that all non-initial cluster variables in an acyclic skew-symmetric quantum cluster algebra are contained in the dual canonical basis. With these results in mind we

Effects of Long-Period Ground Motion on Distant Basins: The 1906 San Francisco Earthquake and Comparison with Japanese Cases

NASA Astrophysics Data System (ADS)

Koketsu, K.; Ikegami, Y.; Kimura, T.; Miyake, H.

2006-12-01

Large earthquakes at shallow depths can excite long-period ground motions affecting large-scale structures in distant sedimentary basins. For example, the 1985 Michoacan, Mexico, earthquake caused 20,000 fatalities in Mexico City at an epicentral distance of 400 km, and the 2003 Tokachi-oki, Japan, earthquake damaged oil tanks in the Yufutsu basin 250 km away (Koketsu et al., 2005). Similar long-range effects were also observed during the 2004 off Kii-peninsula earthquake (Miyake and Koketsu, 2005). In order to examine whether the 1906 San Francisco earthquake and the Los Angeles (LA) basin are in such a case or not, we simulate long- period ground motions in almost whole California caused by the earthquake using the finite element method (FEM) with a voxel mesh (Koketsu et al., 2004). The LA basin is located at a distance of about 600 km from the source region of the 1906 San Francisco earthquake. The 3-D heterogeneous velocity structure model for the ground motion simulation is constructed based on the SCEC Unified Velocity Model for southern California and USGS Bay Area Velocity Model for northern California. The source model of the earthquake is constructed according to Wald et al. (1993). Since we use a mesh with intervals of 500m, the voxel FEM can compute seismic waves with frequencies lower than 0.2 Hz. Although ground motions in the south of the source region are smaller than those in the north because of the rupture directivity effect, we can see fairly developed long- period ground motions in the LA basin in the preliminary result of Kimura et al. (2006). However, we obtained only 8cm/s and 25km/s for PGV and peak velocity response spectrum in the LA basin. We modeled the velocity structure up to a depth of only 20km neglecting the Moho reflections, and we did not include layers with Vs smaller than 1.0 km/s. In this study, we include deeper parts and use a more accurate velocity structure model with low-velocity sediments of Vs smaller than 1.0 km/s.

Mechanisms of Fe biofortification and mitigation of Cd accumulation in rice (Oryza sativa L.) grown hydroponically with Fe chelate fertilization.

PubMed

Chen, Zhe; Tang, Ye-Tao; Zhou, Can; Xie, Shu-Ting; Xiao, Shi; Baker, Alan J M; Qiu, Rong-Liang

2017-05-01

Cadmium contaminated rice from China has become a global food safety issue. Some research has suggested that chelate addition to substrates can affect metal speciation and plant metal content. We investigated the mitigation of Cd accumulation in hydroponically-grown rice supplied with EDTANa 2 Fe(II) or EDDHAFe(III). A japonica rice variety (Nipponbare) was grown in modified Kimura B solution containing three concentrations (0, 10, 100 μΜ) of the iron chelates EDTANa 2 Fe(II) or EDDHAFe(III) and 1 μΜ Cd. Metal speciation in solution was simulated by Geochem-EZ; growth and photosynthetic efficiency of rice were evaluated, and accumulation of Cd and Fe in plant parts was determined. Net Cd fluxes in the meristematic zone, growth zone, and maturation zone of roots were monitored by a non-invasive micro-test technology. Expression of Fe- and Cd-related genes in Fe-sufficient or Fe-deficient roots and leaves were studied by QRT-PCR. Compared to Fe deficiency, a sufficient or excess supply of Fe chelates significantly enhanced rice growth by elevating photosynthetic efficiency. Both Fe chelates increased the Fe content and decreased the Cd content of rice organs, except for the Cd content of roots treated with excess EDDHAFe(III). Compared to EDDHAFe(III), EDTANa 2 Fe(II) exhibited better mitigation of Cd accumulation in rice by generating the EDTANa 2 Cd complex in solution, decreasing net Cd influx and increasing net Cd efflux in root micro-zones. Application of EDTANa 2 Fe(II) and EDDHAFe(III) also reduced Cd accumulation in rice by inhibiting expression of genes involved in transport of Fe and Cd in the xylem and phloem. The 'win-win' situation of Fe biofortification and Cd mitigation in rice was achieved by application of Fe chelates. Root-to-stem xylem transport of Cd and redistribution of Cd in leaves by phloem transport can be regulated in rice through the use of Fe chelates that influence Fe availability and Fe-related gene expression. Fe fertilization

Development of incremental dynamical downscaling and analysis system for regional scale climate change projections

NASA Astrophysics Data System (ADS)

Wakazuki, Yasutaka; Hara, Masayuki; Fujita, Mikiko; Ma, Xieyao; Kimura, Fujio

2013-04-01

Regional scale climate change projections play an important role in assessments of influences of global warming and include statistical (SD) and dynamical downscaling (DD) approaches. One of DD methods is developed basing on the pseudo-global-warming (PGW) method developed by Kimura and Kitoh (2007) in this study. In general, DD uses regional climate model (RCM) with lateral boundary data. In PGW method, the climatological mean difference estimated by GCMs are added to the objective analysis data (ANAL), and the data are used as the lateral boundary data in the future climate simulations. The ANAL is also used as the lateral boundary conditions of the present climate simulation. One of merits of the PGW method is that influences of biases of GCMs in RCM simulations are reduced. However, the PGW method does not treat climate changes in relative humidity, year-to-year variation, and short-term disturbances. The developing new downscaling method is named as the incremental dynamical downscaling and analysis system (InDDAS). The InDDAS treat climate changes in relative humidity and year-to-year variations. On the other hand, uncertainties of climate change projections estimated by many GCMs are large and are not negligible. Thus, stochastic regional scale climate change projections are expected for assessments of influences of global warming. Many RCM runs must be performed to make stochastic information. However, the computational costs are huge because grid size of RCM runs should be small to resolve heavy rainfall phenomena. Therefore, the number of runs to make stochastic information must be reduced. In InDDAS, climatological differences added to ANAL become statistically pre-analyzed information. The climatological differences of many GCMs are divided into mean climatological difference (MD) and departures from MD. The departures are analyzed by principal component analysis, and positive and negative perturbations (positive and negative standard deviations

A web-based survey of erection hardness score and its relationship to aging, sexual behavior, confidence, and risk factors in Japan.

PubMed

Kimura, Masaki; Shimura, Satoru; Tai, Toshihiro; Kobayashi, Hideyuki; Baba, Shiro; Kano, Munehide; Nagao, Koichi

2013-12-01

Erection hardness is an elemental component of men's sexual quality of life that can be easily measured by the Erection Hardness Score (EHS). However, there are few published data regarding EHS, and there is little understanding of its relationships to aging, men's sexual behavior, sexual confidence, and risk factors in Japan. To assess EHS and how it correlates to aging, sexual behaviors, sexual self-confidence, and risk factors in a Japanese population database. A web-based cross-sectional nationwide survey conducted between March and May 2009 in Japan. EHS, lifestyle factors, comorbidities, general health, sexual confidence, frequency of sexual behaviors, and attitudes toward treatment of erectile dysfunction (ED). A total of 7,710 men with a mean age of 39.3 ± 13.0 years participated in this survey. In 6,528 participants who were not using phosphodiesterase type 5 inhibitors, 3,540 (54.2%) had EHS ≤ 3 and 1,196 (18.3%) had EHS ≤ 2. We found a significant age-dependent decrease in EHS, sexual confidence, and frequency of sexual activities. Sexual confidence was strongly associated with higher EHS but was also associated with older age groups, presence of offspring, awareness of better general health, and greater frequency of sexual activity. In age-adjusted multivariate logistic regression, risk factors for a lower EHS (defined as EHS ≤ 2) were heavy smoking, which was defined as more than two packs per day (odds ratio [OR], 1.7) or a history of metabolic syndrome (OR, 1.4), hypertension (OR, 1.2), and diabetes mellitus (OR, 1.4). EHS correlates to various elements, such as aging, sexual behaviors, sexual confidence, and ED-related risk factors, and can be a valuable tool in clinical practice for monitoring and treating ED and thereby improving the quality of life for men and their sexual partners. Kimura M, Shimura S, Tai T, Kobayashi H, Baba S, Kano M, and Nagao K. A web-based survey of Erection Hardness Score and its relationship to aging, sexual

Morphological and molecular characteristics of Malayfilaria sofiani Uni, Mat Udin & Takaoka n. g., n. sp. (Nematoda: Filarioidea) from the common treeshrew Tupaia glis Diard & Duvaucel (Mammalia: Scandentia) in Peninsular Malaysia.

PubMed

Uni, Shigehiko; Mat Udin, Ahmad Syihan; Agatsuma, Takeshi; Saijuntha, Weerachai; Junker, Kerstin; Ramli, Rosli; Omar, Hasmahzaiti; Lim, Yvonne Ai-Lian; Sivanandam, Sinnadurai; Lefoulon, Emilie; Martin, Coralie; Belabut, Daicus Martin; Kasim, Saharul; Abdullah Halim, Muhammad Rasul; Zainuri, Nur Afiqah; Bhassu, Subha; Fukuda, Masako; Matsubayashi, Makoto; Harada, Masashi; Low, Van Lun; Chen, Chee Dhang; Suganuma, Narifumi; Hashim, Rosli; Takaoka, Hiroyuki; Azirun, Mohd Sofian

2017-04-20

The filarial nematodes Wuchereria bancrofti (Cobbold, 1877), Brugia malayi (Brug, 1927) and B. timori Partono, Purnomo, Dennis, Atmosoedjono, Oemijati & Cross, 1977 cause lymphatic diseases in humans in the tropics, while B. pahangi (Buckley & Edeson, 1956) infects carnivores and causes zoonotic diseases in humans in Malaysia. Wuchereria bancrofti, W. kalimantani Palmieri, Pulnomo, Dennis & Marwoto, 1980 and six out of ten Brugia spp. have been described from Australia, Southeast Asia, Sri Lanka and India. However, the origin and evolution of the species in the Wuchereria-Brugia clade remain unclear. While investigating the diversity of filarial parasites in Malaysia, we discovered an undescribed species in the common treeshrew Tupaia glis Diard & Duvaucel (Mammalia: Scandentia). We examined 81 common treeshrews from 14 areas in nine states and the Federal Territory of Peninsular Malaysia for filarial parasites. Once any filariae that were found had been isolated, we examined their morphological characteristics and determined the partial sequences of their mitochondrial cytochrome c oxidase subunit 1 (cox1) and 12S rRNA genes. Polymerase chain reaction (PCR) products of the internal transcribed spacer 1 (ITS1) region were then cloned into the pGEM-T vector, and the recombinant plasmids were used as templates for sequencing. Malayfilaria sofiani Uni, Mat Udin & Takaoka, n. g., n. sp. is described based on the morphological characteristics of adults and microfilariae found in common treeshrews from Jeram Pasu, Kelantan, Malaysia. The Kimura 2-parameter distance between the cox1 gene sequences of the new species and W. bancrofti was 11.8%. Based on the three gene sequences, the new species forms a monophyletic clade with W. bancrofti and Brugia spp. The adult parasites were found in tissues surrounding the lymph nodes of the neck of common treeshrews. The newly described species appears most closely related to Wuchereria spp. and Brugia spp., but differs from these in

A Web-Based Survey of Erection Hardness Score and Its Relationship to Aging, Sexual Behavior, Confidence, and Risk Factors in Japan

PubMed Central

Kimura, Masaki; Shimura, Satoru; Tai, Toshihiro; Kobayashi, Hideyuki; Baba, Shiro; Kano, Munehide; Nagao, Koichi

2013-01-01

Introduction Erection hardness is an elemental component of men's sexual quality of life that can be easily measured by the Erection Hardness Score (EHS). However, there are few published data regarding EHS, and there is little understanding of its relationships to aging, men's sexual behavior, sexual confidence, and risk factors in Japan. Aim To assess EHS and how it correlates to aging, sexual behaviors, sexual self-confidence, and risk factors in a Japanese population database. Methods A web-based cross-sectional nationwide survey conducted between March and May 2009 in Japan. Main Outcome Measures EHS, lifestyle factors, comorbidities, general health, sexual confidence, frequency of sexual behaviors, and attitudes toward treatment of erectile dysfunction (ED). Results A total of 7,710 men with a mean age of 39.3 ± 13.0 years participated in this survey. In 6,528 participants who were not using phosphodiesterase type 5 inhibitors, 3,540 (54.2%) had EHS ≤ 3 and 1,196 (18.3%) had EHS ≤ 2. We found a significant age-dependent decrease in EHS, sexual confidence, and frequency of sexual activities. Sexual confidence was strongly associated with higher EHS but was also associated with older age groups, presence of offspring, awareness of better general health, and greater frequency of sexual activity. In age-adjusted multivariate logistic regression, risk factors for a lower EHS (defined as EHS ≤ 2) were heavy smoking, which was defined as more than two packs per day (odds ratio [OR], 1.7) or a history of metabolic syndrome (OR, 1.4), hypertension (OR, 1.2), and diabetes mellitus (OR, 1.4). Conclusions EHS correlates to various elements, such as aging, sexual behaviors, sexual confidence, and ED-related risk factors, and can be a valuable tool in clinical practice for monitoring and treating ED and thereby improving the quality of life for men and their sexual partners. Kimura M, Shimura S, Tai T, Kobayashi H, Baba S, Kano M, and Nagao K. A web-based survey of

Climate Change Implications and Use of Early Warning Systems for Global Dust Storms

NASA Astrophysics Data System (ADS)

Harriman, L.

2014-12-01

transport from eastern Australia: a proxy for Holocene aridity and ENSO-type climate variability, Earth Planet Sci. Lett., 282. [4] Kimura, R. (2012), Factors contributing to dust storms in source regions producing the yellow-sand phenomena observed in Japan from 1993 to 2002, J. Arid Environ. 80

Where is the game? Wild meat products authentication in South Africa: a case study.

