78 FR 22239 - Endangered Species; File No. 16556

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-15

... Fisheries Science Center (NEFSC; Responsible Party: Dr. William Karp), 166 Water St., Woods Hole, MA 02543... research. ADDRESSES: The permit and related documents are available for review upon written request or by... request for a scientific research permit to take loggerhead, leatherback, Kemp's ridley, and green sea...

Rickettsial Illnesses as Important Causes of Febrile Illness in Chittagong, Bangladesh

PubMed Central

Kingston, Hugh W.; Hossain, Mosharraf; Leopold, Stije; Anantatat, Tippawan; Tanganuchitcharnchai, Ampai; Sinha, Ipsita; Plewes, Katherine; Maude, Richard J.; Chowdhury, M.A. Hassan; Paul, Sujat; Uddin, Rabiul Alam Mohammed Erfan; Siddiqui, Mohammed Abu Naser; Zahed, Abu Shahed; Abu Sayeed, Abdullah; Rahman, Mohammed Habibur; Barua, Anupam; Uddin, Mohammed Jasim; Sattar, Mohammed Abdus; Dondorp, Arjen M.; Blacksell, Stuart D.; Day, Nicholas P.J.; Ghose, Aniruddha; Hossain, Amir

2018-01-01

We conducted a yearlong prospective study of febrile patients admitted to a tertiary referral hospital in Chittagong, Bangladesh, to assess the proportion of patients with rickettsial illnesses and identify the causative pathogens, strain genotypes, and associated seasonality patterns. We diagnosed scrub typhus in 16.8% (70/416) and murine typhus in 5.8% (24/416) of patients; 2 patients had infections attributable to undifferentiated Rickettsia spp. and 2 had DNA sequence–confirmed R. felis infection. Orientia tsutsugamushi genotypes included Karp, Gilliam, Kato, and TA763-like strains, with a prominence of Karp-like strains. Scrub typhus admissions peaked in a biphasic pattern before and after the rainy season, whereas murine typhus more frequently occurred before the rainy season. Death occurred in 4% (18/416) of cases; case-fatality rates were 4% each for scrub typhus (3/70) and murine typhus (1/28). Overall, 23.1% (96/416) of patients had evidence of treatable rickettsial illnesses, providing important evidence toward optimizing empirical treatment strategies. PMID:29553921

Analysis of the cross-reactivity of various 56 kDa recombinant protein antigens with serum samples collected after Orientia tsutsugamushi infection by ELISA.

PubMed

Chao, Chien-Chung; Huber, Erin S; Porter, Terrisita B; Zhang, Zhiwen; Ching, Wei-Mei

2011-06-01

Orientia tsutsugamushi, the etiologic agent of scrub typhus, has a highly expressed and immunodominant 56-kD outer membrane protein. This protein is one of the leading candidates for diagnosis and vaccine development for scrub typhus. Previous studies using recombinant 56-kD protein (r56s) derived from Karp strain (Kpr56) in a mouse model have shown good homologous protection but only moderate to poor heterologous protection. We evaluated the cross-reactivity of recombinant 56-kD proteins from Karp, Kato, Gilliam, TA763, and three chimeric 56-kD proteins. Not all r56s are equally reactive with strain-specific serum samples. These data provide a first glance of how reactive these r56s are toward the antiserum of different strains and which r56 exhibits the broadest reactivity. A formulation of this combination has the potential to provide broad protection against the heterologous challenge and to be used in a highly sensitive diagnostic assay.

History of Higher Education Annual, 1985.

ERIC Educational Resources Information Center

Karp, Alan; And Others

1985-01-01

This volume of the History of Higher Education Annual contains five articles. Alan Karp's essay, "John Calvin and the Geneva Academy: Roots of the Board of Trustees," discusses the reoganization and government of the Geneva Academy and Calvin's unsuccessful struggle to establish a church independent of lay control. Institutional…

An Analysis of the President’s Budgetary Proposals for Fiscal Year 2010

DTIC Science & Technology

2009-06-01

Ozanne, Frank Russek, Marika Santoro, Kurt Seibert, Sven Sinclair, and David Weiner carried out the modeling . Barry Blom of CBO’s Projections Unit...Baseline Policy Assumptions 15 Ways in Which the President’s Proposals Would Affect the Economy 15 The Models and Their Results 21 The Potential Economic...Effects of Selected Proposals in the President’s 2010 Budget 27 The Models Used to Analyze the Supply-Side Macroeconomic Effects of the President’s

Exploring the Role of First-Year Experiences in Enhancing Equity & Outcomes. Insights on Equity and Outcomes. Issue 14

ERIC Educational Resources Information Center

Rockey, Marci; Congleton, Randi

2016-01-01

Weak connections between students and their academic and social environment can hinder commitment and lead to departure (Deil-Amen, 2011; Karp, Hughes, & O'Gara, 2010). Given their influence on college retention and completion, higher levels of academic and social integration should be a priority. Rather than focus on why students leave, it is…

A Holistic Conception of Nonacademic Support: How Four Mechanisms Combine to Encourage Positive Student Outcomes in the Community College

ERIC Educational Resources Information Center

Mechur Karp, Melinda

2016-01-01

Despite their best efforts, community colleges continue to see low rates of student persistence and degree attainment. Although such outcomes can be attributed in large part to students' lack of academic readiness, nonacademic issues also play a part. Building on Karp's 2011 framework of nonacademic support, this chapter explores the evidence that…

Inclusive Classrooms: A Basic Qualitative Study of K-8 Urban Charter School Teachers

ERIC Educational Resources Information Center

Williams, Regina N.

2017-01-01

The rapid growth of charter schools has been accompanied with numerous questions related to special education such as whether or not charter schools and their unique missions can actually meet the needs of students with disabilities (Karp, 2012). This basic qualitative study explores the practices and procedures used by primary school teachers to…

Expression and Refolding of Truncated Recombinant Major Outer Membrane Protein Antigen (r56) of Orientia tsutsugamushi and Its Use in Enzyme-Linked Immunosorbent Assays

PubMed Central

Ching, W.-M.; Wang, H.; Eamsila, C.; Kelly, D. J.; Dasch, G. A.

1998-01-01

The variable 56-kDa major outer membrane protein of Orientia tsutsugamushi is the immunodominant antigen in human scrub typhus infections. The gene encoding this protein from Karp strain was cloned into the expression vector pET11a. The recombinant protein (r56) was expressed as a truncated nonfusion protein (amino acids 80 to 456 of the open reading frame) which formed an inclusion body when expressed in Escherichia coli BL21. Refolded r56 was purified and compared to purified whole-cell lysate of the Karp strain of O. tsutsugamushi by immunoglobulin G (IgG) enzyme-linked immunosorbent assay (ELISA) for reactivity with rabbit sera prepared against eight antigenic prototypes of O. tsutsugamushi as well as several other species of Rickettsiales and nonrickettsial antigens. Refolded r56 exhibited broad reactivity with the rabbit antisera against the Orientia prototypes, and the ELISA reactions with the r56 and Karp whole-cell lysate antigens correlated well (r = 0.81, n = 22, sensitivity compared to that of standard ELISA of 91%). Refolded r56 did not react with most antisera against other rickettsial species or control antigens (specificity = 92%, n = 13) using a positive cutoff value determined with eight uninfected rabbit sera. Refolded r56 was evaluated further by ELISA, using 128 sera obtained from patients with suspected scrub typhus from Korat, Thailand, and 74 serum specimens from healthy Thai soldiers. By using the indirect immunoperoxidase assay as the reference assay, the recombinant antigen exhibited a sensitivity and specificity of 93% or greater for detection of both IgG and IgM in the ELISA at 1:400 serum dilution. These results strongly suggest that purified r56 is a suitable candidate for replacing the density gradient-purified, rickettsia-derived, whole-cell antigen currently used in the commercial dipstick assay available in the United States. PMID:9665960

Expression and refolding of truncated recombinant major outer membrane protein antigen (r56) of Orientia tsutsugamushi and its use in enzyme-linked immunosorbent assays.

PubMed

Ching, W M; Wang, H; Eamsila, C; Kelly, D J; Dasch, G A

1998-07-01

The variable 56-kDa major outer membrane protein of Orientia tsutsugamushi is the immunodominant antigen in human scrub typhus infections. The gene encoding this protein from Karp strain was cloned into the expression vector pET11a. The recombinant protein (r56) was expressed as a truncated nonfusion protein (amino acids 80 to 456 of the open reading frame) which formed an inclusion body when expressed in Escherichia coli BL21. Refolded r56 was purified and compared to purified whole-cell lysate of the Karp strain of O. tsutsugamushi by immunoglobulin G (IgG) enzyme-linked immunosorbent assay (ELISA) for reactivity with rabbit sera prepared against eight antigenic prototypes of O. tsutsugamushi as well as several other species of Rickettsiales and nonrickettsial antigens. Refolded r56 exhibited broad reactivity with the rabbit antisera against the Orientia prototypes, and the ELISA reactions with the r56 and Karp whole-cell lysate antigens correlated well (r = 0.81, n = 22, sensitivity compared to that of standard ELISA of 91%). Refolded r56 did not react with most antisera against other rickettsial species or control antigens (specificity = 92%, n = 13) using a positive cutoff value determined with eight uninfected rabbit sera. Refolded r56 was evaluated further by ELISA, using 128 sera obtained from patients with suspected scrub typhus from Korat, Thailand, and 74 serum specimens from healthy Thai soldiers. By using the indirect immunoperoxidase assay as the reference assay, the recombinant antigen exhibited a sensitivity and specificity of 93% or greater for detection of both IgG and IgM in the ELISA at 1:400 serum dilution. These results strongly suggest that purified r56 is a suitable candidate for replacing the density gradient-purified, rickettsia-derived, whole-cell antigen currently used in the commercial dipstick assay available in the United States.

NREL Develops Novel Method to Produce Renewable Acrylonitrile | News | NREL

Science.gov Websites

to Produce Renewable Acrylonitrile December 7, 2017 Research paves the way for cost-competitive , and Eric Karp, part of the NREL team working on a cost-competitive, sustainable process for creating traditional process in terms of cost and yield. Now, new NREL research is showing promise toward achieving

Mathematics and Social Justice: A Symbiotic Pedagogy

ERIC Educational Resources Information Center

Bond, Gareth; Chernoff, Egan J.

2015-01-01

Mathematics can be defined as "the science of pattern and order" (Van de Walle, Folk, Karp, & Bay-Williams, 2009, p. 10). But because there is often a perceived spectrum of approachability to mathematics (based on common misconceptions that envision the subject as a sort of elitist wizardry) it is important to bear in mind different…

On the Computational Complexity of Stochastic Scheduling Problems,

DTIC Science & Technology

1981-09-01

Survey": 1979, Ann. Discrete Math . 5, pp. 287-326. i I (.4) Karp, R.M., "Reducibility Among Combinatorial Problems": 1972, R.E. Miller and J.W...Weighted Completion Time Subject to Precedence Constraints": 1978, Ann. Discrete Math . 2, pp. 75-90. (8) Lawler, E.L. and J.W. Moore, "A Functional

Effects of Expertise and Cognitive Style on Information Use in Tactical Decision Making

DTIC Science & Technology

1988-06-01

environmental situation. Demographic Characteristics Age Gender Rank/Command Level 5 Personality Characteristics Decision making style Cognitive style Learning...individuals with diverse decision making patterns to use a standard approach will adversely affect their decision making abilities. Further, the findings...Minneapolis MN: University of Minnesota, Cognitive, Science Research Group. Karp, S.A. (1963). Field dependence and overcoming embeddedness . J. Consult

Molecular characterization of Orientia tsutsugamushi serotypes causing scrub typhus outbreak in southern region of Andhra Pradesh, India.

PubMed

Usha, K; Kumar, E; Kalawat, Usha; Kumar, B Siddhartha; Chaudhury, A; Gopal, D V R Sai

2016-10-01

Scrub typhus is a vector-borne zoonotic infection caused by Orientiatsutsugamushi. Local epidemiology of the circulating serotypes of scrub typhus is not available from most parts of India. We conducted this study for the diagnosis of scrub typhus using IgM ELISA and to detect O. tsutsugamushi serotypes circulating in southern Andhra Pradesh, India. Samples were collected from patients clinically suspected to have scrub typhus and were subjected to IgM ELISA to measure IgM antibodies against O. tsutsugamushi. Nested polymerase chain reaction (PCR) was performed targeting strain-specific regions in ELISA-positive samples. Of a total of 663 samples, 258 (38.91%) were found to be positive by IgM ELISA. Serotypes could be detected in 230 (34.69%) samples only. Only two serotypes, Karp and Kawasaki, were found in the serum samples, with the former being predominant. The dual infection of Karp and Kawasaki serotypes was found in seven patients. Other serotypes such as Gilliam, Kuroki and Kato were not detected in the samples. The nested PCR products proved useful in presumptively identifying the endemic O. tsutsugamushi serotypes. The present study could be significant in understanding scrub typhus epidemiology in this region.

Discovery Systems for Manufacturing

DTIC Science & Technology

1994-01-01

Rev. Letters, 68, Number 10, pp 1500-1503, 1992. Karp, Peter D., Hypothesis Formation and Qualitative Reasoning in Molecular Biology, Ph.D. Thesis ...1-4 2.5.1.2 Evaluating Attributes ........................ 2-17 1.21.4 The Simulated Laboratory ..............1-4 2.5.2 Nearest...4-11vs. Conventional Ae Cs R ............... 2-6 4.33 Initialize Simulator ......... ........... 4-112.4.12.1 Similarities

Critical transition in the constrained traveling salesman problem.

PubMed

Andrecut, M; Ali, M K

2001-04-01

We investigate the finite size scaling of the mean optimal tour length as a function of density of obstacles in a constrained variant of the traveling salesman problem (TSP). The computational experience pointed out a critical transition (at rho(c) approximately 85%) in the dependence between the excess of the mean optimal tour length over the Held-Karp lower bound and the density of obstacles.