PubMed

D'Amato, Maria Eugenia; Alechine, Evguenia; Cloete, Kevin Wesley; Davison, Sean; Corach, Daniel

2013-03-01

Wild animals' meat is extensively consumed in South Africa, being obtained either from ranching, farming or hunting. To test the authenticity of the commercial labels of meat products in the local market, we obtained DNA sequence information from 146 samples (14 beef and 132 game labels) for barcoding cytochrome c oxidase subunit I and partial cytochrome b and mitochondrial fragments. The reliability of species assignments were evaluated using BLAST searches in GenBank, maximum likelihood phylogenetic analysis and the character-based method implemented in BLOG. The Kimura-2-parameter intra- and interspecific variation was evaluated for all matched species. The combined application of similarity, phylogenetic and character-based methods proved successful in species identification. Game meat samples showed 76.5% substitution, no beef samples were substituted. The substitutions showed a variety of domestic species (cattle, horse, pig, lamb), common game species in the market (kudu, gemsbok, ostrich, impala, springbok), uncommon species in the market (giraffe, waterbuck, bushbuck, duiker, mountain zebra) and extra-continental species (kangaroo). The mountain zebra Equus zebra is an International Union for Conservation of Nature (IUCN) red listed species. We also detected Damaliscus pygargus, which is composed of two subspecies with one listed by IUCN as 'near threatened'; however, these mitochondrial fragments were insufficient to distinguish between the subspecies. The genetic distance between African ungulate species often overlaps with within-species distance in cases of recent speciation events, and strong phylogeographic structure determines within-species distances that are similar to the commonly accepted distances between species. The reliability of commercial labeling of game meat in South Africa is very poor. The extensive substitution of wild game has important implications for conservation and commerce, and for the consumers making decisions on the basis of

Where is the game? Wild meat products authentication in South Africa: a case study

PubMed Central

2013-01-01

Background Wild animals’ meat is extensively consumed in South Africa, being obtained either from ranching, farming or hunting. To test the authenticity of the commercial labels of meat products in the local market, we obtained DNA sequence information from 146 samples (14 beef and 132 game labels) for barcoding cytochrome c oxidase subunit I and partial cytochrome b and mitochondrial fragments. The reliability of species assignments were evaluated using BLAST searches in GenBank, maximum likelihood phylogenetic analysis and the character-based method implemented in BLOG. The Kimura-2-parameter intra- and interspecific variation was evaluated for all matched species. Results The combined application of similarity, phylogenetic and character-based methods proved successful in species identification. Game meat samples showed 76.5% substitution, no beef samples were substituted. The substitutions showed a variety of domestic species (cattle, horse, pig, lamb), common game species in the market (kudu, gemsbok, ostrich, impala, springbok), uncommon species in the market (giraffe, waterbuck, bushbuck, duiker, mountain zebra) and extra-continental species (kangaroo). The mountain zebra Equus zebra is an International Union for Conservation of Nature (IUCN) red listed species. We also detected Damaliscus pygargus, which is composed of two subspecies with one listed by IUCN as ‘near threatened’; however, these mitochondrial fragments were insufficient to distinguish between the subspecies. The genetic distance between African ungulate species often overlaps with within-species distance in cases of recent speciation events, and strong phylogeographic structure determines within-species distances that are similar to the commonly accepted distances between species. Conclusions The reliability of commercial labeling of game meat in South Africa is very poor. The extensive substitution of wild game has important implications for conservation and commerce, and for the

Pre-mRNA Processing Factor Prp18 Is a Stimulatory Factor of Influenza Virus RNA Synthesis and Possesses Nucleoprotein Chaperone Activity.

PubMed

Minakuchi, M; Sugiyama, K; Kato, Y; Naito, T; Okuwaki, M; Kawaguchi, A; Nagata, K

2017-02-01

The genome of influenza virus (viral RNA [vRNA]) is associated with the nucleoprotein (NP) and viral RNA-dependent RNA polymerases and forms helical viral ribonucleoprotein (vRNP) complexes. The NP-vRNA complex is the biologically active template for RNA synthesis by the viral polymerase. Previously, we identified human pre-mRNA processing factor 18 (Prp18) as a stimulatory factor for viral RNA synthesis using a Saccharomyces cerevisiae replicon system and a single-gene deletion library of Saccharomyces cerevisiae (T. Naito, Y. Kiyasu, K. Sugiyama, A. Kimura, R. Nakano, A. Matsukage, and K. Nagata, Proc Natl Acad Sci USA, 104:18235-18240, 2007, https://doi.org/10.1073/pnas.0705856104). In infected Prp18 knockdown (KD) cells, the synthesis of vRNA, cRNA, and viral mRNAs was reduced. Prp18 was found to stimulate in vitro viral RNA synthesis through its interaction with NP. Analyses using in vitro RNA synthesis reactions revealed that Prp18 dissociates newly synthesized RNA from the template after the early elongation step to stimulate the elongation reaction. We found that Prp18 functions as a chaperone for NP to facilitate the formation of NP-RNA complexes. Based on these results, it is suggested that Prp18 accelerates influenza virus RNA synthesis as an NP chaperone for the processive elongation reaction. Templates for viral RNA synthesis of negative-stranded RNA viruses are not naked RNA but rather RNA encapsidated by viral nucleocapsid proteins forming vRNP complexes. However, viral basic proteins tend to aggregate under physiological ionic strength without chaperones. We identified the pre-mRNA processing factor Prp18 as a stimulatory factor for influenza virus RNA synthesis. We found that one of the targets of Prp18 is NP. Prp18 facilitates the elongation reaction of viral polymerases by preventing the deleterious annealing of newly synthesized RNA to the template. Prp18 functions as a chaperone for NP to stimulate the formation of NP-RNA complexes. Based on

[Genetic evidence for recombination and mutation in the emergence of human enterovirus 71].

PubMed

Liu, Ai-Ping; Tan, Hui; Xie, Qun; Chen, Bai-Tang; Liu, Xiao-Feng; Zhang, Yong

2014-09-01

We wished to understand the genetic recombination and phylogenetic characteristics of human en- terovirus A71 (EV-A71) and to explore its potential virulence-related sites. Full-length genomes of three EV-A71 strains isolated from patients in Chenzhou City (China) were sequenced and analyzed. Possible re- combination events and crossover sites were analyzed with Recombination Detection Program v4. 1. 6 by comparison with the complete genome sequences of 231 strains of EV-A71. Similarly, plot and bootscanning analyses were undertaken with SimPlot v3. 5. 1. Phylogenetic trees based on the sequences of VP1 regions were constructed with MEGA v5. 2 using the Kimura two-parameter model and neighbor-joining method. Results suggested that recombination events were detected among the three EV-A71 isolates from Chenzhou City. The common main parent sequence was from JF799986 isolated from samples in Guang- zhou City (China) in 2009, and the minor parent sequence was TW/70516/08. Intertypic recombination e- vents were found in the C4b strain (strain SHZH98 isolated in 1998) and C4a strain (Fuyang strain isola- ted in 2008) with the prototype strains of CVA4 and CVA14 in the 3D region. The chi-square test was used to screen-out potential virulence-related sites with nucleotide substitutions of different types of hand, foot, and mouth disease (HFMD) cases using SPSS v19.0. Results suggested that there were no significant nucleotide substitutions between death cases and severe-HFMD cases. Eighteen significant nucleotide substitutions were found between death/severe-HFMD cases and mild-HFMD cases, and all these 18 substitutions were distributed only in P2 and P3 regions. Intertypic recombination among the predominant circulating EV-A71 strains in the Chinese mainland and other EV-A strains probably dates before 1998, and intratypic recombination might have occurred frequently in the HFMD outbreak from 2008 to 2012. Substitutions in the non-capsid region may be correlated with the

Present-day Circum-Antarctic Simulations using the POPSICLES Coupled Ice Sheet-Ocean Model

NASA Astrophysics Data System (ADS)

Asay-Davis, X.; Martin, D. F.; Price, S. F.; Maltrud, M. E.; Collins, W.

2014-12-01

We present POPSICLES simulation results covering the full Antarctic Ice Sheet and the Southern Ocean spanning the period 1990 to 2010. Simulations are performed at 0.1o (~5 km) ocean resolution and with adaptive ice-sheet model resolution as fine as 500 m. We compare time-averaged melt rates below a number of major ice shelves with those reported by Rignot et al. (2013) as well as other recent studies. We also present seasonal variability and decadal trends in submarine melting from several Antarctic regions. Finally, we explore the influence on basal melting and system dynamics resulting from two different choices of climate forcing: a "normal-year" climatology and the CORE v. 2 forcing data (Large and Yeager 2008).POPSICLES couples the POP2x ocean model, a modified version of the Parallel Ocean Program (Smith and Gent, 2002), and the BISICLES ice-sheet model (Cornford et al., 2012). POP2x includes sub-ice-shelf circulation using partial top cells (Losch, 2008) and boundary layer physics following Holland and Jenkins (1999), Jenkins (2001), and Jenkins et al. (2010). Standalone POP2x output compares well with standard ice-ocean test cases (e.g., ISOMIP; Losch, 2008) and other continental-scale simulations and melt-rate observations (Kimura et al., 2013; Rignot et al., 2013). BISICLES makes use of adaptive mesh refinement and a 1st-order accurate momentum balance similar to the L1L2 model of Schoof and Hindmarsh (2009) to accurately model regions of dynamic complexity, such as ice streams, outlet glaciers, and grounding lines. Results of BISICLES simulations have compared favorably to comparable simulations with a Stokes momentum balance in both idealized tests (MISMIP-3D; Pattyn et al., 2013) and realistic configurations (Favier et al. 2014).A companion presentation, "Response of the Antarctic Ice Sheet to ocean forcing using the POPSICLES coupled ice sheet-ocean model" in session C024 covers the ice-sheet response to these melt rates in the coupled simulation

Cognitive and Behavioral Skills Exercises Completed by Patients with Major Depression During Smartphone Cognitive Behavioral Therapy: Secondary Analysis of a Randomized Controlled Trial.

PubMed

Furukawa, Toshi A; Horikoshi, Masaru; Fujita, Hirokazu; Tsujino, Naohisa; Jinnin, Ran; Kako, Yuki; Ogawa, Sei; Sato, Hirotoshi; Kitagawa, Nobuki; Shinagawa, Yoshihiro; Ikeda, Yoshio; Imai, Hissei; Tajika, Aran; Ogawa, Yusuke; Akechi, Tatsuo; Yamada, Mitsuhiko; Shimodera, Shinji; Watanabe, Norio; Inagaki, Masatoshi; Hasegawa, Akio

2018-01-11

tasks, engaged in different types of activities, and also filled in more cognitive restructuring worksheets than the latter. Activities such as "test-drive a new car," "go to a coffee shop after lunch," or "call up an old friend" were found to be particularly rewarding. All cognitive restructuring strategies were found to significantly decrease the distress level, with "What would be your advice to a friend who has a similar problem?" found more helpful than some other strategies. The CBT program offered via smartphone and connected to the remote server is not only effective in alleviating depression but also opens a new avenue in gathering information of what and how each participant may utilize the program. The activities and strategies found useful in this analysis will provide valuable information in brush-ups of the program itself and of mobile health (mHealth) in general. Japanese Clinical Trials Registry UMIN CTR 000013693; https://upload.umin.ac.jp/cgi-open-bin/ctr_e/ ctr_view.cgi?recptno=R000015984 (Archived by WebCite at http://www.webcitation.org/6u6pxVwik). ©Toshi A Furukawa, Masaru Horikoshi, Hirokazu Fujita, Naohisa Tsujino, Ran Jinnin, Yuki Kako, Sei Ogawa, Hirotoshi Sato, Nobuki Kitagawa, Yoshihiro Shinagawa, Yoshio Ikeda, Hissei Imai, Aran Tajika, Yusuke Ogawa, Tatsuo Akechi, Mitsuhiko Yamada, Shinji Shimodera, Norio Watanabe, Masatoshi Inagaki, Akio Hasegawa. Originally published in JMIR Mental Health (http://mental.jmir.org), 11.01.2018.

Three-Dimensional Numerical Modeling of Crustal Growth at Active Continental Margins

NASA Astrophysics Data System (ADS)

Zhu, G.; Gerya, T.; Tackley, P. J.

2011-12-01

the finger-like plumes. We demonstrate the potential applicability of our model to clustering of arc magmatism in several subduction zones, such as Baja California (Ramos-Velázquez et al., Revista Mexicana de Ciencias Geológicas,2008), North Island of New Zealand (Booden et al., J. Volcanol. Geotherm. Res., 2010), Northeast Japan (Kimura and Yoshida,Journal of Petrology, 2006); Ecuador (Schütte et al., Tectonophysics,2010) and Lesser Antilles (Labanieh et al., EPSL,2010).

PREFACE: 3rd International Workshop on "State of the Art in Nuclear Cluster Physics"

NASA Astrophysics Data System (ADS)

Yamada, Taiichi; Kanada-En'yo, Yoshiko

2014-12-01

The 3rd International Workshop on "State of the Art in Nuclear Cluster Physics"(SOTANCP3) was held at KGU Kannai Media Center, Kanto Gakuin University, Yokohama, Japan, from May 26 to 30, 2014. Yokohama is the second largest city in Japan, about 25 km southeast of Tokyo. The first workshop of the series was held in Strasbourg, France, in 2008 and the second one was in Brussels, Belgium, in 2010. The purpose of SOTANCP3 was to discuss the present status and future perspectives of the nuclear cluster physics. The following nine topics were selected in order to cover most of the scientific programme and highlight an area where new ideas have emerged over recent years: (1) Cluster structures and many-body correlations in stable and unstable nuclei (2) Clustering aspects of nuclear reactions and resonances (3) Alpha condensates and analogy with condensed matter approaches (4) Role of tensor force in cluster physics and ab initio approaches (5) Clustering in hypernuclei (6) Nuclear fission, superheavy nuclei, and cluster decay (7) Cluster physics and nuclear astrophysics (8) Clustering in nuclear matter and neutron stars (9) Clustering in hadron and atomic physics There were 122 participants, including 53 from 17 foreign countries. In addition to invited talks, we had many talks selected from contributed papers. There were plenary, parallel, and poster sessions. Poster contributions were also presented as four-minute talks in parallel sessions. This proceedings contains the papers presented in invited and selected talks together with those presented in poster sessions. We would like to express our gratitude to the members of the International Advisory Committee and those of the Organizing Committee for their efforts which made this workshop successful. In particular we would like to present our great thanks to Drs. Y. Funaki, W. Horiuchi, N. Itagaki, M. Kimura, T. Myo, and T. Yoshida. We would like also to thank the following organizations for their sponsors: RCNP

Species Delimitation and Global Biosecurity

PubMed Central

Boykin, Laura M.; Armstrong, Karen F.; Kubatko, Laura; De Barro, Paul

2012-01-01

Species delimitation directly impacts on global biosecurity. It is a critical element in the decisions made by national governments in regard to the flow of trade and to the biosecurity measures imposed to protect countries from the threat of invasive species. Here we outline a novel approach to species delimitation, “tip to root”, for two highly invasive insect pests, Bemisia tabaci (sweetpotato whitefly) and Lymantria dispar (Asian gypsy moth). Both species are of concern to biosecurity, but illustrate the extremes of phylogenetic resolution that present the most complex delimitation issues for biosecurity; B. tabaci having extremely high intra-specific genetic variability and L. dispar composed of relatively indistinct subspecies. This study tests a series of analytical options to determine their applicability as tools to provide more rigorous species delimitation measures and consequently more defensible species assignments and identification of unknowns for biosecurity. Data from established DNA barcode datasets (COI), which are becoming increasingly considered for adoption in biosecurity, were used here as an example. The analytical approaches included the commonly used Kimura two-parameter (K2P) inter-species distance plus four more stringent measures of taxon distinctiveness, (1) Rosenberg’s reciprocal monophyly, (P(AB)),1 (2) Rodrigo’s (P(randomly distinct)),2 (3) genealogical sorting index, (gsi),3 and (4) General mixed Yule-coalescent (GMYC).4,5 For both insect datasets, a comparative analysis of the methods revealed that the K2P distance method does not capture the same level of species distinctiveness revealed by the other three measures; in B. tabaci there are more distinct groups than previously identified using the K2P distances and for L. dipsar far less variation is apparent within the predefined subspecies. A consensus for the results from P(AB), P(randomly distinct) and gsi offers greater statistical confidence as to where genetic limits

Feasibility of nuclear ribosomal region ITS1 over ITS2 in barcoding taxonomically challenging genera of subtribe Cassiinae (Fabaceae).

PubMed

Mishra, Priyanka; Kumar, Amit; Rodrigues, Vereena; Shukla, Ashutosh K; Sundaresan, Velusamy

2016-01-01

The internal transcribed spacer (ITS) region is situated between 18S and 26S in a polycistronic rRNA precursor transcript. It had been proved to be the most commonly sequenced region across plant species to resolve phylogenetic relationships ranging from shallow to deep taxonomic levels. Despite several taxonomical revisions in Cassiinae, a stable phylogeny remains elusive at the molecular level, particularly concerning the delineation of species in the genera Cassia, Senna and Chamaecrista . This study addresses the comparative potential of ITS datasets (ITS1, ITS2 and concatenated) in resolving the underlying morphological disparity in the highly complex genera, to assess their discriminatory power as potential barcode candidates in Cassiinae. A combination of experimental data and an in-silico approach based on threshold genetic distances, sequence similarity based and hierarchical tree-based methods was performed to decipher the discriminating power of ITS datasets on 18 different species of Cassiinae complex. Lab-generated s equences were compared against those available in the GenBank using BLAST and were aligned through MUSCLE 3.8.31 and analysed in PAUP 4.0 and BEAST1.8 using parsimony ratchet, maximum likelihood and Bayesian inference (BI) methods of gene and species tree reconciliation with bootstrapping. DNA barcoding gap was realized based on the Kimura two-parameter distance model (K2P) in TaxonDNA and MEGA. Based on the K2P distance, significant divergences between the inter- and intra-specific genetic distances were observed, while the presence of a DNA barcoding gap was obvious. The ITS1 region efficiently identified 81.63% and 90% of species using TaxonDNA and BI methods, respectively. The PWG-distance method based on simple pairwise matching indicated the significance of ITS1 whereby highest number of variable (210) and informative sites (206) were obtained. The BI tree-based methods outperformed the similarity-based methods producing well

Transmembrane helix M6 in sarco(endo)plasmic reticulum Ca(2+)-ATPase forms a functional interaction site with phospholamban. Evidence for physical interactions at other sites.

PubMed

Asahi, M; Kimura, Y; Kurzydlowski, K; Tada, M; MacLennan, D H

1999-11-12

In an earlier study (Kimura, Y., Kurzydlowski, K., Tada, M., and MacLennan, D. H. (1997) J. Biol. Chem. 272, 15061-15064), mutation of amino acids on one face of the phospholamban (PLN) transmembrane helix led to loss of PLN inhibition of sarco(endo)plasmic reticulum Ca(2+)-ATPase (SERCA) molecules. This helical face was proposed to form a site of PLN interaction with a transmembrane helix in SERCA molecules. To determine whether predicted transmembrane helices M4, M5, M6, or M8 in SERCA1a interact with PLN, SERCA1a mutants were co-expressed with wild-type PLN and effects on Ca(2+) dependence of Ca(2+) transport were measured. Wild-type inhibitory interactions shifted apparent Ca(2+) affinity of SERCA1a by an average of -0.34 pCa units, but four of the seven mutations in M4 led to a more inhibitory shift in apparent Ca(2+) affinity, averaging -0.53 pCa units. Seven mutations in M5 led to an average shift of -0.32 pCa units and seven mutations in M8 led to an average shift of -0.30 pCa units. Among 11 mutations in M6, 1, Q791A, increased the inhibitory shift (-0.59 pCa units) and 5, V795A (-0.11), L802A (-0.07), L802V (-0.04), T805A (-0.11), and F809A (-0.12), reduced the inhibitory shift, consistent with the view that Val(795), Leu(802), Thr(805), and Phe(809), located on one face of a predicted M6 helix, form a site in SERCA1a for interaction with PLN. Those mutations in M4, M6, or M8 of SERCA1a that enhanced PLN inhibitory function did not enhance PLN physical association with SERCA1a, but mutants V795A and L802A in M6, which decreased PLN inhibitory function, decreased physical association, as measured by co-immunoprecipitation. In related studies, those PLN mutants that gained inhibitory function also increased levels of co-immunoprecipitation of wild-type SERCA1a and those that lost inhibitory function also reduced association, correlating functional interaction sites with physical interaction sites. Thus, both functional and physical data confirm that PLN

DNA Barcoding Reveals Cryptic Diversity within Commercially Exploited Indo-Malay Carangidae (Teleosteii: Perciformes)

PubMed Central

Mat Jaafar, Tun Nurul Aimi; Taylor, Martin I.; Mohd Nor, Siti Azizah; de Bruyn, Mark; Carvalho, Gary R.

2012-01-01

Background DNA barcodes, typically focusing on the cytochrome oxidase I gene (COI) in many animals, have been used widely as a species-identification tool. The ability of DNA barcoding to distinguish species from a range of taxa and to reveal cryptic species has been well documented. Despite the wealth of DNA barcode data for fish from many temperate regions, there are relatively few available from the Southeast Asian region. Here, we target the marine fish Family Carangidae, one of the most commercially-important families from the Indo-Malay Archipelago (IMA), to produce an initial reference DNA barcode library. Methodology/Principal Findings Here, a 652 bp region of COI was sequenced for 723 individuals from 36 putative species of Family Carangidae distributed within IMA waters. Within the newly-generated dataset, three described species exhibited conspecific divergences up to ten times greater (4.32–4.82%) than mean estimates (0.24–0.39%), indicating a discrepancy with assigned morphological taxonomic identification, and the existence of cryptic species. Variability of the mitochondrial DNA COI region was compared within and among species to evaluate the COI region's suitability for species identification. The trend in range of mean K2P distances observed was generally in accordance with expectations based on taxonomic hierarchy: 0% to 4.82% between individuals within species, 0% to 16.4% between species within genera, and 8.64% to 25.39% between genera within families. The average Kimura 2-parameter (K2P) distance between individuals, between species within genera, and between genera within family were 0.37%, 10.53% and 16.56%, respectively. All described species formed monophyletic clusters in the Neighbour-joining phylogenetic tree, although three species representing complexes of six potential cryptic species were detected in Indo-Malay Carangidae; Atule mate, Selar crumenophthalmus and Seriolina nigrofasciata. Conclusion/Significance This study confirms

Development of piggy-back basins in the Sub-Himalaya: structure of the Triyuga Valley in eastern Nepal from seismic reflection profiles

NASA Astrophysics Data System (ADS)

Lee, Y. S.; Almeida, R. V.; Hubbard, J.; Liberty, L. M.; Foster, A. E.; Sapkota, S. N.

2017-12-01

The foreland fold and thrust belt in the Nepal Himalaya has developed over the last 2 My (Mugnier et al., 2004; Van der Beek et al., 2006), and is generally referred to as the Main Frontal Thrust system (MFT; Gansser, 1964). The thrust faults there are spaced 5-30 km apart. Where the faults are furthest from each other, they create piggy-back basins, known as "dun" valleys in the Himalaya. The easternmost of these basins in Nepal is the Triyuga river valley, a 35 km wide basin where the range front abruptly steps 15 km to the south. This dun valley is thought to be the youngest of Nepal, initiating in the Late Pleistocene (Kimura, 1999). In order to understand the sub-surface structure and development of the Triyuga Valley, we analyse high resolution seismic reflection profiles across the three basin-surrounding structures, as well as a north-south profile across the basin proper, in combination with field observations. These datasets reveal that the edges of the forward step are defined by three orthogonal thrust fronts, with abrupt changes in vergence direction. Sharp geometric changes along the range front may have implications for the propagation of earthquakes along the MFT. The surface rupture of the Nepal-Bihar 1934 earthquake was inferred to go around this thrust front (Sapkota et al., 2013), however field observations suggest that although past earthquakes have likely ruptured the surface here, these faults did not slip in 1934. Further, analogue models suggest that the filling of the basin with sediments may affect the activation of out of sequence thrusts (Toscani et al., 2014). This is consistent with field evidence of Quaternary reactivation of the Main Boundary Thrust north of the Triyuga Valley. We also compare these seismic profiles to one across the Jalthal anticline, an incipient structure forming 50 km south of the range front in easternmost Nepal (a section thought to have ruptured in 125; Nakata et al., 1998). We suggest that this may be an

The 2007 Boso Slow Slip Event and the associated earthquake swarm

NASA Astrophysics Data System (ADS)

Sekine, S.; Hirose, H.; Kimura, H.; Obara, K.

2007-12-01

In the Boso Peninsula, which is located in southeast of the Japan mainland, slow slip events (SSE) have been observed by the GEONET GPS array operated by the Geographical Survey Institute Japan and the NIED tiltmeter network every 6-7 years (Ozawa et al.,2003; NIED 2003). The unique characteristics of the Boso SSE are that earthquake swarm activities have also occurred in association with the SSE. The latest activity of the SSE and the earthquake swarm took place in August 2007. On 13th August, an earthquake swarm began to occur at east off Boso Peninsula and the slow tilt deformations also started. The earthquake sources migrated to the NNE direction, which is the same direction of the relative plate motion of the subducting Philippine Sea Plate with respect to the overriding plate. The largest earthquake in this episode (Mw 5.3) occurred on 16th and the second largest one (Mw 5.2) on 18th. Most of the larger earthquakes show low- angle thrust type focal mechanisms that are consistent with the plate motion and the geometry of the subduction plate interface. The tilt changes seem to stop on 17th and the activity of the swarm rapidly decreases after 19th. The maximum tilt change of 0.8 micro radian with northwest down tilting was observed at KT2H, the nearest station from the source region. Based on the tilt records around Boso Peninsula, we estimate a fault model for the SSE using genetic algorithm inversion to non-linear parameter and the weighted least squares method to linear parameters. As a result, the estimated moment magnitude and the amount of slip are 6.4 and 10 cm, respectively. The size and the location of the SSE are similar to the previous episodes. The estimated fault plane is very consistent with the configuration of the plate interface (Kimura et al., 2006). Most of the earthquakes are located on the deeper edge of the estimated SSE fault area. The coincidence of the swarm and the SSE suggests a causal relation between them and may help us to

Mega-thrust and Intra-slab Earthquakes Beneath Tokyo Metropolitan Area

NASA Astrophysics Data System (ADS)

Hirata, N.; Sato, H.; Koketsu, K.; Hagiwara, H.; Wu, F.; Okaya, D.; Iwasaki, T.; Kasahara, K.

2006-12-01

In central Japan the Philippine Sea plate (PSP) subducts beneath the Tokyo Metropolitan area, the Kanto region, where it causes mega-thrust earthquakes, such as the 1703 Genroku earthquake (M8.0) and the 1923 Kanto earthquake (M7.9) which had 105,000 fatalities. The vertical proximity of this down going lithospheric plate is of concern because the greater Tokyo urban region has a population of 42 million and is the center of approximately 40% of the nation's economic activities. A M7+ earthquake in this region at present has high potential to produce devastating loss of life and property with even greater global economic repercussions. The M7+ earthquake is evaluated to occur with a probability of 70% in 30 years by the Earthquake Research Committee of Japan. In 2002, a consortium of universities and government agencies in Japan started the Special Project for Earthquake Disaster Mitigation in Urban Areas, a project to improve information needed for seismic hazards analyses of the largest urban centers. Assessment in Kanto of the seismic hazard produced by the Philippine Sea Plate (PSP) mega-thrust earthquakes requires identification of all significant faults and possible earthquake scenarios and rupture behavior, regional characterizations of PSP geometry and the overlying Honshu arc physical properties (e.g., seismic wave velocities, densities, attenuation), and local near-surface seism ic site effects. Our study addresses (1) improved regional characterization of the PSP geometry based on new deep seismic reflection profiles (Sato etal.,2005), reprocessed off-shore profiles (Kimura et al.,2005), and a dense seismic array in the Boso peninsular (Hagiwara et al., 2006) and (2) identification of asperities of the mega-thrust at the top of the PSP. We qualitatively examine the relationship between seismic reflections and asperities inferred by reflection physical properties. We also discuss the relation between deformation of PSP and intra-slab M7+ earthquakes: the

Evidence of new species for malaria vector Anopheles nuneztovari sensu lato in the Brazilian Amazon region.

PubMed

Scarpassa, Vera Margarete; Cunha-Machado, Antonio Saulo; Saraiva, José Ferreira

2016-04-12

Anopheles nuneztovari sensu lato comprises cryptic species in northern South America, and the Brazilian populations encompass distinct genetic lineages within the Brazilian Amazon region. This study investigated, based on two molecular markers, whether these lineages might actually deserve species status. Specimens were collected in five localities of the Brazilian Amazon, including Manaus, Careiro Castanho and Autazes, in the State of Amazonas; Tucuruí, in the State of Pará; and Abacate da Pedreira, in the State of Amapá, and analysed for the COI gene (Barcode region) and 12 microsatellite loci. Phylogenetic analyses were performed using the maximum likelihood (ML) approach. Intra and inter samples genetic diversity were estimated using population genetics analyses, and the genetic groups were identified by means of the ML, Bayesian and factorial correspondence analyses and the Bayesian analysis of population structure. The Barcode region dataset (N = 103) generated 27 haplotypes. The haplotype network suggested three lineages. The ML tree retrieved five monophyletic groups. Group I clustered all specimens from Manaus and Careiro Castanho, the majority of Autazes and a few from Abacate da Pedreira. Group II clustered most of the specimens from Abacate da Pedreira and a few from Autazes and Tucuruí. Group III clustered only specimens from Tucuruí (lineage III), strongly supported (97 %). Groups IV and V clustered specimens of A. nuneztovari s.s. and A. dunhami, strongly (98 %) and weakly (70 %) supported, respectively. In the second phylogenetic analysis, the sequences from GenBank, identified as A. goeldii, clustered to groups I and II, but not to group III. Genetic distances (Kimura-2 parameters) among the groups ranged from 1.60 % (between I and II) to 2.32 % (between I and III). Microsatellite data revealed very high intra-population genetic variability. Genetic distances showed the highest and significant values (P = 0.005) between Tucuruí and

Ethnobotanical survey of herbal tea plants from the traditional markets in Chaoshan, China.