Kepler AutoRegressive Planet Search: Motivation & Methodology

NASA Astrophysics Data System (ADS)

Caceres, Gabriel; Feigelson, Eric; Jogesh Babu, G.; Bahamonde, Natalia; Bertin, Karine; Christen, Alejandra; Curé, Michel; Meza, Cristian

2015-08-01

The Kepler AutoRegressive Planet Search (KARPS) project uses statistical methodology associated with autoregressive (AR) processes to model Kepler lightcurves in order to improve exoplanet transit detection in systems with high stellar variability. We also introduce a planet-search algorithm to detect transits in time-series residuals after application of the AR models. One of the main obstacles in detecting faint planetary transits is the intrinsic stellar variability of the host star. The variability displayed by many stars may have autoregressive properties, wherein later flux values are correlated with previous ones in some manner. Auto-Regressive Moving-Average (ARMA) models, Generalized Auto-Regressive Conditional Heteroskedasticity (GARCH), and related models are flexible, phenomenological methods used with great success to model stochastic temporal behaviors in many fields of study, particularly econometrics. Powerful statistical methods are implemented in the public statistical software environment R and its many packages. Modeling involves maximum likelihood fitting, model selection, and residual analysis. These techniques provide a useful framework to model stellar variability and are used in KARPS with the objective of reducing stellar noise to enhance opportunities to find as-yet-undiscovered planets. Our analysis procedure consisting of three steps: pre-processing of the data to remove discontinuities, gaps and outliers; ARMA-type model selection and fitting; and transit signal search of the residuals using a new Transit Comb Filter (TCF) that replaces traditional box-finding algorithms. We apply the procedures to simulated Kepler-like time series with known stellar and planetary signals to evaluate the effectiveness of the KARPS procedures. The ARMA-type modeling is effective at reducing stellar noise, but also reduces and transforms the transit signal into ingress/egress spikes. A periodogram based on the TCF is constructed to concentrate the signal

Molecular Cloning and Sequence Analysis of the Sta58 Major Antigen Gene of Rickettsia tsutsugamushi: Sequence homology and Antigenic Comparison of Sta58 to the 60-Kilodalton Family of Stress Proteins

DTIC Science & Technology

1990-05-01

Sta58 antigen and the Sta56 strain- GroES, C. burnetii HtpA, Mycobacterium tuberculosis 12- specific major antigen of R. tsutsugamushi (strain Karp...kb HindlIl fragment carrying the gene for the Sta58 tuberculosis, and Mycobacterium smegmatis (65-kDa anti- protein was subjected to DNA sequence...the Hsp6O and HsplO proteins. R. tsu., R. isutsugamushi; M. lep., Mvtcobacteriutn leprae : C. bur., C. burneiii; Synech.. Synechococcus strain 6301; T

Development of a Test Battery to Assess Mental Flexibility Based on Sternberg’s Theory of Successful Intelligence

DTIC Science & Technology

2008-01-01

on such tests as the Embedded Figures Test ( EFT ) (Witkin et al., 1971) or the Rod and Frame Test (RFT) (Witkin, Dyk, Faterson, Goodenough, & Karp...one starts to tap sources of individual differences measured little or not at all by such tests. Thus, when assessing intelligence, it is important to...in requiring verbal skills or the ability to analyze one’s own ideas-Sternberg & Lubart, 1995) but also tap skills beyond those measured even by

Proceedings of the 14th Annual Review Conference on Atmospheric Transmission Models (14th) Held at Hanscom Air Force Base, Massachusetts on 11-12 June 1991,

DTIC Science & Technology

1992-02-26

MIE 0 MEM a HUM 0.00 101 M4OBS 0.00 DEGUS FE 1.001 I.~ r1 40 N 99 IM 14 BANU2. S1 E CELL Calculated at 260K 04;.g of 056.N 072.44 00.M 904.00 920. of...o.374 Karp (1978) At a,, Fourier transform K~ ohp (1973) all 2.1 weighted samn of Lorentz and Gaul function 10- 4 relative to peak Value Pierluasi

Analysis of polypeptide composition and antigenic components of Rickettsia tsutsugamushi by polyacrylamide gel electrophoresis and immunoblotting.

PubMed Central

Tamura, A; Ohashi, N; Urakami, H; Takahashi, K; Oyanagi, M

1985-01-01

Polyacrylamide gel electrophoresis of lysates of purified Rickettsia tsutsugamushi revealed as many as 30 polypeptide bands, including major bands corresponding to molecular sizes of 70, 60, 54 to 56, and 46 to 47 kilodaltons. Compared with the polypeptide composition of the rickettsiae of Gilliam, Karp, and Kato strains and a newly isolated Shimokoshi strain, the major polypeptide in the Kato strain (54-56K) and in the Karp strain (46-47K) migrated a little faster and slower, respectively, than the corresponding polypeptides in the other strains. The largest major polypeptide (54-56K) was digestible by the treatment of intact rickettsiae with trypsin and variable in content in separate preparations, suggesting that the polypeptide exists on the rickettsial surface and is easily degraded during the handling of these microorganisms. Several surface polypeptides of rickettsiae, including the 54-56K and 46-47K polypeptides, were detected by radioiodination of intact rickettsiae followed by polyacrylamide gel electrophoresis of the lysate; however, the 70K and 60K polypeptides were not labeled. Immunoblotting experiments with hyperimmune sera prepared in guinea pigs against each strain demonstrated that the 70K, 54-56K, and 46-47K polypeptides showed antigenic activities. The 54-56K polypeptide appeared to be strain specific, whereas the 70K and 46-47K polypeptides cross-reacted with the heterologous antisera. Images PMID:3922893

High order local absorbing boundary conditions for acoustic waves in terms of farfield expansions

NASA Astrophysics Data System (ADS)

Villamizar, Vianey; Acosta, Sebastian; Dastrup, Blake

2017-03-01

We devise a new high order local absorbing boundary condition (ABC) for radiating problems and scattering of time-harmonic acoustic waves from obstacles of arbitrary shape. By introducing an artificial boundary S enclosing the scatterer, the original unbounded domain Ω is decomposed into a bounded computational domain Ω- and an exterior unbounded domain Ω+. Then, we define interface conditions at the artificial boundary S, from truncated versions of the well-known Wilcox and Karp farfield expansion representations of the exact solution in the exterior region Ω+. As a result, we obtain a new local absorbing boundary condition (ABC) for a bounded problem on Ω-, which effectively accounts for the outgoing behavior of the scattered field. Contrary to the low order absorbing conditions previously defined, the error at the artificial boundary induced by this novel ABC can be easily reduced to reach any accuracy within the limits of the computational resources. We accomplish this by simply adding as many terms as needed to the truncated farfield expansions of Wilcox or Karp. The convergence of these expansions guarantees that the order of approximation of the new ABC can be increased arbitrarily without having to enlarge the radius of the artificial boundary. We include numerical results in two and three dimensions which demonstrate the improved accuracy and simplicity of this new formulation when compared to other absorbing boundary conditions.

Entropy Production during Fatigue as a Criterion for Failure. The Critical Entropy Threshold: A Mathematical Model for Fatigue.