PubMed

Li, Dong-Lin; Zheng, Xi-Long; Duan, Lei; Deng, Shuang-Wen; Ye, Wen; Wang, Ai-Hua; Xing, Fu-Wu

2017-06-09

Herbal tea, which refers to "cooling tea", "cool beverage", or "liáng chá" in China, includes a range of drinks with heat-clearing and detoxification qualities. Herbal tea plants are great contributive to the health and prosperity of Chaoshan people. The aim of the study was to document herbal tea plant species used and commercialized as "liáng chá" in Chaoshan area, to facilitate the use and development of herbal tea enterprises, and to promote the further development of national herbal tea. Information and data were obtained from all 83 stall holders in 12 traditional markets, semi-structured informant interviews were carried out individually with the stall holders, 10 questions were asked. In this study, 186 species of herbal tea plants belonging to 65 families and 156 genera were indicated by 83 stall holders, with Asteraceae being the most prevalent family with 22 species. Herbs are main sources of herbal tea plants in Chaoshan area, with whole plants (97 species) being the most used parts. Herbal drinks are mostly consumed for heat-clearing and detoxification, and a large number of plant species were reported to treat coughs, colds, dysentery, dampness and sore throats. The most cited species were Hedyotis corymbosa (L.) Lam. (47 times mentioned), Hedyotis diffusa Willd. (46), Plantago asiatica L. (43), Houttuynia cordata Thunb (42), Centella asiatica (L.) Urban (36), Desmodium styracifolium (Osbeck) Merr. (35) and Morus alba L. (31), and 5 protected species were recorded in the list of the nationally protected species of China: Dendrobium officinale Kimura et Migo, Dendrobium nobile Lindl., Anoectochilus formosanus Hayata, Bulbophyllum odoratissimum (J. E. Smith) Lindl. and Pholidota chinensis Lindl. The selling price of most fresh herbal tea plants in the market varied from￥10-16/kg, with the profit margin of sales ranging from 12.5% to 20%. The consumption of herbal tea for one family costs about ￥3-5/day. Chaoshan herbal teas, prepared by diverse

P - ρ - T data for H2O up to 260 GPa under laser-driven shock loading

NASA Astrophysics Data System (ADS)

Kimura, T.; Ozaki, N.; Sano, T.; Okuchi, T.; Shimizu, K.; Miyanishi, K.; Terai, T.; Kakeshita, T.; Sakawa, Y.; Kodama, R.

2014-12-01

.109-138. 2S. P. Lyon and J. D. Johnson, Los Alamos Technical Report No. LA-UR-92-3407, 1992. 3F. H. Ree, Lawrence Livemore Laboratory Technical Report No. UCRL-52190, 1976. 4M. French et al., Phys. Rev. B 79, 054107 (2009). 5M. D. Knudson et al., Phys. Rev. Lett. 108, 091102 (2012). 6 R. Redmer et al., Icarus 211, 798 (2011). 7T. Kimura et al., J. Chem. Phys. 140, 074501 (2014).

Seismic velocity structure and spatial distribution of reflection intensity off the Boso Peninsula, Central Japan, revealed by an ocean bottom seismographic experiment

NASA Astrophysics Data System (ADS)

Kono, Akihiro; Sato, Toshinori; Shinohara, Masanao; Mochizuki, Kimihiro; Yamada, Tomoaki; Uehira, Kenji; Shinbo, Takashi; Machida, Yuuya; Hino, Ryota; Azuma, Ryosuke

2016-04-01

Off the Boso Peninsula, central Japan, where the Sagami Trough is in the south and the Japan Trench is in the east, there is a triple junction where the Pacific plate (PAC), the Philippine Sea plate (PHS) and the Honshu island arc (HIA) meet each other. In this region, the PAC subducts beneath the PHS and the HIA, and the PHS subducts beneath the HIA. Due to the subduction of 2 oceanic plates, numerous seismic events took place in the past. In order to understand these events, it is important to image structure of these plates. Hence, many researchers attempted to reveal the substructure from natural earthquakes and seismic experiments. Because most of the seismometers are placed inland area and the regular seismicity off Boso is inactive, it is difficult to reveal the precise substructure off Boso area using only natural earthquakes. Although several marine seismic experiments using active sources were conducted, vast area remains unclear off Boso Peninsula. In order to improve the situation, a marine seismic experiment, using airgun as an active source, was conducted from 30th July to 4th of August, 2009. The survey line has 216 km length and 20 Ocean Bottom Seismometers (OBSs) were placed on it. We estimated 2-D P-wave velocity structure from the airgun data using the PMDM (Progressive Model Development Method; Sato and Kenett, 2000) and the FAST (First Arrival Seismic Tomography ; Zelt and Barton, 1998). Furthermore, we identified the probable reflection phases from the data and estimated the location of reflectors using Travel time mapping method (Fujie et al. 2006). We found some reflection phases from the data, and the reflectors are located near the region where P-wave velocity is 5.0 km/s. We interpret that the reflectors indicate the plate boundary between the PHS and the HIA. The variation of the intensity of reflection along the upper surface of PHS seems to be consistent with the result from previous reflection seismic experiment conducted by Kimura et

[What is impaired consciousness? Revisiting impaired consciousness as psychiatric concept].

PubMed

Kanemoto, Kousuke

2004-01-01

observation of an additional 3 cases, descriptions of naissance of the first word (taken from the autobiography of Helen Keller), visual object agnosia, and chronic schizophrenia with schizophasia were discussed to examine the relationship between impairments of recursive consciousness and semantic generation dysfunction. Attempts to bridge semantic generation and recursive consciousness, performed by psychopathologists such as Bin Kimura and Hiroyuki Koide, were also briefly discussed. In light of these case presentations and related discussions, we re-examined traditional theories of impaired consciousness, including Mayer-Gross's Gestalt theory, later replaced by Conrad and Henri Ey's theory related to intentionality. Furthermore, we attempted to link Denett's theory of consciousness to those traditional theories as well as to our own postulations, and neuropsychological data such as those of implicit memory and blindsight. Finally, the significance of Freud's unconsciousness in the framework of neuroscience was discussed.

Snow drift: acoustic sensors for avalanche warning and research

NASA Astrophysics Data System (ADS)

Lehning, M.; Naaim, F.; Naaim, M.; Brabec, B.; Doorschot, J.; Durand, Y.; Guyomarc'h, G.; Michaux, J.-L.; Zimmerli, M.

-term monitoring. Optical sensors (Schmidt, 1977; Brown and Pomeroy, 1989; Sato and Kimura, 1993) have been very successful for research applications, but suffer from the fact that they give a single flux value at one specific height. In addition, they have not been used, to our knowledge, for long-term monitoring applications or at remote sites. New developments of acoustic sensors have taken place recently (Chritin et al., 1999; Font et al., 1998). Jaedicke (2001) gives examples of possible applications of acoustic snow drift sensors. He emphasizes the advantages of acoustic sensors for snow drift monitoring at remote locations, but could not present any evaluation of the accuracy of the measurements. We present a complete evaluation of the new acoustic sensors for snow drift and discuss their applications for research or avalanche warning. We compare the suitability of sensors for operational applications.

EDITORIAL: Focus on Advances in Surface and Interface Science 2008 FOCUS ON ADVANCES IN SURFACE AND INTERFACE SCIENCE 2008

NASA Astrophysics Data System (ADS)

Scheffler, Matthias; Schneider, Wolf-Dieter

2008-12-01

Iori, K Sakamoto, H Narita, A Kimura, M Taniguchi, S Qiao, K Hasegawa, K Shimada, H Namatame and S Blügel Activated associative desorption of C + O → CO from Ru(001) induced by femtosecond laser pulses S Wagner, H Öström, A Kaebe, M Krenz, M Wolf, A C Luntz and C Frischkorn Surface structure of Sn-doped In2O3 (111) thin films by STM Erie H Morales, Yunbin He, Mykola Vinnichenko, Bernard Delley and Ulrike Diebold Coulomb oscillations in three-layer graphene nanostructures J Güttinger, C Stampfer, F Molitor, D Graf, T Ihn and K Ensslin Adsorption processes of hydrogen molecules on SiC(001), Si(001) and C(001) surfaces Xiangyang Peng, Peter Krüger and Johannes Pollmann Fermi surface nesting in several transition metal dichalcogenides D S Inosov, V B Zabolotnyy, D V Evtushinsky, A A Kordyuk, B Büchner, R Follath, H Berger and S V Borisenko Probing molecule-surface interactions through ultra-fast adsorbate dynamics: propane/Pt(111) A P Jardine, H Hedgeland, D Ward, Y Xiaoqing, W Allison, J Ellis and G Alexandrowicz A novel method achieving ultra-high geometrical resolution in scanning tunnelling microscopy R Temirov, S Soubatch, O Neucheva, A C Lassise and F S Tautz

Secondary overprinting of S-Se-Te signatures in the Earth's mantle: Implications for the Late Veneer

NASA Astrophysics Data System (ADS)

Koenig, S.; Luguet, A.; Lorand, J.; Pearson, D.

2013-12-01

towards sub-chondritic Se/Te ratios (i.e. Se/Te < 2). On the other hand, harzburgites that preserve depletion signatures show suprachondritic Se/Te ratios (< 31). Altogether this shows that metasomatic enrichment of mantle rocks may lead to a systematic bias and hence underestimation of the current Se/Te estimate of the primitive mantle. The metasomatic origin of the reported S, Se and Te ratios in peridotites that reflect the control of metasomatic BMS and PGMs[5;6] furthermore show that not all whole rock signatures in the Earth's mantle that scatter around near-chondritic values are primary and hence challenge the simple conception that these features may readily solve the long-standing conundrum of the Late Veneer composition. Refs: [1] Rose-Weston et al. (2009) GCA 73, 4598-4615; [2] Kimura et al. (1974) GCA 38, 683-701; [3] Lorand and Alard (2010) 67, 4137-4151; [4] Wang and Becker (2013) Nature 499, 328-331; [5] König et al. (2012) GCA 86, 354-366; [6] König et al. (2013, in press), EPSL.

Upward extension of the Nankai accretionary prism megasplay fault into slope basin strata. Insights from drilling at IODP Expedition 338 Site C0022

NASA Astrophysics Data System (ADS)

Fabbri, O.; Oohashi, K.; Kanagawa, K.; Yamaguchi, A.

2013-12-01

Megasplay faults have been recognized on seismic reflection profiles across several convergent margins in the world. Understanding the behavior of these faults during large to very large inter-plate earthquakes is a major challenge in assessing strong-motion and tsunami hazards at or near subduction zones. One of the goals of the IODP NanTroSEIZE project is to drill across and to obtain data from the megasplay fault crossing the Nankai accretionary prism off Kii peninsula (Kumano transect), SW Japan. This fault is considered to have been activated during the 1944 Tonankai earthquake (Baba et al., 2006 ; Moore et al., 2007). Drilling and coring during IODP Expedition 316 (Expedition 316 Scientists, 2009) showed that the megasplay fault at 300 mbsf at Site C0004 consists in a 60 m thick package of fractured and brecciated rocks. Combined analysis of 3D reflection data in the vicinity of Site C0004 and core data from sites C0004 and C0008 (Strasser et al., 2009 ; Kimura et al., 2011) suggest that the lower boundary of the megasplay fault ceased activity at about 1.55 Ma while its upper boundary has remained active since about 1.95 Ma and probably 1.24 Ma. In order to determine whether the megasplay fault upper boundary crosscuts slope sediments or is sealed by them, drilling at IODP Site C0022 was carried out during Expedition 338. Two 420 m deep holes were drilled: C0022A (LWD) and C0022B (coring). At Hole C0022A, LWD resistivity images show that the 85-105.5 mbsf interval is fractured and extends above and below a ca. 1 m thick interval characterized by a low resistivity value at 100-101 mbsf. Structures observed in cores from Hole C0022B confirm LWD data. While gently dipping elsewhere, bedding in the 73-146 mbsf interval is steep, commonly exceeding 30°. This bedding dip increase may be a consequence of fault activity (folding ?). Though the low-resistivity interval at 100-101 mbsf could not be sampled at Hole C0022B (no recovery between 95.5 and 99.5 mbsf

Monitoring the Galaxy - Highlights from the MAXI mission

NASA Astrophysics Data System (ADS)

Mihara, Tatehiro

Monitor of All-sky X-ray Image (MAXI) is an X-ray all-sky monitor on the International Space Station. It is equipped with Gas Slit Camera (GSC) and Solid-state Slit Camera (SSC). Since it was mounted to the Japanese experimental module in 2009, it has been scanning the whole sky in every 92 minutes with ISS rotation. The data are processed automatically and distributed through http://maxi.riken.jp homepage. MAXI issued 136 to Astronomers Telegram and 47 to Gamma-ray burst Coordinated Network so far. There are many transient X-ray sources in our galaxy. The most remarkable one is a new source. MAXI discovered 12 MAXI sources, 6 of which are blackhole binaries. MAXI J0158-744 was a source in a new category (Morii et al. 2013). It was a very bright (10(40) erg s(-1) ) and very rapid (< 1 hour) nova consisting of a unusual pair of binary, which was a Ne-white dwarf and a Be star. The monitoring results are published as the 37-month catalog (Hiroi et al. 2012) which contains 500 sources above 0.6 mCrab in 4-10 keV in high Galactic-latitude (|b| > 10 deg). SSC with X-ray CCD has detected diffuse soft X-rays in the all-sky, such as Cygnus super bubble (Kimura et al. 2013) and north polar spur, as well as it found Ne line from the rapid soft X-ray nova MAXI J0158-744. Be X-ray binary pulsars (BeXBP) are also transients. They have outbursts at the periastron passage. However, the outburst does not occur in every orbit. Some sources stay in quiescence for tens of years, then suddenly start outbursts repeating for several years. All-sky monitor is then essential to study such kinds of sources. For example, cyclotron feature is often seen in the high energy X-ray band of BeXBP, from which magnetic fields of the poles are measured. MAXI detection of outburst and following SUZAKU pointing observation are very effective. We observed two BeXBP, GX 304-1 in 2010 and GRO J1008-57 in 2012 in MAXI-Suzaku collaboration and succeeded to catch them at the outburst peaks (600mCrab and 450

PREFACE: 3rd International Workshop on Materials Analysis and Processing in Magnetic Fields (MAP3)

NASA Astrophysics Data System (ADS)

Sakka, Yoshio; Hirota, Noriyuki; Horii, Shigeru; Ando, Tsutomu

2009-07-01

the journal Science and Technology of Advanced Materials. All articles have been refereed by experts in the field. Both of these journals are fully accessible electronically and can be cited and referenced in the usual way. It is our hope that the reader will enjoy and profit from the MAP3 Proceedings. Hitoshi Wada (Kashiwa, Japan) Chair Eric Beaugon (Grenoble, France) Hans J Schneider-Muntau (Tallahassee, USA) Co-chair Advisory Board Shigeo Asai (Nagoya, Japan) Koichi Kitazawa (Tokyo, Japan) Mitsuhiro Motokawa (Sendai, Japan) Shoogo Ueno (Fukuoka, Japan) Robert Tournier (Grenoble, France) Justin Schwartz (Tallahassee, USA) J C Maan (Nijmegen, Netherland) Scientific Committee Yoshifumi Tanimoto (Hiroshima, Japan) Masuhiro Yamaguchi (Yokohama, Japan) Tsunehisa Kimura (Kyoto, Japan) Yoshio Sakka (Tsukuba Japan) Ryoichi Aogaki (Tokyo, Japan) Jyunji Miyakoshi (Hirosaki, Japan) Kazuo Watanabe (Sendai, Japan) James M Valles Jr. (Providence, USA) Joon Pyo Park (Pohang, Korea) Qiang Wang (Shenyang, China) Nicole Pamme (Hull, UK) Sophie Rivoirard (Grenoble, France) P C M Christianen (Nijmegen, Netherland) Local Organizing Committee Isao Yamamoto Masafumi Yamato Shigeru Horii Norihito Sogoshi Masateru Ikehata Noriyuki Hirota Tsutomu Ando Proceedings Editorial Board Yoshio Sakka Noriyuki Hirota Shigeru Horii Tsutomu Ando Conference photograph

PREFACE: Nanoelectronics, sensors and single molecule biophysics Nanoelectronics, sensors and single molecule biophysics

NASA Astrophysics Data System (ADS)

Tao, Nongjian

2012-04-01

�száros, Koji Yoshida, Artem Mishchenko, Murat Gulcur, Martin R Bryce and Thomas Wandlowski Single-molecule conductance determinations on HS(CH2)4O(CH2)4SH and HS(CH2)2O(CH2)2O(CH2)2SH, and comparison with alkanedithiols of the same lengthLisa E Scullion, Edmund Leary, Simon J Higgins and Richard J Nichols Metal atomic contact under electrochemical potential controlManabu Kiguchi and Kei Murakoshi Rectification in substituted atomic wires: a theoretical insightYoshihiro Asai High-fidelity chemical patterning on oxide-free germaniumJ Nathan Hohman, Moonhee Kim, Jeffrey A Lawrence, Patrick D McClanahan and Paul S Weiss

Study on characteristic frequencies of ELF emissions and estimation of ion constituents in the vicinity of magnetic equator

NASA Astrophysics Data System (ADS)

Matsuda, S.; Kasahara, Y.; Goto, Y.

2012-12-01

. However, it remains several different interpretations depending on the species of ions and their ion constituents. In this study, we set up the following two hypotheses which shall satisfy dozens of such phenomena observed in 1989 and 1990: 1) Constituents of major ions in the plasmasphere (i.e., H^{+}, He^{+}) happened to coincide the condition that gives observed lower cut-off frequency along the trajectory. 2) There exists minor ions (i.e., D^{+}, T^{+}) that have cyclotron frequencies at 1/n of proton's cyclotron frequency. We examine the validity of the above hypotheses referring electron density and Dst index of the corresponding period. The present study could be a promising technique to estimate ion constituents from plasma wave observation by Akebono in the radiation belt. It is also noted that it can be also applicable to the ERG mission, which is expected to provide important clues for solving plasma dynamics in the Earth's radiation belt by means of integrated observation of electric and magnetic fields, particles and waves. [1] Y. Kasahara, A. Sawada, M. Yamamoto, I. Kimura, S. Kokubun, and K. Hayashi, Ion Cyclotron Emissions Observed by the Satellite Akebono in the vicinity of the Magnetic Equator, Radio Science, 27, 347-362, 1992.

The amino acid and hydrocarbon contents of the Paris meteorite, the most primitive CM chondrite

NASA Astrophysics Data System (ADS)

Martins, Zita; Modica, Paola; Zanda, Brigitte; Le Sergeant d'Hendecourt, Louis

2015-04-01

or contribution from interstellar precursors. In summary, the soluble organic content of the primitive CM chondrite Paris possibly relates to late phases of condensed phase chemistry in molecular clouds. References: [1] Blanchard et al. (2011) Abstract #5322. Meteoritics and Planetary Science 46:A21. [2] Caillet Komorowski et al. (2011) Abstract #5289. Meteoritics and Planetary Science 46:A35. [3] Kimura et al. (2011) Meteoritics & Planetary Science 46:431-442. [4] Bourot-Denise et al. (2010) Abstract #1533. 41st LPSC. CD-ROM. [5] Merouane et al. (2011) Proceedings, EPSC-DPS Joint Meeting, pp.902. [6] Merouane et al. (2012) The Astrophysical Journal 756:154-160. [7] Remusat et al. (2010) The Astrophysical Journal 713:1048-1058. [8] Remusat et al. (2011) Abstract #5327. Meteoritics and Planetary Science 46:A197. [9] Martins et al. Meteoritics and Planetary Science, under review. [10] Glavin et al. (2006) Meteoritics & Planetary Science 41:889-902. [11] Glavin et al. (2010) Abstract #5131. Meteoritics and Planetary Science 45:A64. [12] Pizzarello et al. (2003) GCA 67:1589-1595. [13] Glavin and Dworkin (2009) PNAS 106:5487-5492. [14] Elsila et al. (2005) GCA 69:1349-1357.

Evolution and mass extinctions as lognormal stochastic processes

NASA Astrophysics Data System (ADS)

Maccone, Claudio

2014-10-01

-terrestrial civilizations existing in the Galaxy (as a consequence of the central limit theorem of statistics). (5) But the most striking new result is that the well-known `Molecular Clock of Evolution', namely the `constant rate of Evolution at the molecular level' as shown by Kimura's Neutral Theory of Molecular Evolution, identifies with growth rate of the entropy of our Evo-SETI model, because they both grew linearly in time since the origin of life. (6) Furthermore, we apply our Evo-SETI model to lognormal stochastic processes other than GBMs. For instance, we provide two models for the mass extinctions that occurred in the past: (a) one based on GBMs and (b) the other based on a parabolic mean value capable of covering both the extinction and the subsequent recovery of life forms. (7) Finally, we show that the Markov & Korotayev (2007, 2008) model for Darwinian Evolution identifies with an Evo-SETI model for which the mean value of the underlying lognormal stochastic process is a cubic function of the time. In conclusion: we have provided a new mathematical model capable of embracing molecular evolution, SETI and entropy into a simple set of statistical equations based upon b-lognormals and lognormal stochastic processes with arbitrary mean, of which the GBMs are the particular case of exponential growth.

Coupling of the Matched Gravity and Electromagnetic Fields of the Sun with Jupiter and its Moons Together in Nearest Portion of Jupiter's Orbit to the Sun as the Main Cause of the Peak of Approximately 11 Yearly Solar Cycles and Hazards from Solar Storms

NASA Astrophysics Data System (ADS)

Gholibeigian, Kazem; Gholibeigian, Hassan

2016-04-01

strongest variable GEFs in solar system after the Sun. For example, Ganymede is the largest moon of Jupiter and in the Solar System. Completing an orbit in roughly seven days. It means that it generates 52 GEFs oscillations (loading, unloading) per year in solar cycle while it is rotating around the Jupiter. New observations of the planet's extreme ultraviolet emissions show that bright explosions of Jupiter's aurora by the planet-moon interaction, not by solar activity [Tomoki Kimura, JAEA]. Coupling of Jupiter's GEFs and its moons with the Sun generate very strong GEFs and approximately 11 yearly solar cycles. The peaks of each cycle is when the Jupiter passes from the nearest portion of its orbit to the Sun. which some of its peaks generate gigantic solar storms and hazards to the Earth. The Earth passes from between of Sun and Jupiter eleven times in each solar cycle and may be under shooting of storms from the both side specially during 2-3 years in cycle's peak.

PREFACE: Atomically controlled fabrication technology: new physics and functional device realization Atomically controlled fabrication technology: new physics and functional device realization

NASA Astrophysics Data System (ADS)

Kuwahara, Yuji; Kasai, Hideaki

2011-10-01

, J L Hutchison, D C Smith, P Ashburn and C H de Groot Mechanism of atomic-scale passivation and flattening of semiconductor surfaces by wet-chemical preparationsKenta Arima, Katsuyoshi Endo, Kazuto Yamauchi, Kikuji Hirose, Tomoya Ono and Yasuhisa Sano Real-space calculations for electron transport properties of nanostructuresTomoya Ono, Shigeru Tsukamoto, Yoshiyuki Egami and Yoshitaka Fujimoto Thermally activated magnetization reversal in monatomic magnetic chains on surfaces studied by classical atomistic spin-dynamics simulationsDavid S G Bauer, Phivos Mavropoulos, Samir Lounis and Stefan Blügel An atomically controlled Si film formation process at low temperatures using atmospheric-pressure VHF plasmaK Yasutake, H Kakiuchi, H Ohmi, K Inagaki, Y Oshikane and M Nakano Single-nanometer focusing of hard x-rays by Kirkpatrick-Baez mirrorsKazuto Yamauchi, Hidekazu Mimura, Takashi Kimura, Hirokatsu Yumoto, Soichiro Handa, Satoshi Matsuyama, Kenta Arima, Yasuhisa Sano, Kazuya Yamamura, Koji Inagaki, Hiroki Nakamori, Jangwoo Kim, Kenji Tamasaku, Yoshinori Nishino, Makina Yabashi and Tetsuya Ishikawa Surface magnetism in O2 dissociation—from basics to applicationY Kunisada, M C Escaño and H Kasai Real-space finite-difference approach for multi-body systems: path-integral renormalization group method and direct energy minimization methodAkira Sasaki, Masashi Kojo, Kikuji Hirose and Hidekazu Goto Electrical conduction of organic ultrathin films evaluated by an independently driven double-tip scanning tunneling microscopeK Takami, S Tsuruta, Y Miyake, M Akai-Kasaya, A Saito, M Aono and Y Kuwahara

Evaluation of magnifying colonoscopy in the diagnosis of serrated polyps.

PubMed

Ishigooka, Shinya; Nomoto, Masahito; Obinata, Nobuyuki; Oishi, Yoshichika; Sato, Yoshinori; Nakatsu, Satoko; Suzuki, Midori; Ikeda, Yoshiko; Maehata, Tadateru; Kimura, Tomoaki; Watanabe, Yoshiyuki; Nakajima, Takashi; Yamano, Hiro-o; Yasuda, Hiroshi; Itoh, Fumio

2012-08-28

To elucidate the colonoscopic features of serrated lesions of the colorectum using magnifying colonoscopy. Broad division of serrated lesions of the colorectum into hyperplastic polyps (HPs), traditional serrated adenomas (TSAs), and sessile serrated adenomas/polyps (SSA/Ps) has been proposed on the basis of recent molecular biological studies. However, few reports have examined the colonoscopic features of these divisions, including magnified colonoscopic findings. This study examined 118 lesions excised in our hospital as suspected serrated lesions after magnified observation between January 2008 and September 2011. Patient characteristics (sex, age), conventional colonoscopic findings (location, size, morphology, color, mucin) and magnified colonoscopic findings (pit pattern diagnosis) were interpreted by five colonoscopists with experience in over 1000 colonoscopies, and were compared with histopathological diagnoses. The pit patterns were categorized according to Kudo's classification, but a more detailed investigation was also performed using the subclassification [type II-Open (type II-O), type II-Long (type II-L), or type IV-Serrated (type IV-S)] proposed by Kimura T and Yamano H. Lesions comprised 23 HPs (23/118: 19.5%), 39 TSAs (39/118: 33.1%: with cancer in one case), 50 SSA/Ps (50/118: 42.4%: complicated with cancer in three cases), and six others (6/118: 5.1%). We excluded six others, including three regular adenomas, one hamartoma, one inflammatory polyp, and one juvenile polyp for further analysis. Conventional colonoscopy showed that SSA/Ps were characterized as larger in diameter than TSAs and HPs (SSA/P vs HP, 13.62 ± 8.62 mm vs 7.74 ± 3.24 mm, P < 0.001; SSA/Ps vs TSA, 13.62 ± 8.62 mm vs 9.89 ± 5.73 mm, P < 0.01); common in the right side of the colon [HPs, 30.4% (7/23): TSAs, 20.5% (8/39): SSA/P, 84.0% (42/50), P < 0.001]; flat-elevated lesion [HPs, 30.4% (7/23): TSAs, 5.1% (2/39): SSA/Ps, 90.0% (45/50), P < 0.001]; normal-colored or pale

Physical properties of dust particles in different comets inferred from observations and experimental simulations

NASA Astrophysics Data System (ADS)

Hadamcik, E.; Levasseur-Regourd, A. C.

2007-08-01

numerous levitating samples (compact and fluffy) with the PROGRA2 experiment, either in reduced gravity conditions (parabolic flights) [10,11], or lifted by an air-draught (laboratory conditions) [12,13]. The variations of the polarization are correlated to variations in the size of the grains and aggregates and are a function of the complex refractive index and its evolution. The correlation between the variations of the scattered intensity and the linear polarization maps allows us to disentangle different physical properties of the dust. The results are compared to results obtained from previous observations by the same methods. References [1] E. Hadamcik and A.C. Levasseur-Regourd, JQSRT 79-80, 661-678 (2003) [2] A.C. Levasseur-Regourd, E. Hadamcik, JQSRT 79-80, 903-910 (2003) [3] E. Hadamcik, A.C. Levasseur-Regourd, A&A 403, 757- 768 (2003) [4] L. Kolokolova et al., In: Comets II, M.C. Festou et al. (eds), pp 577 (2004) [5] E. Hadamcik, A.C. Levasseur-Regourd, Icarus 166, 188-194 (2003) [6] E. Hadamcik et al., Icarus, accepted. [7] J. Lasue, A.C. Levasseur-Regourd, JQSRT 100, 220-236 (2006) [8] H. Kimura et al., A&A 449, 1243-1254 (2006) [9] A.C. Levasseur-Regourd et al., PSS, in press, available on line (2007) [10] J.-B. Renard et al. Appl. Opt 41, 609-618 (2002) [11] J.-B. Renard et al., Adv. Space Res. 31, 2511-2518 (2003) [12] E. Hadamcik et al., JQSRT 100, 143-156 (2006) [13] E. Hadamcik et al., Icarus, in press, available on line (2007)

Evaluation of chikungunya virus infection in children from India during 2009-2010: A cross sectional observational study.