DTIC Science & Technology

1983-08-15

Measurement of Material Damping," Experimental Mechanics, 297-302 (Aug 1977). 4. Feltner, C. E., and J. D. Morrow, " Microplastic Strain Hysteresis Energy as...Code OOKB, CP5, Room 606 Washington, DC 20360 Mr. Richard R. Graham, II Code 5243, Bldg. NC4 Naval Sea Systems Command "* Washington, DC 20362 Mr. Al...Harbage, Jr. Code 2723 DTNSRDC Annapolis, MD 21402 L’r. Martih Kandl Code 5231 Naval Sea Systems Command *i Washington, DC 20362 S. Karpe David W

Interprocess Communication Protocols for Computer Networks

DTIC Science & Technology

1975-12-01

this value without maintaining any state information about itp partner CCP. The receiving CCP returns a SYN giving its own ISN, or can reject...34Packet Arrival and Buffer Statistics in a Packet Switching Node," IBM Research Report RZ 594 {.s;Zni02),. September 1973. [Cochi73] B. J. Cochi...rwid 0. P. Karp, "Protocol for a Computer Netuork," IBM Sustem Journa! 12. 1, 1973, pp. 94-105. [ricKen2ie741 A. fl. McKenzie

Failure Mode and Effects Analysis (FMEA) Introductory Overview

DTIC Science & Technology

2012-06-14

Failure Mode and Effects Analysis ( FMEA ) Introductory Overview TARDEC Systems Engineering Risk Management Team POC: Kadry Rizk or Gregor Ratajczak...2. REPORT TYPE Briefing Charts 3. DATES COVERED 01-05-2012 to 23-05-2012 4. TITLE AND SUBTITLE Failure Mode and Effects Analysis ( FMEA ) 5a...18 WELCOME Welcome to “An introductory overview of Failure Mode and Effects Analysis ( FMEA )”, A brief concerning the use and benefits of FMEA

Tsunami mitigation - redistribution of energy

NASA Astrophysics Data System (ADS)

Kadri, Usama

2017-04-01

.1007/1-4020-3607-8 3 3. E. Check, 2005. Natural disasters: Roots of recovery. Nature 438, 910-911, doi:10.1038/438910a. 4. A. M. Fridman, L. S. Alperovich, L. Shemer, L. Pustil'nik, D. Shtivelman, A. G. Marchuk, D. Liberzon, 2010. Tsunami wave suppression using submarine barriers. Phys. Usp. 53 809-816, doi:10.3367/UFNe.0180.201008d.0843. 5. U. Kadri, M. Stiassnie, 2013. Generation of an acoustic-gravity wave by two gravity waves, and their mutual interaction. J. Fluid Mech. 735, R6, doi:10.1017/jfm.2013.539. 6. U. Kadri, 2015. Wave motion in a heavy compressible fluid: revisited. European Journal of Mechanics - B/Fluids, 49(A), 50-57, doi:10.1016/j.euromechflu.2014.07.008 7. U. Kadri, T.R. Akylas, 2016. On resonant triad interactions of acoustic-gravity waves. J. Fluid Mech., 788, R1(12 pages), doi:10.1017/jfm.2015.721. 8. U. Kadri, 2016. Triad resonance between a surface-gravity wave and two high frequency hydro-acoustic waves. Eur. J. Mech. B/Fluid, 55(1), 157-161, doi:10.1016/j.euromechflu.2015.09.008.

Development of a 39.5 GHz Karp traveling wave tube for use in space

NASA Technical Reports Server (NTRS)

Jacquez, A.; Wilson, D.

1988-01-01

A millimeter-wave TWT was developed using a dispersive, high-impedance forward wave interaction structure based on a ladder, with non-space-harmonic interaction, for a tube with high gain per inch and high efficiency. The 'Tunneladder' interaction structure combines ladder properties modified to accommodate Pierce gun beam optics on a radially magnetized PM focusing structure. The development involved the fabrication of chemically milled, shaped ladders diffusion brazed to each ridge of a double ridged waveguide. Cold-test data are presented, representing the omega-Beta and impedance characteristics of the modified ladder circuit These results were used in small and large-signal computer programs to predict TWT gain and efficiency. A laboratory model tube was designed and fabricated, including all major subassemblies.

EDITORIAL: Bioengineering nanotechnology: towards the clinic Bioengineering nanotechnology: towards the clinic

NASA Astrophysics Data System (ADS)

Zhao, Weian; Karp, Jeffrey M.; Ferrari, Mauro; Serda, Rita

2011-12-01

special issue highlights some of the most recent advances in the exciting field of bioengineering nanotechnology. The themes covered in this issue include nanoparticle systems for tracking transplanted stem cells using a variety of imaging modalities, synthesis of smart nanomaterials for drug delivery and targeting specific intracellular organalles, elucidating how physical cues provided by nano- or micro-fabricated scaffolds impact cell phenotype, novel nanocomposite materials for biosensing, biomimetic assembly of nanostructures for studying molecular interactions, and high content analysis for assessing nanotoxicity. We believe next-generation nanomaterials that are currently under development will transform our understanding of biological mechanisms, and revolutionize clinical practice through ushering in new diagnostics and therapeutic paradigms. As nanotechnology becomes increasingly accessible to research laboratories, significant advances leading to paradigm shifts in basic biology and medicine will require connecting the right technology to the right problem and ensuring that the most pertinent criteria are correctly identified and addressed. References [1] Peer D et al Nat. Nanotechnol. 2 751-60 [2] Wang A Z, Langer R S and Farokhzad O C 2011 Annu. Rev. Med. doi: 10.1146/annurev-med-040210-162544 [3] Farokhzad O C and Langer R 2006 Adv. Drug Deliv. Rev. 58 1456-9 [4] Zhao W and Karp J M 2009 Nat. Mater. 8 453-4 [5] Ferreira L, Karp J M, Nobre L and Langer R 2008 Cell Stem Cell 3 136-46 [6] Zhao W and Karp J M 2009 ChemBioChem 10 2308-10 [7] Zhao W et al 2011 Nat. Nanotechnol. 6 524-31 [8] Stephan M T, Moon J J, Um S H, Bershteyn A and Irvine D J 2010 Nat. Med. 16 1035-41 [9] Sarkar D, Ankrum J A, Teo G S, Carman C V and Karp J M 2011 Biomaterials 32 3053-61

Propagation of acoustic-gravity waves in arctic zones with elastic ice-sheets

NASA Astrophysics Data System (ADS)

Kadri, Usama; Abdolali, Ali; Kirby, James T.

2017-04-01

We present an analytical solution of the boundary value problem of propagating acoustic-gravity waves generated in the ocean by earthquakes or ice-quakes in arctic zones. At the surface, we assume elastic ice-sheets of a variable thickness, and show that the propagating acoustic-gravity modes have different mode shape than originally derived by Ref. [1] for a rigid ice-sheet settings. Computationally, we couple the ice-sheet problem with the free surface model by Ref. [2] representing shrinking ice blocks in realistic sea state, where the randomly oriented ice-sheets cause inter modal transition at the edges and multidirectional reflections. We then derive a depth-integrated equation valid for spatially slowly varying thickness of ice-sheet and water depth. Surprisingly, and unlike the free-surface setting, here it is found that the higher acoustic-gravity modes exhibit a larger contribution. These modes travel at the speed of sound in water carrying information on their source, e.g. ice-sheet motion or submarine earthquake, providing various implications for ocean monitoring and detection of quakes. In addition, we found that the propagating acoustic-gravity modes can result in orbital displacements of fluid parcels sufficiently high that may contribute to deep ocean currents and circulation, as postulated by Refs. [1, 3]. References [1] U. Kadri, 2016. Generation of Hydroacoustic Waves by an Oscillating Ice Block in Arctic Zones. Advances in Acoustics and Vibration, 2016, Article ID 8076108, 7 pages http://dx.doi.org/10.1155/2016/8076108 [2] A. Abdolali, J. T. Kirby and G. Bellotti, 2015, Depth-integrated equation for hydro-acoustic waves with bottom damping, J. Fluid Mech., 766, R1 doi:10.1017/jfm.2015.37 [3] U. Kadri, 2014. Deep ocean water transportation by acoustic?gravity waves. J. Geophys. Res. Oceans, 119, doi:10.1002/ 2014JC010234

Early Diagnosis of Scrub Typhus with a Rapid Flow Assay Using Recombinant Major Outer Membrane Protein Antigen (r56) of Orientia tsutsugamushi

PubMed Central

Ching, W.-M.; Rowland, D.; Zhang, Z.; Bourgeois, A. L.; Kelly, D.; Dasch, G. A.; Devine, P. L.