PubMed

Raghavendhar, B Siva; Ray, Pratima; Ratagiri, Vinod H; Sharma, B S; Kabra, Sushil K; Lodha, Rakesh

2016-06-01

Chikungunya virus, a small (about 60-70 nm diameter), spherical, enveloped, positive, single stranded RNA virus is transmitted by Aedes mosquitoes. After a short period of incubation (3-5 days) symptoms like fever with joint pains and others start appearing. After a gap of 20 years, this virus re-emerged during 2006-2008 in India causing a major outbreak of CHIKV in India. This study was conducted subsequent to the major outbreak in order to evaluate the proportion of chikungunya virus infection in children with suggestive symptoms at three geographical locations of India. Lineage of circulating strains and changes in the E1 structural polypeptide were also determined. Blood samples were collected (in Sodium citrate vacutainer tubes) during 1st June 2009 to 31st May 2010 from children (age 0 ≤ 18 years) suspected to have chikungunya infection, that is, those who presented with sudden onset of fever and/or joint pain, myalgia, and headache from three regions of India, All India Institute of Medical Sciences (AIIMS) in New Delhi, Karnataka Institute of Medical Sciences (KIMS) in Hubli and Sawai Mansingh Medical College (SMS) in Jaipur. Detection of CHIKV antibodies in all acute-phase patient plasma samples was done by IgM ELISA and for samples within ≤5 days of fever, a one-step RT-PCR was carried out on a block thermo-cycler targeting 294 bp region of E1 gene that codes for the viral envelope protein. Comparison of nucleotide and amino acid sequences from few positive samples of two regions was done with African S-27 reference strain using BioEdit. A phylogenetic tree was constructed using MEGA 6 by using the Maximum Likelihood method based on the Kimura 2-parameter model. Out of the 723 acute phase samples tested from three geographical locations of India, Chikungunya virus infection was detected in 249/723 (34.44%) subjects by either IgM Elisa (180/723) or RT-PCR (69/412). RT-PCR was employed in samples collected from children with ≤5 days of fever. Maximum

Detailed seismic velocity structure beneath the Hokkaido corner, NE Japan: Collision process of the forearc sliver

NASA Astrophysics Data System (ADS)

Kita, S.; Hasegawa, A.; Okada, T.; Nakajima, J.; Matsuzawa, T.; Katsumata, K.

2010-12-01

1. Introduction In south-eastern Hokkaido, the Kuril forearc sliver is colliding with the northeastern Japan arc due to the oblique subduction of the Pacific plate. This collision causes the formation of the Hidaka mountain range since the late Miocene (Kimura, 1986) and delamination of the lower-crust materials of the Kuril forearc sliver, which would be expected to descend into the mantle wedge below (e.g., Ito 2000; Ito and Iwasaki, 2002). In this study, we precisely investigated the three-dimensional seismic velocity structure beneath the Hokkaido corner to examine the collision of two forearcs in this area by using both of data from a dense temporary seismic network deployed in this area (Katsumata et al. [2006]) and those from the Kiban observation network, which covers the entire Japanese Islands with a station separation of 15-20 km. 2. Data and method The double-difference tomography method (Zhang and Thurber, 2003; 2006) was applied to a large number of arrival time data of 201,527 for P-waves and 150,963 for S-waves that were recorded at 125 stations from 10,971 earthquakes that occurred from 1999 to 2010. Grid intervals were set at 10 km in the along-arc direction, 12.5 km perpendicular to it, and 5-10 km in the vertical direction. 3. Results and discussion Inhomogeneous seismic velocity structure was clearly imaged in the Hokkaido corner at depths of 0-120 km. A high-velocity anomaly of P- and S- waves with a volume of 20 km x 90 km x 35km was detected just beneath the main zone of the Hidaka metamorphic belt at depths of 0-35 km. This high-velocity anomaly is continuously distributed from the depths of the mantle wedge to the surface. The western edge of the anomaly exactly corresponds to the Hidaka main thrust (HMT) at the surface. The highest velocity value in the anomaly corresponds to those of the uppermost mantle material (e.g. peridotite). The location of them at depths of 0-35km is also consistent with that of the Horoman-Peridotite belt, which

Grain Formation Processes in Oxygen-Rich Circumstellar Outflows: Testing the Metastable Eutectic Condensation Hypothesis and Measuring Atom-Grain & Grain-Grain Sticking Coefficients (A Sub-orbital Investigation)

NASA Astrophysics Data System (ADS)

Nuth, Joseph

An experimentally-based model of grain formation in oxygen-rich circumstellar outflows that includes vapor-solid nucleation, grain growth, thermal annealing and grain aggregation in sufficient detail to predict the spectral energy distribution (SED) of the shells for comparison with observations of a wide range of stellar sources still lacks critical data. In order to gather this data we propose to conduct a series of laboratory experiments using our proven experimental system and microgravity condensation, growth and grain aggregation experiments on sounding rockets with a flight-proven payload provided by Dr. Yuki Kimura of Hokkaido University. We have proposed that solids from a hydrogen-rich, supersaturated, Fe-Mg-SiO vapor condense at metastable eutectic points in this ternary phase diagram. Because the FeOMgO system is totally miscible (has no eutectic or metastable eutectic compositions), this predicts that condensates will be pure Mg-silicate or Fe-silicate grains and that no primary condensate will be a mixed Fe-Mg-silicate. We have shown that this observation leads to a logical explanation as to why pure magnesium olivine and enstatite minerals are detected in circumstellar winds rather than the mixed Mg-Fe-silicate grains that might otherwise be expected (Rietmeijer, Nuth & Karner, 1999). This simplifying hypothesis has been built into our models of circumstellar condensation and growth. However, these experimental results require confirmation and testing since they should apply to other, quite similar condensable systems. We propose to test this hypothesis by condensing solids from the Fe-Mg-AlO ternary vapor system. Since FeO-MgO miscibility also applies to this system, the primary condensates from such a vapor should consist of pure amorphous Fe-aluminates and Mg-aluminates. No mixed Fe-Mg-spinels should be detected as primary condensates if this hypothesis is correct, just as none were detected for the FeO-MgO-SiO system. Confirmation of this

Controllable Quantum States Mesoscopic Superconductivity and Spintronics (MS+S2006)

NASA Astrophysics Data System (ADS)

Takayanagi, Hideaki; Nitta, Junsaku; Nakano, Hayato

2008-10-01

Mesoscopic effects in superconductors. Tunneling measurements of charge imbalance of non-equilibrium superconductors / R. Yagi. Influence of magnetic impurities on Josephson current in SNS junctions / T. Yokoyama. Nonlinear response and observable signatures of equilibrium entanglement / A. M. Zagoskin. Stimulated Raman adiabatic passage with a Cooper pair box / Giuseppe Falci. Crossed Andreev reflection-induced giant negative magnetoresistance / Francesco Giazotto -- Quantum modulation of superconducting junctions. Adiabatic pumping through a Josephson weak link / Fabio Taddei. Squeezing of superconducting qubits / Kazutomu Shiokawa. Detection of Berrys phases in flux qubits with coherent pulses / D. N. Zheng. Probing entanglement in the system of coupled Josephson qubits / A. S. Kiyko. Josephson junction with tunable damping using quasi-particle injection / Ryuta Yagi. Macroscopic quantum coherence in rf-SQUIDs / Alexey V. Ustinov. Bloch oscillations in a Josephson circuit / D. Esteve. Manipulation of magnetization in nonequilibrium superconducting nanostructures / F. Giazotto -- Superconducting qubits. Decoherence and Rabi oscillations in a qubit coupled to a quantum two-level system / Sahel Ashhab. Phase-coupled flux qubits: CNOT operation, controllable coupling and entanglement / Mun Dae Kim. Characteristics of a switchable superconducting flux transformer with a DC-SQUID / Yoshihiro Shimazu. Characterization of adiabatic noise in charge-based coherent nanodevices / E. Paladino -- Unconventional superconductors. Threshold temperatures of zero-bias conductance peak and zero-bias conductance dip in diffusive normal metal/superconductor junctions / Iduru Shigeta. Tunneling conductance in 2DEG/S junctions in the presence of Rashba spin-orbit coupling / T. Yokoyama. Theory of charge transport in diffusive ferromagnet/p-wave superconductor junctions / T. Yokoyama. Theory of enhanced proximity effect by the exchange field in FS bilayers / T. Yokoyama. Theory of

Evo-SETI SCALE to measure Life on Exoplanets

NASA Astrophysics Data System (ADS)

Maccone, Claudio

2016-04-01

that the GBM exponential may be regarded as the geometric locus of all the peaks of a one-parameter (i.e. the peak time p) family of b-lognormals. Since b-lognormals are pdf-s, the area under each of them always equals 1 (normalization condition) and so, going from left to right on the time axis, the b-lognormals become more and more ;peaky;, and so they last less and less in time. This is precisely what happened in human history: civilizations that lasted millennia (like Ancient Greece and Rome) lasted just centuries (like the Italian Renaissance and Portuguese, Spanish, French, British and USA Empires) but they were more and more advanced in the ;level of civilization;. This ;level of civilization; is what physicists call ENTROPY. Also, in refs. Maccone [3] and [4], this author proved that, for all GBMs, the (Shannon) Entropy of the b-lognormals in his Peak-Locus Theorem grows LINEARLY in time. The Molecular Clock, well known to geneticists since 50 years, shows that the DNA base-substitutions occur LINEARLY in time since they are neutral with respect to Darwinian selection. In simple words: DNA evolved by obeying the laws of quantum physics only (microscopic laws) and not by obeying assumed ;Darwinian selection laws; (macroscopic laws). This is Kimura's neutral theory of molecular evolution. The conclusion is that the Molecular Clock and the b-lognormal Entropy are the same thing. At last, we reach the new, original result justifying the publication of this paper. On exoplanets, molecular evolution is proceeding at about the same rate as it did proceed on Earth: rather independently of the physical conditions of the exoplanet, if the DNA had the possibility to evolve in water initially. Thus, Evo-Entropy, i.e. the (Shannon) Entropy of the generic b-lognormal of the Peak-Locus Theorem, provides the Evo-SETI SCALE to measure the evolution of life on exoplanets.

PREFACE: Selected invited contributions from the International Conference on Magnetism (Karlsruhe, Germany, 26-31 July 2009) Selected invited contributions from the International Conference on Magnetism (Karlsruhe, Germany, 26-31 July 2009)

NASA Astrophysics Data System (ADS)

Goll, Gernot; Löhneysen, Hilbert v.; Loidl, Alois; Pruschke, Thomas; Richter, Manuel; Schultz, Ludwig; Sürgers, Christoph; Wosnitza, Jochen

2010-04-01

in a plenary talk. The IUPAP Young Scientist Award on Magnetism was presented to S O Valenzuela, E Saitoh and T Kimura. The sessions were held in the Stadthalle Karlsuhe operated by the Karlsruher Messe- und Kongress-GmbH (KMK). We are grateful to Ms M Mäkelburg (KMK) for organizing the conference site impeccably. The conference was attended by 1552 participants from 48 countries, with approximately 50 per cent from overseas. The program entailed six plenary talks (40 min each), with 16 half-plenary and 41 invited talks (30 min) and 298 contributed talks (15 min). Extended lunch breaks and evenings were devoted to poster sessions, with a total of 1632 posters presented. All submitted papers were reviewed in order to meet the standards of Journal of Physics: Condensed Matter and Journal of Physics: Conference Series. The referees made every effort to ensure that the manuscripts submitted for publication in the proceedings reached a high standard. The tremendous work in organizing the paper classification and refereeing procedures was carried out by the Publication Committee which was headed by J Wosnitza, and comprised, in addition, Th Pruschke, M Richter and L Schultz. We also thank G Douglas, IOP Publishing, for his support with the preparation of these proceedings. We gratefully acknowledge the help of L Behrens, E Maass and B Schelske in preparing the conference. The conference would not have been possible without G Goll (conference secretary) and C Sürgers (finances). I thank them for their help. Thanks also go to the many students in blue t-shirts who helped to manage the conference. We are grateful for the financial support of Universität Karlsruhe (TH) and Forschungszentrum Karlsruhe (both institutions merged to form the Karlsruhe Institute of Technology (KIT) as of 1 October 2009), the International Union of Pure and Applied Physics (IUPAP), the City of Karlsruhe, Deutsche Forschungsgemeinschaft (German National Science Foundation), and the European

Uplifting of the Jiamusi Block in the eastern Central Asian Orogenic Belt, NE China: evidence from basin provenance and geochronology

NASA Astrophysics Data System (ADS)

Liu, Yongjiang; Wen, Quanbo; Han, Guoqing; Li, Wei

2010-05-01

the Paleo-Asian Ocean the Jiamusi Block underwent a very rapid exhumation in the late Permian. In the early Mesozoic the area went into a basin developing stage and formed a large basin as a whole during the Early Cretaceous. In the Late Cretaceous the Jiamusi Block started uplifting and the basin was broken into isolate small basins. References: Bureau of Geology and Mineral Resources of Heilongjiang Province. Regional geology of Heilongjiang Province. Beijing: Geological Publishing House, 1993.578-581. Cao Chengrun, Zheng Qingdao. Structural evolution feature and its significance of hydrocarbon exploration in relict basin formation, Eastern Heilongjiang province. Journal of Jilin university (Earth Science Edition), 2003, 33(2):167-172. Lang Xiansheng. Biologic Assemblage features of Coal-bearing Strata in Shuangyashan-Jixian coal-field. Coal geology of China, 2002, 14(2):7-12. Piao Taiyuan , Cai Huawei , Jiang Baoyu. On the Cretaceous coal-bearing Strata in Eastern Heilongjiang. Journal Of Stratigraphy, 2005, 29:489-496. Wang Jie , He Zhonghua , Liu Zhaojun , Du Jiangfeng , Wang Weitao. Geochemical characteristics of Cretaceous detrital rocks and their constraint on provenance in Jixi Basin. Global Geology，2006, 25(4):341-348. DickinsonW R and Christopher A. Suczek. Plate Tectonics and Sandstone Composition. AAPG B. 1979,63(12 ):2164-2182. DickinsonW R, Beard L S, Brakenridge G R, et al. Provenance of North American Phanerozoic sandstones in relation to tectonic setting. Bull Geo-Soc Amer, 1983, 94: 222-235. Maruyama S, Seno T. Orogeny and relative plate motions: Example of the Japanese Islands. Tectonophysics, 1986，127(3-4):305-329. Maruyama S, Isozaki Y, Kimura Gand Terabayashi M C.Paleogeographic maps of the Japanese Islands: plate tectonic systhesis from 750 Ma to the present. Island Arc, 1997,6:121-142.

Shallow Moho with aseismic upper crust and deep Moho with seismic lower crust beneath the Japanese Islands obtained by seismic tomography using data from dense seismic network

NASA Astrophysics Data System (ADS)

Matsubara, Makoto; Obara, Kazushige

2015-04-01

. The Moho discontinuity deepens over 35 km in the collision zone like as Kanto Mountains, the volcanic underplating zone as the Tohoku backbone range, and non-tension region like as Chugoku Mountains. These regions associated with deep Moho are characterized by the crustal seismicity within the depth range from 20 to 30 km. The iso-depth contour of 35 km beneath the southwestern Japan is consistent with that derived from the receiver function method (Shiomi et al. 2006). There are nonvolcanic tremors and short-time slow slip events (SSE) beneath the southwestern Japan (eg. Obara, 2002). Matsubara et al. (2009) consider that the tremors and SSEs occur along the contact zone of Moho discontinuity beneath the Eurasian plate and the subducting Philippine Sea plate beneath southwestern Japan. Our Moho model is consistent with this since they exist along the southern edge of the Moho discontinuity of the continental Eurasian plate. Reference: Hirata, N., Sakai, S., Nakagawa, S., Ishikawa, M., Sato, H., Kasahara, K., Kimura, H. and Honda, R. (2012) A new tomographic image on the Philippine Sea Slab beneath Tokyo - Implication to seismic hazard in the Tokyo metropolitan region, EOS, Transactions, AGU, T11C-06. Kita, S., T. Okada, A. Hasegawa, J. Nakajima, and T. Matsuzawa (2010) Anomalous deepening of a seismic belt in the upper-plane of the double seismic zone in the Pacific slab beneath the Hokkaido corner: Possible evidence for thermal shielding caused by subducted forearc crust materials, Earth Planet. Science Lett., 290, 415-426. Matsubara, M. and K. Obara (2011) The 2011 Off the Pacific Coast of Tohoku earthquake related to a strong velocity gradient with the Pacific plate, Earth Planets Space, 63, 663-667. Matsubara, M., K. Obara, and K. Kasahara (2009) High-Vp/Vs zone accompanying non-volcanic tremors and slow-slip events beneath southwestern Japan, Tectonophysics, 472, 6-17, doi:10.1016/j.tecto.2008.06.013. Obara, K. (2002) Nonvolcanic deep tremor associated with

Diffusion in fractal wakes and convective thermoelectric flows

NASA Astrophysics Data System (ADS)

Vila, Teresa; Tellez, Jackson; Sanchez, Jesus Maria; Sotillos, Laura; Diez, Margarita; Redondo, Jose Manuel

2014-05-01

fronts like removable plate experiments [7] for Rayleigh-Taylor flows. The evolution of the turbulent mixing layer and its complex configuration is studied taking into account the dependence on the initial modes at the early stages and its spectral, self-similar information [8,9]. Spectral and Fractal analysis on the images has been used in order to estimate dominant mixing structures as well as the dispersion relations of basic instabilities [2,10]. [1] Redondo J.M. (1992) Termodinámica de los procesos irreversibles, efectos termoeléctricos Rev. Termoelectricidad 2, 16-29.AIT.Pamplona. [2] Mahjoub O.B., Redondo J.M. and Babiano A.(2000) "Hyerarchy flux in nonhomogeneous flows" in Turbulent diffusion in the environment Eds. Redondo J.M. and Babiano A. 249-260. [3] Redondo J.M., Sanchez J.M. Pascual I. Noriega, G.F.(1995)."Thermoelectric regulation for electric cabinets".XVI International Conference in Thermoelectrics, 02-G20. Ed. V. Vedernikov. 456-468. St. Petersburg, Russia. [4] Kuramitsu, M.; Redondo, J.M.; Noriega, G. (2003) Measurements of anisotropy, thermoelectric behaviour and multi-fractal aspects of FeSi and of complex custom made TE materials Twenty-Second International Conference on Thermoelectric- ICT,IEEE, DOI:10.1109/ICT.2003.1287570, 541-545. [5] López González-Nieto, P., Cano, J. L. and Redondo, J. M., "Buoyant mixing processes generated in turbulent pluma arrays" in Experimental and Modelling Micrometeorology, Física de la Tierra, vol. 19, pp. 205-219, 2007. [6] Kimura R. and Iga, I. (1995) Bubble Convection in Mixing in Geophysical Flows Eds. Redondo J.M: and Metais, 35-51. Ed CIMNE, Barcelona. [7] Linden, P. F., Redondo, J. M. and Caulfield, C. P.: (1992), Advances in Compressible Turbulent Mixing, edited by W.P. Dannevik, A.C. Buckingham and C.E. Leith, Princenton University. [8] Nicolleau, F.C.G.A.; Cambon, C.; Redondo, J.M.; Vassilicos, J.C.; Reeks, M.; Nowakowski, A.F. (Eds.) New Approaches in Modeling Multiphase Flows and Dispersion in

Strong Coupling Gauge Theories in LHC ERA

NASA Astrophysics Data System (ADS)

Fukaya, H.; Harada, M.; Tanabashi, M.; Yamawaki, K.

2011-01-01

conformal Higgs / Kazumoto Haba, Shinya Matsuzaki and Koichi Yamawaki -- Phase structure of topologically massive gauge theory with fermion / Yuichi Hoshino -- New regularization in extra dimensional model and renormalization group flow of the cosmological constant / Shoichi Ichinose -- Spectral analysis of dense two-color QCD / T. Kanazawa, T. Wettig and N. Yamamoto -- NJL model with dimensional regularization at finite temperature / T. Fujihara ... [et al.] -- A new method of evaluating the dynamical chiral symmetry breaking scale and the chiral restoration temperature in general gauge theories by using the non-perturbative renormalization group analyses with general 4-Fermi effective interaction space / Ken-Ichi Aoki, Daisuke Sato and Kazuhiro Miyashita -- The effective chiral Lagrangian with vector mesons and hadronic [symbol] decays / D. Kimura ... [et al.] -- Spontaneous SUSY breaking with anomalous U(1) symmetry in metastable vacua and moduli stabilization / Hiroyuki Nishino -- A new description of the lattice Yang-Mills theory and non-abelian magnetic monopole dominance in the string tension / Akihiro Shibata -- Thermodynamics with unbroken center symmetry in two-flavor QCD / S. Takemoto, M. Harada and C. Sasaki -- Masses of vector bosons in two-color QCD based on the hidden local symmetry / T. Yamaoka, M. Harada and C. Nonaka -- Walking dynamics from string duals / Maurizio Piai -- The quark mass dependence of the nucleon mass in AdS/QCD / Hyo Chul Ahn -- Structure of thermal quasi-fermion in QED/QCD from the Dyson-Schwinger equation / Hisao Nakkagawa -- Critical behaviors of sigma-mode and pion in holographic superconductors / Cheonsoo Park.

EDITORIAL: Invited papers from ISAMMA 2010 (Sendai, Japan, 12-16 July 2010) Invited papers from ISAMMA 2010 (Sendai, Japan, 12-16 July 2010)

NASA Astrophysics Data System (ADS)

Takahashi, M.; Saito, H.

2011-02-01

Yanagihara, Yuta Toyoda and Eiji Kita Monte Carlo simulations of the magnetocaloric effect in magnetic Ni-Mn-X (X = Ga, In) Heusler alloys V D Buchelnikov, V V Sokolovskiy, S V Taskaev, V V Khovaylo, A A Aliev, L N Khanov, A B Batdalov, P Entel, H Miki and T Takagi Changes in electronic states and magnetic free energy in La1-zCez(FexSi1-x)13 magnetic refrigerants A Fujita, S Fujieda and K Fukamichi Garnet composite films with Au particles fabricated by repetitive formation for enhancement of Faraday effect H Uchida, Y Mizutani, Y Nakai, A A Fedyanin and M Inoue Control of magnetic domain wall displacement using spin current in small in-plane magnetic field in Permalloy nanowires Yoshihiko Togawa, Takashi Kimura, Ken Harada, Akira Tonomura and Yoshichika Otani Magnetic-field tunable transmittance in a ferrofluid-filled silicon nitride photonic crystal slab H M Lee, L Horng and J C Wu Evaluation of a miniature magnetostrictive actuator using Galfenol under tensile stress Toshiyuki Ueno, Hidemitsu Miura and Sotoshi Yamada Sub-nm resolution depth profiling of the magnetic structure of thin films by the depth-resolved x-ray magnetic circular dichroism technique K Amemiya and M Sakamaki

List of Participants

NASA Astrophysics Data System (ADS)

2011-09-01

KhodelVictorKurchatov Institute, Moscowvak@wuphys.wustl.edu KimuraMasaakiHokkaido University, Sapporomasaaki@nucl.sci.hokudai.ac.jp LacroixDenisGANIL, Caenlacroix@ganil.fr LiangHaozhaoPeking University, Beijinghzliang@pku.edu.cn MargueronJérômeIPN Orsayjerome.margueron@ipno.in2p3.fr MassotElisabethIPN Orsaymassot@ipno.in2p3.fr MengJiePeking University, Beijingmengj@pku.edu.cn MillerTomaszWarsaw University of Technologymillert@student.mini.pw.edu.pl MoghrabiKassemIPN Orsaymoghrabi@ipno.in2p3.fr NapolitaniPaoloIPN Orsaynapolita@ipno.in2p3.fr NeffThomasGSI Darmstadtt.neff@gsi.de NguyenVan GiaiIPN Orsaynguyen@ipno.in2p3.fr OtsukaTakaharuUniversity of Tokyootsuka@phys.s.u-tokyo.ac.jp PilletNathalie-MarieCEA-DAM, Arpajonnathalie.pillet@cea.fr QiChongKTH Stockholmchongq@kth.se RamananSunethraICTP Triestesramanan@ictp.it RingPeterTU Munichring@ph.tum.de Rios HuguetArnauUniversity of Surreya.rios@surrey.ac.uk RivetMarie-FranceIPN Orsayrivet@ipno.in2p3.fr RobledoLuisUniversidad Autonoma de Madridluis.robledo@uam.es Roca MazaXavierINFN Milanoxavier.roca.maza@mi.infn.it RöpkeGerdRostock Universitygerd.roepke@uni-rostock.de RowleyNeilIPN Orsayrowley@ipno.in2p3.fr SagawaHiroyukiUniversity of Aizusagawa@u-aizu.ac.jp SandulescuNicolaeIFIN-HH, Bucharestsandulescu@theory.nipne.ro SchuckPeterIPN Orsayschuck@ipno.in2p3.fr SedrakianArmenGoethe Universität Frankfurtsedrakian@th.physik.uni-frankfurt.de SeveryukhinAlexeyJINR Dubnasever@theor.jinr.ru SogoTakaakiIPN Orsaysogo@ipno.in2p3.fr SomàVittorioCEA Saclayvittorio.soma@cea.fr StrinatiGiancarloUniversità di Camerinogiancarlo.strinati@gmail.com SuharaTadahiroKyoto Universitysuhara@ruby.scphys.kyoto-u.ac.jp SukhoruchkinSergeiPetersburg Nuclear Physics Institutesergeis@pnpi.spb.ru SuzukiToruTokyo Metropolitan Universitysuzukitr@tmu.ac.jp SuzukiToshioNihon University, Tokyosuzuki@chs.nihon-u.ac.jp TarpanovDimitarINRNE, Sofiadimitert@yahoo.co.uk Tohsaki-SuzukiAkihiroOsaka Universitytohsaki@rcnp.osaka-u.ac.jp TypelStefanGSI Darmstadts

Proceedings of the 8th International Symposium on Foundations of Quantum Mechanics in the Light of New Technology

NASA Astrophysics Data System (ADS)

Ishioka, Sachio; Fujikawa, Kazuo

2006-06-01

-Horne-Zeilinger states in Josephson systems / T. Fujii, M. Nishida, N. Hatakenaka -- Quantum-dot systems. Tunable tunnel and exchange couplings in double quantum dots / S. Tarucha, T. Hatano, M. Stopa. Coherent transport through quantum dots / S. Katsumoto ... [et al.]. Electrically pumped single-photon sources towards 1.3 [symbol]m / X. Xu ... [et al.]. Aharonov-Bohm-type effects in antidot arrays and their decoherence / M. Kato ... [et al.]. Nonequilibrium Kondo dot connected to ferromagnetic leads / Y. Utsumi ... [et al.]. Full counting-statistics in a single-electron transistor in the presence of strong quantum fluctuations / Y. Utsumi -- Anomalous Hall effect and Spin-Hall effect. Geometry and the anomalous Hall effect in ferromagnets / N. P. Ong, W.-L. Lee. Control of spin chirality, Berry phase, and anomalous Hall effect / Y. Tokura, Y. Taguchi. Quantum geometry and Hall effect in ferromagnets and semiconductors / N. Nagaosa. Spin-Hall effect in a semiconductor two-dimensional hole gas with strong spin-orbit coupling / J. Wunderlich ... [et al.]. Intrinsic spin Hall effect in semiconductors / S. Murakami -- Spin related phenomena. Theory of spin transfer phenomena in magnetic metals and semiconductors / A. S. Núñez, A. H. MacDonald. Spin filters of semiconductor nanostructures / T. Dietl, G. Grabecki, J. Wróbel. Experimental study on current-driven domain wall motion / T. Ono ... [et al.]. Magnetization reversal of ferromagnetic nano-dot by non local spin injection / Y. Otani, T. Kimura. Theory of current-driven domain wall dynamics / G. Tatara ... [et al.]. Magnetic impurity states and ferromagnetic interaction in diluted magnetic semiconductors / M. Ichimura ... [et al.]. Geometrical effect on spin current in magnetic nano-structures / M. Ichimura, S. Takahashi, S. Maekawa. Ferromagnetism in anatase TiO[symbol] codoped with Co and Nb / T. Hitosugi ... [et al.] -- Superconductivity in nano-systems. Nonlinear quantum effects in nanosuperconductors / C. Carballeira ... [et al

CALL FOR PAPERS: Special issue: One hundred years of PVI, the Fuchs Painlevé equation

NASA Astrophysics Data System (ADS)

Clarkson, P. A.; Joshi, N.; Mazzocco, M.; Nijhoff, F. W.; Noumi, M.