2001-01-01

The variable 56-kDa major outer membrane protein of Orientia tsutsugamushi is the immunodominant antigen in human scrub typhus infections. We developed a rapid immunochromatographic flow assay (RFA) for the detection of immunoglobulin M (IgM) and IgG antibodies to O. tsutsugamushi. The RFA employs a truncated recombinant 56-kDa protein from the Karp strain as the antigen. The performance of the RFA was evaluated with a panel of 321 sera (serial bleedings of 85 individuals suspected of scrub typhus) which were collected in the Pescadore Islands, Taiwan, from 1976 to 1977. Among these 85 individuals, IgM tests were negative for 7 cases by both RFA and indirect fluorescence assay (IFA) using Karp whole-cell antigen. In 29 cases specific responses were detected by the RFA earlier than by IFA, 44 cases had the same detection time, and 5 cases were detected earlier by IFA than by RFA. For IgG responses, 4 individuals were negative with both methods, 37 cases exhibited earlier detection by RFA than IFA, 42 cases were detected at the same time, and 2 cases were detected earlier by IFA than by RFA. The sensitivities of RFA detection of antibody in sera from confirmed cases were 74 and 86% for IgM and IgG, respectively. When IgM and IgG results were combined, the sensitivity was 89%. A panel of 78 individual sera collected from patients with no evidence of scrub typhus was used to evaluate the specificity of the RFA. The specificities of the RFA were 99% for IgM and 97% for IgG. The sensitivities of IFA were 53 and 73% for IgM and IgG, respectively, and were 78% when the results of IgM and IgG were combined. The RFA test was significantly better than the IFA test for the early detection of antibody to scrub typhus in primary infections, while both tests were equally sensitive with reinfected individuals. PMID:11238230

Light curves for bump Cepheids computed with a dynamically zoned pulsation code

NASA Technical Reports Server (NTRS)

Adams, T. F.; Castor, J. I.; Davis, C. G.

1980-01-01

The dynamically zoned pulsation code developed by Castor, Davis, and Davison was used to recalculate the Goddard model and to calculate three other Cepheid models with the same period (9.8 days). This family of models shows how the bumps and other features of the light and velocity curves change as the mass is varied at constant period. The use of a code that is capable of producing reliable light curves demonstrates that the light and velocity curves for 9.8 day Cepheid models with standard homogeneous compositions do not show bumps like those that are observed unless the mass is significantly lower than the 'evolutionary mass.' The light and velocity curves for the Goddard model presented here are similar to those computed independently by Fischel, Sparks, and Karp. They should be useful as standards for future investigators.

Genotypic characterization of Orientia tsutsugamushi from patients in two geographical locations in Sri Lanka.

PubMed

Premaratna, Ranjan; Blanton, Lucas S; Samaraweera, Dilhar N; de Silva, G Nalika N; Chandrasena, Nilmini T G A; Walker, David H; de Silva, H J

2017-01-13

To date more than 20 antigenically distinct strains of Orientia tsutsugamushi (OT) reported within the tsutsugamushi triangle that cause an undifferentiated acute febrile illness in humans. Genotypic characterization of OT in different geographic regions or within the same country, is important in order to establish effective diagnostics, clinical management and to develop effective vaccines. Genetic and antigenic characterization of OT causing human disease in OT-endemic regions is not known for Sri Lanka. Adult patients and children who were admitted with an acute febrile illness and presumed to having acute scrub typhus based on presence of an eschar and other supporting clinical features were recruited. Eschar biopsies and buffy coat samples collected from patients who were confirmed having OT by IFA were further studied by real time PCR (Orientia 47 kD) and nested PCR (Orientia 56 kD) amplification. DNA sequences were obtained for 56 kD gene amplicons and phylogenetic comparisons were analyzed using currently available data in GenBank [Neucleotide substitution per 100 residues, 1000 Bootstrap Trials]. Twenty eschar biopsies (Location1,19, Location 2,1) and eight buffy coat samples (Location1,6, Location2,2) examined by real time PCR revealed Orientia amplicons in 16 samples. DNA sequences were obtained for the 56 kD gene amplicons in 12 eschars and 4 buffy coat samples. The genotypes of the Location1 samples revealed that, 7 exhibiting close homology with JP1 [distantly related to UT177 Thai (Karp related)], five had close homology with Kato strain, two had close homology with JGv and JG AF [Distantly related to Kawasaki M63383] and one had close homology with Gilliam strain. The Location 2 strain was closely related to Kuroki-Boryong L04956, the genotype which is distributed in far eastern Asia. Similar to other patients in the cohort this patient also had never travelled out of Sri Lanka. We observed all three main OT genotypes in Sri Lanka, and the majority

Kepler AutoRegressive Planet Search

NASA Astrophysics Data System (ADS)

Caceres, Gabriel Antonio; Feigelson, Eric

2016-01-01

The Kepler AutoRegressive Planet Search (KARPS) project uses statistical methodology associated with autoregressive (AR) processes to model Kepler lightcurves in order to improve exoplanet transit detection in systems with high stellar variability. We also introduce a planet-search algorithm to detect transits in time-series residuals after application of the AR models. One of the main obstacles in detecting faint planetary transits is the intrinsic stellar variability of the host star. The variability displayed by many stars may have autoregressive properties, wherein later flux values are correlated with previous ones in some manner. Our analysis procedure consisting of three steps: pre-processing of the data to remove discontinuities, gaps and outliers; AR-type model selection and fitting; and transit signal search of the residuals using a new Transit Comb Filter (TCF) that replaces traditional box-finding algorithms. The analysis procedures of the project are applied to a portion of the publicly available Kepler light curve data for the full 4-year mission duration. Tests of the methods have been made on a subset of Kepler Objects of Interest (KOI) systems, classified both as planetary `candidates' and `false positives' by the Kepler Team, as well as a random sample of unclassified systems. We find that the ARMA-type modeling successfully reduces the stellar variability, by a factor of 10 or more in active stars and by smaller factors in more quiescent stars. A typical quiescent Kepler star has an interquartile range (IQR) of ~10 e-/sec, which may improve slightly after modeling, while those with IQR ranging from 20 to 50 e-/sec, have improvements from 20% up to 70%. High activity stars (IQR exceeding 100) markedly improve. A periodogram based on the TCF is constructed to concentrate the signal of these periodic spikes. When a periodic transit is found, the model is displayed on a standard period-folded averaged light curve. Our findings to date on real

Models and algorithm of optimization launch and deployment of virtual network functions in the virtual data center

NASA Astrophysics Data System (ADS)

Bolodurina, I. P.; Parfenov, D. I.