2005-10-01

This is a call for contributions to a special issue of Journal of Physics A: Mathematical and General entitled `One hundred years of Painlevé VI, the Fuchs Painlevé equation'. The motivation behind this special issue is to celebrate the centenary of the discovery of this famous differential equation. The Editorial Board has invited P A Clarkson, N Joshi, M Mazzocco, F W Nijhoff and M Noumi to serve as Guest Editors for the issue. The nonlinear ordinary differential equation, which is nowadays known as the Painlevé VI (PVI) equation, is one of the most important differential equations in mathematical physics. It was discovered 100 years ago by Richard Fuchs (son of the famous mathematician Lazarus Fuchs) and reported for the first time in Comptes Rendus de l'Academie des Sciences Paris 141 555 8 (1905). Gambier, in his seminal paper of 1906, included this equation as the top equation in the list of what are now known as the six Painlevé transcendental equations. The Painlevé list emerged from the work on the classification of all ordinary second-order differential equations whose general solution are `uniform', in the sense that there are no movable (i.e. as a function of the initial data) singularities (meaning branch points) worse than poles. The latter is known as the Painlevé property. As the top equation in the Painlevé list of transcendental equations, the importance of PVI can be appreciated by recognizing that this is a universal differential equation, which is the most general (in terms of number of free parameters) of the known second order ODEs defining nonlinear special functions. As such, parallels can be drawn between the role played by PVI transcendents in the nonlinear case and the hypergeometric functions at the linear level. In fact, the monograph From Gauss to Painlevé by K Iwasaki, H Kimura, S Shimomura and M Yoshida (Vieweg, 1991), draws very clearly the line stretching over more than 150 years of special function theory in which PVI is

Physics of Unstable Nuclei

NASA Astrophysics Data System (ADS)

Khoa, Dao Tien; Egelhof, Peter; Gales, Sydney; Giai, Nguyen Van; Motobayashi, Tohru

2008-04-01

. -- Thermal pairing in nuclei / N. D. Dang -- Molecular-orbital and di-nuclei states in Ne and F isotopes / M. Kimura -- Low-momentum interactions for nuclei / A. Schwenk -- Nonrelativistic nuclear energy functionals including the tensor force / G. Colo et al. -- New aspects on dynamics in nuclei described by covariant density functional theory / P. Ring, D. Pena -- Theoretical studies on ground-state properties of superheavy nuclei / Z. Z. Ren et al. -- New results in the study of superfluid nuclei: many-body effects, spectroscopic factors / P. F. Bortignon et al. -- New Effective nucleon-nucleon interaction for the mean-field approximation / V. K. Au et al. -- Linear response calculations with the time-dependent Skyrme density functional / T. Nakatsukasa et al. -- Dissipative dynamics with exotic beams / M. Di Toro et al. -- Exploring the symmetry energy of asymmetric nuclear matter with heavy ion reactions / M. B. Tsang -- Invariant mass spectroscopy of halo nuclei / T. Nakamura et al. -- Core [symbol] structures in [symbol]C, [symbol]C and [symbol]C up to high excitation energies / H. G. Bohlen et al. -- Light neutron-rich nuclei studied by alpha-induced reactions / S. Shimoura -- Fusion and direct reactions around the Coulomb barrier for the system [symbol]He + [symbol]Zn / V. Scuderi et al. -- Analyzing power measurement for proton elastic scattering on [symbol]He / S. Sakaguchi et al. -- Knockout reaction spectroscopy of exotic nuclei / J. A. Tostevin -- Exotic nuclei, quantum phase transitions, and the evolution of structure / R. F. Casten -- Structure of exotic nuclei in the medium mass region / T. Otsuka -- Pairing correlations in halo nuclei / H. Sagawa, K. Hagino -- Experimental approach to high-temperature Stellar reactions with low-energy RI beams / S. Kubono et al. -- Transition to quark matter in neutron stars / G. X. Peng et al. -- Research at VATLY: main themes and recent results / P. N. Diep et al. -- Study of the astrophysical reaction [symbol

PREFACE: International Conference on Magnetism (ICM 2009)

NASA Astrophysics Data System (ADS)

Goll, Gernot; Löhneysen, Hilbert v.; Loidl, Alois; Pruschke, Thomas; Richter, Manuel; Schultz, Ludwig; Sürgers, Christoph; Wosnitza, Jochen

2010-11-01

Mayor of Karlsruhe, Ms M Mergen, and the Chairman of the Executive Board of Forschungszentrum Karlsruhe, E Umbach. ICM 2009 was attended by the Nobel Laureates P W Anderson, A Fert and P Grünberg who gave plenary talks. A special highlight was the presentation of the Magnetism Award and Néel Medal to S S P Parkin who presented his newest results in a plenary talk as well. The IUPAP Young Scientist Award on Magnetism was given to S O Valenzuela, E Saitoh and T Kimura. The sessions were held in the Stadthalle Karlsuhe operated by the Karlsruher Messe- und Kongress-GmbH (KMK). We are grateful to Ms M Mäkelburg (KMK) for a perfect organization at the conference site. The conference was attended by 1552 participants from 48 countries, with about 50 percent from overseas (see figure). The program entailed six plenary talks (40 minutes each), with 16 half-plenary and 41 invited talks (30 minutes) and 298 contributed talks (15 minutes). Extended lunch breaks and evenings were devoted to the poster sessions, with a total of 1632 posters presented. Attendance breakdown All submitted papers were reviewed in order to meet the standards of Journal of Physics: Condensed Matter and Journal of Physics: Conference Series. The referees made every effort possible to ensure that the manuscripts submitted for publication in the proceedings reach a high standard. The tremendous work in organizing the paper classification and refereeing procedures was carried out by the Publication Committee which was headed by J Wosnitza, and comprised, in addition, Th Pruschke, M Richter and L Schultz. We also thank G Douglas, IOP Publishing, for his efficient support with the preparation of these proceedings. We gratefully acknowledge the help of L Behrens, E Maass and B Schelske in preparing the conference. The conference would not have been possible without G Goll (conference secretary) and C Sürgers (finance). I thank them for their great help. Thanks go to the many students in blue T-shirts who

Energy of Extra-Terrestrial Civilizations according to Evo-SETI Theory

NASA Astrophysics Data System (ADS)

Maccone, Claudio

2018-03-01

with respect to Darwinian selection. This is Kimura's neutral theory of molecular evolution. The conclusion is that the Molecular Clock and the linear increase of EvoEntropy in time are just the same thing! In other words, we derived the Molecular Clock mathematically as a part of our Evo-SETI Theory. In addition, our EvoEntropy, i.e. the Shannon Entropy of the b-lognormal (with the minus sign reversed and starting at zero at the time of the origin of Life on Earth) is just the new Evo-SETI Scale to measure the evolution of life on Exoplanets (measured in bits). That was the situation prior to the present paper, firstly presented at the SETI II Session of the Adelaide IAC in October 2017. In fact, just as classical thermodynamics entails both energy and entropy, so our Evo-SETI Theory needs entailing the energy used by a living Species or Civilization along its whole lifetime in addition to its entropy (i.e. Molecular Clock). In other words still, while the Molecular Clock is a measure of the advancement in evolution, the energy required to get that advancement is another topic not faced by this author prior to 2017. However, in the present paper we were able to add the consideration of energy in addition to entropy by replacing the b-lognormal probability densities previously used by a new curve, finite in the time, that we call "logpar". This logpar is made up by an ascending b-lognormal in the time between the birth and the peak of the living organism, followed by a descending parabola in the time between its peak and death. The logpar curve is not normalized to one: the area under the logpar curve may be any positive number since it represents the energy requested by the organism to live over its entire lifetime "birth-to-death". In other words still, we mathematically demonstrate in this paper that just three instants (birth b, peak p and death d) must be assigned in order to make the mathematical logpar curve perfectly described. The history of the Roman

Proceedings of the 9th International Symposium on Foundations of Quantum Mechanics in the Light of New Technology

NASA Astrophysics Data System (ADS)

Ishioka, Sachio; Fujikawa, Kazuo

2009-06-01

phenomena. Dynamical magnetoelectric effects in multiferroics / Y. Tokura. Exchange-stabilization of spin accumulation in the two-dimensional electron gas with Rashba-type of spin-orbit interaction / H. M. Saarikoski, G. E. W. Bauer. Electronic Aharonov-Casher effect in InGaAs ring arrays / J. Nitta, M. Kohda, T. Bergsten. Microscopic theory of current-spin interaction in ferromagnets / H. Kohno ... [et al.]. Spin-polarized carrier injection effect in ferromagnetic semiconductor / diffusive semiconductor / superconductor junctions / H. Takayanagi ... [et al.]. Low voltage control of ferromagnetism in a semiconductor P-N junction / J. Wunderlich ... [et al.].Measurement of nanosecond-scale spin-transfer torque magnetization switching / K. Ito ... [et al.]. Current-induced domain wall creep in magnetic wires / J. Ieda, S. Maekawa, S. E. Barnes. Pure spin current injection into superconducting niobium wire / K. Ohnishi, T. Kimura, Y. Otani. Switching of a single atomic spin induced by spin injection: a model calculation / S. Kokado, K. Harigaya, A. Sakuma. Spin transfer torque in magnetic tunnel junctions with synthetic ferrimagnetic layers / M. Ichimura ... [et al.]. Gapless chirality excitations in one-dimensional spin-1/2 frustrated magnets / S. Furukawa ... [et al.] -- Dirac fermions in condensed matter. Electronic states of graphene and its multi-layers / T. Ando, M. Koshino. Inter-layer magnetoresistance in multilayer massless dirac fermions system [symbol]-(BEDT-TTF)[symbol]I[symbol] / N. Tajima ... [et al.]. Theory on electronic properties of gapless states in molecular solids [symbol]-(BEDT-TTF)[symbol]I[symbol] / A. Kobayashi, Y. Suzumura, H. Fukuyama. Hall effect and diamagnetism of bismuth / Y. Fuseya, M. Ogata, H. Fukuyama. Quantum Nernst effect in a bismuth single crystal / M. Matsuo ... [et al.] -- Quantum dot systems. Kondo effect and superconductivity in single InAs quantum dots contacted with superconducting leads / S. Tarucha ... [et al.]. Electron transport

PREFACE: 11th IAEA Technical Meeting on H-mode Physics and Transport Barriers

NASA Astrophysics Data System (ADS)

Takizuka, Tomonori

2008-07-01

(University of Tsukuba, Japan) K Itoh (National Institute for Fusion Science, Japan) S-I Itoh (Kyushu University, Japan) F Jenko (Max-Plank-Institut für Plasmaphysik, Germany) D Kalupin (Institut für Plasmaphysik, Forschungszentrum Jülich GmbH, Germany) Y Kamada (Japan Atomic Energy Agency, Japan) N Kasuya (National Institute for Fusion Science, Japan) I Katanuma (University of Tsukuba, Japan) M Kimura (Kyushu University, Japan) A Kirk (EURATOM/UKAEA Fusion Association, UK) S Kitajima (Tohoku University, Japan) S Kobayashi (Kyoto University, Japan) T Kobuchi (Tohoku University, Japan) J Kohagura (University of Tsukuba, Japan) P T Lang (Max-Plank-Institut für Plasmaphysik, Germany) S V Lebedev (Ioffe Institute, Russia) A W Leonard (General Atomics, USA) J Q Li (Kyoto University, Japan) A Malaquias (International Atomic Energy Agency) Y R Martin (Centre de Recherches en Physique des Plasmas, EPFL, Switzerland) C J McDevitt (University of California, San Diego, USA) D C McDonald (EURATOM/UKAEA Fusion Association, UK) H Meyer (EURATOM/UKAEA Fusion Association, UK) C A Michael (National Institute for Fusion Science, Japan) K Miki (Kyushu University, Japan) R Minami (University of Tsukuba, Japan) T Minami (National Institute for Fusion Science, Japan) Y Miyata (University of Tsukuba, Japan) N Miyato (Japan Atomic Energy Agency, Japan) Y Motegi (University of Tsukuba, Japan) V Mukhovatov (ITER Organization) S Murakami (Kyoto University, Japan) Y Nagashima (Kyushu University, Japan) Y Nakashima (University of Tsukuba, Japan) T Numakura (University of Tsukuba, Japan) S Ohshima (National Institute for Fusion Science, Japan) T Oishi (National Institute for Fusion Science, Japan) T Onjun (Sirindhorn International Institute of Technology, Thailand) T H Osborne (GENERAL Atomics, USA) N Oyama (Japan Atomic Energy Agency, Japan) T Ozeki (Japan Atomic Energy Agency, Japan) V Parail (EURATOM/UKAEA Fusion Association, UK) A Polevoi (ITER Organization, France) J E Rice (MIT Plasma Science

Radicals and Non-Equilibrium Processes in Low-Temperature Plasmas

NASA Astrophysics Data System (ADS)

Petrović, Zoran; Mason, Nigel; Hamaguchi, Satoshi; Radmilović-Radjenović, Marija

2007-06-01

discharges, plasma chemistry - particularly in oxygen containing plasmas, modeling of plasmas and plasma surface interactions in complex comprehensive plasma codes, modeling of the development of surface profiles and kinetics of surface collisions, plasma treatment of materials, plasma processing and applications in thin film deposition, nanoscale device production and many other applications. Yet all the papers, one way or the other, address the key issues of the next generation of plasma technologies in the micro and nano electronic industry. The issue of radicals and also of electron molecule collisions is addressed by J Tennyson who presents a guide into using a code for R-matrix calculations of electron-molecule collisions at low and intermediate energies. Related experimental results are presented by T Field who showed recent measurements of electron radical attachment cross sections, by T Märk who discusses electron impact ionization/dissociation of molecules and subsequent production of energetic radicals, and by M Kimura and his coauthors who discuss productions of radicals and ions by electron and photon impacts on CH4. Finally T Maddern and M Brunger share with us the first results from the new very complex system for comprehensive measurements of electron radical cross sections, the first example being CF2. B Marinković mainly focuses on recent results of his group having in mind the data needs for plasma modeling. Collisions at surfaces are addressed by P Tegeder and more specifically she presents here the evolution of negative ion resonances at surfaces. The electron swarm data as projected onto gaseous dielectrics but also having application in plasma processing is covered by J De Urquijo who attempted to answer the question whether CF3I is a better dielectric than SF6. The basic processes leading to the gas breakdown have been addressed by D Marić and Z Lj Petrović who focus on the transition from Townsend to constricted-normal glow regime while trying to

Mixing and turbulent mixing in fluids, plasma and materials: summary of works presented at the 3rd International Conference on Turbulent Mixing and Beyond

NASA Astrophysics Data System (ADS)

Gauthier, Serge; Keane, Christopher J.; Niemela, Joseph J.; Abarzhi, Snezhana I.

2013-07-01

companion paper Rooker et al provide a very interesting study on the generation and detection of 'whistler waves' induced space plasma turbulence at Gakona (Alaska). Physics of atmosphere. Five papers are devoted to the physics of atmosphere. Byalko presents the first experimental observation of a new hydrodynamic phenomenon, the underwater tornado. Herring and Kimura provide a review on recent results on homogeneous stably stratified turbulence. Pouquet et al use a high-resolution direct numerical simulation of rotating helical turbulence to obtain new numerical results on the inverse energy cascade in rotating flows. Tailleux discusses energy conversion and dissipation in depth in mixing flows. Zagumennyi and Chashechkin study the structure of convective flows driven by density variations in a stratified fluid by means of experiments and numerical simulations. Geophysics and Earth science. Three papers are dedicated to geophysics and Earth science. Jinadasa et al investigate small-scale and lateral intermittency of oceanic microstructure in the pycnocline. Shrira and Townsend review on a plausible mechanism of deep-ocean mixing caused by near-inertial waves in the abyssal ocean. Using numerical simulations, Imazio and Mininni study how helicity affects the spectrum of a passive scalar in rotating turbulent flows. Combustion. Two papers deal with flows with chemical reactions. Meshram used the Lewis-Kraichnan space-time version of Hopf's functional formalism to investigate turbulence with chemical reaction. Watanabe et al carry out experiments on a turbulent plane liquid jet with a second-order chemical reaction. Theoretical aspects of non-equilibrium dynamics. Six papers are devoted to fundamental aspects of non-equilibrium dynamics. Chen et al present state-of-the-art work on exact and direct derivation of macroscopic theoretical description for a flow at arbitrary Knudsen number from the Boltzmann-Bhatnagar-Gross-Krook kinetic theory with constant relaxation time