2017-10-01

The goal of our investigation is optimization of network work in virtual data center. The advantage of modern infrastructure virtualization lies in the possibility to use software-defined networks. However, the existing optimization of algorithmic solutions does not take into account specific features working with multiple classes of virtual network functions. The current paper describes models characterizing the basic structures of object of virtual data center. They including: a level distribution model of software-defined infrastructure virtual data center, a generalized model of a virtual network function, a neural network model of the identification of virtual network functions. We also developed an efficient algorithm for the optimization technology of containerization of virtual network functions in virtual data center. We propose an efficient algorithm for placing virtual network functions. In our investigation we also generalize the well renowned heuristic and deterministic algorithms of Karmakar-Karp.

Geometry Helps to Compare Persistence Diagrams

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

Kerber, Michael; Morozov, Dmitriy; Nigmetov, Arnur

2015-11-16

Exploiting geometric structure to improve the asymptotic complexity of discrete assignment problems is a well-studied subject. In contrast, the practical advantages of using geometry for such problems have not been explored. We implement geometric variants of the Hopcroft--Karp algorithm for bottleneck matching (based on previous work by Efrat el al.), and of the auction algorithm by Bertsekas for Wasserstein distance computation. Both implementations use k-d trees to replace a linear scan with a geometric proximity query. Our interest in this problem stems from the desire to compute distances between persistence diagrams, a problem that comes up frequently in topological datamore » analysis. We show that our geometric matching algorithms lead to a substantial performance gain, both in running time and in memory consumption, over their purely combinatorial counterparts. Moreover, our implementation significantly outperforms the only other implementation available for comparing persistence diagrams.« less

A RICKETTSIAL INFECTION IN CANADIAN VOLES

PubMed Central

Baker, James A.

1946-01-01

From apparently normal voles captured on Grosse Isle, Province of Quebec, Canada, an infective agent has been grown in embryonated eggs, and by inoculation an inapparent infection was established in voles, mice, guinea pigs, hamsters, and rats. No growth of the agent was obtained in the absence of living cells, and the manner of its development in the yolk sac of embryonated eggs, as well as morphological, epidemiological, and pathogenic features, indicates a rickettsial nature. The inability to transmit infection by either cage or intrauterine contact points to a vector, and mites are shown to have a probable part in the epidemiology. Mice infected with the vole agent resist lethal doses of the Karp strain of scrub typhus, and certain epidemiological, morphological, and immunological features support the relationship indicated by the mouse tests. It is therefore concluded that voles on this island have an inapparent infection due to a rickettsia that may be related to the rickettsia of scrub typhus. PMID:19871552

The genotypes of Orientia tsutsugamushi, identified in scrub typhus patients in northern Vietnam.

PubMed

Nguyen, Hang L K; Pham, Hang T T; Nguyen, Tinh V; Hoang, Phuong Vm; Le, Mai T Q; Takemura, Taichiro; Hasebe, Futoshi; Hayasaka, Daisuke; Yamada, Akio; Hotta, Kozue

2017-03-01

There are an estimated one million patients with scrub typhus in the Asia-Pacific region. There are few reports describing the incidence of scrub typhus in Vietnam. Blood samples collected from 63 patients clinically diagnosed as having scrub typhus from July 2015 to September 2016 were subjected to genotyping of Orientia tsutsugamushi. Of these patients, 42 (67%) tested positive for O. tsutsugamushi, and the most common genotype was identified to be Karp (55%). Other genotypes, TA763, Gilliam type in Japan variant, and Kato were also found in 17%, 17% and 12% of patients, respectively. To better understand the epidemiological landscape of scrub typhus in Vietnam, a countrywide study is needed. LC110330-LC110333, LC110336-LC110351 and LC214804-LC214825. © The Author 2017. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Molecular epidemiology and genetic diversity of Orientia tsutsugamushi from patients with scrub typhus in 3 regions of India.

PubMed

Varghese, George M; Janardhanan, Jeshina; Mahajan, Sanjay K; Tariang, David; Trowbridge, Paul; Prakash, John A J; David, Thambu; Sathendra, Sowmya; Abraham, O C

2015-01-01

Scrub typhus, an acute febrile illness that is widespread in the Asia-Pacific region, is caused by the bacterium Orientia tsutsugamushi, which displays high levels of antigenic variation. We conducted an investigation to identify the circulating genotypes of O. tsutsugamushi in 3 scrub typhus-endemic geographic regions of India: South India, Northern India, and Northeast India. Eschar samples collected during September 2010-August 2012 from patients with scrub typhus were subjected to 56-kDa type-specific PCR and sequencing to identify their genotypes. Kato-like strains predominated (61.5%), especially in the South and Northeast, followed by Karp-like strains (27.7%) and Gilliam and Ikeda strains (2.3% each). Neimeng-65 genotype strains were also observed in the Northeast. Clarifying the genotypic diversity of O. tsutsugamushi in India enhances knowledge of the regional diversity among circulating strains and provides potential resources for future region-specific diagnostic studies and vaccine development.

Immunocytochemical methods to study the distribution of Orientia tsutsugamushi in Leptotrombidium (Acari: Trombiculidae) chiggers.

PubMed

Myint, K S; Linthicum, K J; Tanskul, P; Lerdthusnee, K; Vaughn, D W; Manomuth, C; Mongkolsirichaikul, D; Hansukjariya, P; Hastriter, M W

1998-07-01

Immunocytochemical methods were developed and tested for their ability to detect the distribution of Orientia tsutsugamushi in paraffin sections of adult chiggers (Leptotrombidium imphalum Vercammen-Grandjean & Langston). Rickettsial antigen was detected by application of a simple direct or amplified immunocytochemistry procedure and an indirect immunofluorescent procedure. In the direct procedure alkaline phosphatase conjugation to the mouse polyclonal antibody to the Karp strain was followed by the HistoMark Red test system to detect rickettsial antigen. The amplification procedure used a similar method but used an unlabeled primary antibody followed by secondary biotinylated antimouse IgG, streptavidin-alkaline phosphatase, and the HistoMark Red test system. The immunofluorescent procedure included a biotinylated secondary antibody followed by addition of a streptavidin-FITC conjugate. Specific tissue tropisms in infected chiggers were observed in the salivary glands, nervous tissue, and ovaries of adult female mites in all procedures; however, nonspecific fluorescence of the chigger limited definitive identification of tissue tropisms with the indirect immunofluorescent procedure.

Acoustic Gravity Waves Generated by an Oscillating Ice Sheet in Arctic Zone

NASA Astrophysics Data System (ADS)

Abdolali, A.; Kadri, U.; Kirby, J. T., Jr.

2016-12-01

We investigate the formation of acoustic-gravity waves due to oscillations of large ice blocks, possibly triggered by atmospheric and ocean currents, ice block shrinkage or storms and ice-quakes.For the idealized case of a homogeneous weakly compressible water bounded at the surface by ice sheet and a rigid bed, the description of the infinite family of acoustic modes is characterized by the water depth h and angular frequency of oscillating ice sheet ω ; The acoustic wave field is governed by the leading mode given by: Nmax=\\floor {(ω h)/(π c)} where c is the sound speed in water and the special brackets represent the floor function (Fig1). Unlike the free-surface setting, the higher acoustic modes might exhibit a larger contribution and therefore all progressive acoustic modes have to be considered.This study focuses on the characteristics of acoustic-gravity waves generated by an oscillating elastic ice sheet in a weakly compressible fluid coupled with a free surface model [Abdolali et al. 2015] representing shrinking ice blocks in realistic sea state, where the randomly oriented ice sheets cause inter modal transition and multidirectional reflections. A theoretical solution and a 3D numerical model have been developed for the study purposes. The model is first validated against the theoretical solution [Kadri, 2016]. To overcome the computational difficulties of 3D models, we derive a depth-integrated equation valid for spatially varying ice sheet thickness and water depth. We show that the generated acoustic-gravity waves contribute significantly to deep ocean currents compared to other mechanisms. In addition, these waves travel at the sound speed in water carrying information on ice sheet motion, providing various implications for ocean monitoring and detection of ice-quakes. Fig1:Snapshots of dynamic pressure given by an oscillating ice sheet; h=4500m, c=1500m/s, semi-length b=10km, ζ =1m, omega=π rad/s. Abdolali, A., Kirby, J. T. and Bellotti, G

Robust numerical solution of the reservoir routing equation

NASA Astrophysics Data System (ADS)

Fiorentini, Marcello; Orlandini, Stefano

2013-09-01

The robustness of numerical methods for the solution of the reservoir routing equation is evaluated. The methods considered in this study are: (1) the Laurenson-Pilgrim method, (2) the fourth-order Runge-Kutta method, and (3) the fixed order Cash-Karp method. Method (1) is unable to handle nonmonotonic outflow rating curves. Method (2) is found to fail under critical conditions occurring, especially at the end of inflow recession limbs, when large time steps (greater than 12 min in this application) are used. Method (3) is computationally intensive and it does not solve the limitations of method (2). The limitations of method (2) can be efficiently overcome by reducing the time step in the critical phases of the simulation so as to ensure that water level remains inside the domains of the storage function and the outflow rating curve. The incorporation of a simple backstepping procedure implementing this control into the method (2) yields a robust and accurate reservoir routing method that can be safely used in distributed time-continuous catchment models.

Modeling and simulation of magnetic resonance imaging based on intermolecular multiple quantum coherences

NASA Astrophysics Data System (ADS)

Cai, Congbo; Dong, Jiyang; Cai, Shuhui; Cheng, En; Chen, Zhong

2006-11-01

Intermolecular multiple quantum coherences (iMQCs) have many potential applications since they can provide interaction information between different molecules within the range of dipolar correlation distance, and can provide new contrast in magnetic resonance imaging (MRI). Because of the non-localized property of dipolar field, and the non-linear property of the Bloch equations incorporating the dipolar field term, the evolution behavior of iMQC is difficult to deduce strictly in many cases. In such cases, simulation studies are very important. Simulation results can not only give a guide to optimize experimental conditions, but also help analyze unexpected experimental results. Based on our product operator matrix and the K-space method for dipolar field calculation, the MRI simulation software was constructed, running on Windows operation system. The non-linear Bloch equations are calculated by a fifth-order Cash-Karp Runge-Kutta formulism. Computational time can be efficiently reduced by separating the effects of chemical shifts and strong gradient field. Using this software, simulation of different kinds of complex MRI sequences can be done conveniently and quickly on general personal computers. Some examples were given. The results were discussed.

Using pseudoalignment and base quality to accurately quantify microbial community composition

PubMed Central

Novembre, John

2018-01-01

Pooled DNA from multiple unknown organisms arises in a variety of contexts, for example microbial samples from ecological or human health research. Determining the composition of pooled samples can be difficult, especially at the scale of modern sequencing data and reference databases. Here we propose a novel method for taxonomic profiling in pooled DNA that combines the speed and low-memory requirements of k-mer based pseudoalignment with a likelihood framework that uses base quality information to better resolve multiply mapped reads. We apply the method to the problem of classifying 16S rRNA reads using a reference database of known organisms, a common challenge in microbiome research. Using simulations, we show the method is accurate across a variety of read lengths, with different length reference sequences, at different sample depths, and when samples contain reads originating from organisms absent from the reference. We also assess performance in real 16S data, where we reanalyze previous genetic association data to show our method discovers a larger number of quantitative trait associations than other widely used methods. We implement our method in the software Karp, for k-mer based analysis of read pools, to provide a novel combination of speed and accuracy that is uniquely suited for enhancing discoveries in microbial studies. PMID:29659582

Furniture dimensions and postural overload for schoolchildren's head, upper back and upper limbs.

PubMed

Batistão, Mariana Vieira; Sentanin, Anna Cláudia; Moriguchi, Cristiane Shinohara; Hansson, Gert-Åke; Coury, Helenice Jane Cote Gil; de Oliveira Sato, Tatiana

2012-01-01

The aim of this study was to evaluate how the fixed furniture dimensions match with students' anthropometry and to describe head, upper back and upper limbs postures and movements. Evaluation was performed in 48 students from a Brazilian state school. Furniture dimensions were measured with metric tape, movements and postures by inclinometers (Logger Tecknologi, Åkarp, Sweden). Seat height was high for 21% and low for 36% of the students; seat length was short for 45% and long for 9% and table height was high for 53% and low for 28%. Regression analysis showed that seat/popliteal height quotient is explained by 90th percentile of upper back inclination (β=0.410) and 90th percentile of right upper arm elevation (β=-0.293). For seat/thigh length quotient the significant variables were 90th percentile of upper back velocity (β=-0.282) and 90th percentile of right upper arm elevation (β=0.410). This study showed a relationship between furniture mismatch and postural overload. When the seat height is low students increase upper back left inclination and right upper arm elevation; when the seat is short students decrease the upper back flexion velocity and increase right upper arm elevation.

Optimizing the inner loop of the gravitational force interaction on modern processors

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

Warren, Michael S

2010-12-08

We have achieved superior performance on multiple generations of the fastest supercomputers in the world with our hashed oct-tree N-body code (HOT), spanning almost two decades and garnering multiple Gordon Bell Prizes for significant achievement in parallel processing. Execution time for our N-body code is largely influenced by the force calculation in the inner loop. Improvements to the inner loop using SSE3 instructions has enabled the calculation of over 200 million gravitational interactions per second per processor on a 2.6 GHz Opteron, for a computational rate of over 7 Gflops in single precision (700/0 of peak). We obtain optimal performancemore » some processors (including the Cell) by decomposing the reciprocal square root function required for a gravitational interaction into a table lookup, Chebychev polynomial interpolation, and Newton-Raphson iteration, using the algorithm of Karp. By unrolling the loop by a factor of six, and using SPU intrinsics to compute on vectors, we obtain performance of over 16 Gflops on a single Cell SPE. Aggregated over the 8 SPEs on a Cell processor, the overall performance is roughly 130 Gflops. In comparison, the ordinary C version of our inner loop only obtains 1.6 Gflops per SPE with the spuxlc compiler.« less

Development of a rapid and visual nucleotide detection method for a Chinese epidemic strain of Orientia tsutsugamushi based on recombinase polymerase amplification assay and lateral flow test.

PubMed

Qi, Yong; Yin, Qiong; Shao, Yinxiu; Cao, Min; Li, Suqin; Chen, Hongxia; Shen, Wanpeng; Rao, Jixian; Li, Jiameng; Li, Xiaoling; Sun, Yu; Lin, Yu; Deng, Yi; Zeng, Wenwen; Zheng, Shulong; Liu, Suyun; Li, Yuexi

2018-05-01

Orientia tsutsugamushi is an obligate intracellular pathogen that causes scrub typhus. Diagnosing scrub typhus remains a challenge, and a sensitive, specific, simple, and rapid diagnostic test is still needed. A recombinase polymerase amplification (RPA) assay combined with a lateral flow (LF) test targeting the 56-kDa gene of a Karp-like strain of O. tsutsugamushi was developed and optimized. The detection limits, sensitivity, specificity, and simulative clinical performance were evaluated. Primers and probe were screened to establish the RPA assay, and the reaction conditions were optimized. The detection limit was 10 copies/reaction in detecting plasmid DNA and 12 copies/reaction in detecting genomic DNA. The RPA-LF method could differentiate O. tsutsugamushi from other phylogenetically related bacteria. The sensitivity was 100% and specificity was over 90%, when evaluated using infected animal samples or simulative clinical samples. Furthermore, the method was completed in 20min at 37°C followed by a 3-5min incubation at room temperature for the development of an immunochromatographic strip, and the results could be determined visually. This method is promising for wide-ranging use in basic medical units considering that it requires minimal instruments and infrastructure and is highly time-efficient, sensitive, and specific for diagnosing scrub typhus. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Scrub typhus in South India: clinical and laboratory manifestations, genetic variability, and outcome.

PubMed

Varghese, George M; Janardhanan, Jeshina; Trowbridge, Paul; Peter, John V; Prakash, John A J; Sathyendra, Sowmya; Thomas, Kurien; David, Thambu S; Kavitha, M L; Abraham, Ooriapadickal C; Mathai, Dilip

2013-11-01

This study sought to document the clinical and laboratory manifestations, genetic variability, and outcomes of scrub typhus, an often severe infection caused by Orientia tsutsugamushi, in South India. Patients admitted to a large teaching hospital with IgM ELISA-confirmed scrub typhus were evaluated. Clinical examination with a thorough search for an eschar, laboratory testing, chest X-ray, and outcome were documented and analyzed. Additionally, a 410-bp region of the 56-kDa type-specific antigen gene of O. tsutsugamushi was sequenced and compared with isolates from other regions of Asia. Most of the 154 patients evaluated presented with fever and non-specific symptoms. An eschar was found in 86 (55%) patients. Mild hepatic involvement was seen in most, with other organ involvement including respiratory, cardiovascular, and renal. Multi-organ dysfunction was noted in 59 (38.3%), and the fatality rate was 7.8%. Hypotension requiring vasoactive agents was found to be an independent predictor of mortality (p<0.001). The phylogeny of 26 samples showed 17 (65%) clustering with the Kato-like group and eight (31%) with the Karp-like group. The presentation of scrub typhus can be variable, often non-specific, but with potentially severe multi-organ dysfunction. Prompt recognition is key to specific treatment and good outcomes. Further study of the circulating strains is essential for the development of a successful vaccine and sensitive point-of-care testing. Copyright © 2013 International Society for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Isolation of a novel Orientia species (O. chuto sp. nov.) from a patient infected in Dubai.

PubMed

Izzard, Leonard; Fuller, Andrew; Blacksell, Stuart D; Paris, Daniel H; Richards, Allen L; Aukkanit, Nuntipa; Nguyen, Chelsea; Jiang, Ju; Fenwick, Stan; Day, Nicholas P J; Graves, Stephen; Stenos, John

2010-12-01

In July 2006, an Australian tourist returning from Dubai, in the United Arab Emirates (UAE), developed acute scrub typhus. Her signs and symptoms included fever, myalgia, headache, rash, and eschar. Orientia tsutsugamushi serology demonstrated a 4-fold rise in antibody titers in paired serum collections (1:512 to 1:8,192), with the sera reacting strongest against the Gilliam strain antigen. An Orientia species was isolated by the in vitro culture of the patient's acute blood taken prior to antibiotic treatment. The gene sequencing of the 16S rRNA gene (rrs), partial 56-kDa gene, and the full open reading frame 47-kDa gene was performed, and comparisons of this new Orientia sp. isolate to previously characterized strains demonstrated significant sequence diversity. The closest homology to the rrs sequence of the new Orientia sp. isolate was with three strains of O. tsutsugamushi (Ikeda, Kato, and Karp), with a nucleotide sequence similarity of 98.5%. The closest homology to the 47-kDa gene sequence was with O. tsutsugamushi strain Gilliam, with a nucleotide similarity of 82.3%, while the closest homology to the 56-kDa gene sequence was with O. tsutsugamushi strain TA686, with a nucleotide similarity of 53.1%. The molecular divergence and geographically unique origin lead us to believe that this organism should be considered a novel species. Therefore, we have proposed the name "Orientia chuto," and the prototype strain of this species is strain Dubai, named after the location in which the patient was infected.

Isolation of a Novel Orientia Species (O. chuto sp. nov.) from a Patient Infected in Dubai ▿

PubMed Central

Izzard, Leonard; Fuller, Andrew; Blacksell, Stuart D.; Paris, Daniel H.; Richards, Allen L.; Aukkanit, Nuntipa; Nguyen, Chelsea; Jiang, Ju; Fenwick, Stan; Day, Nicholas P. J.; Graves, Stephen; Stenos, John

2010-01-01

In July 2006, an Australian tourist returning from Dubai, in the United Arab Emirates (UAE), developed acute scrub typhus. Her signs and symptoms included fever, myalgia, headache, rash, and eschar. Orientia tsutsugamushi serology demonstrated a 4-fold rise in antibody titers in paired serum collections (1:512 to 1:8,192), with the sera reacting strongest against the Gilliam strain antigen. An Orientia species was isolated by the in vitro culture of the patient's acute blood taken prior to antibiotic treatment. The gene sequencing of the 16S rRNA gene (rrs), partial 56-kDa gene, and the full open reading frame 47-kDa gene was performed, and comparisons of this new Orientia sp. isolate to previously characterized strains demonstrated significant sequence diversity. The closest homology to the rrs sequence of the new Orientia sp. isolate was with three strains of O. tsutsugamushi (Ikeda, Kato, and Karp), with a nucleotide sequence similarity of 98.5%. The closest homology to the 47-kDa gene sequence was with O. tsutsugamushi strain Gilliam, with a nucleotide similarity of 82.3%, while the closest homology to the 56-kDa gene sequence was with O. tsutsugamushi strain TA686, with a nucleotide similarity of 53.1%. The molecular divergence and geographically unique origin lead us to believe that this organism should be considered a novel species. Therefore, we have proposed the name “Orientia chuto,” and the prototype strain of this species is strain Dubai, named after the location in which the patient was infected. PMID:20926708

Loss of PDZ-adaptor protein NHERF2 affects membrane localization and cGMP- and [Ca2+]- but not cAMP-dependent regulation of Na+/H+ exchanger 3 in murine intestine

PubMed Central

Chen, Mingmin; Sultan, Ayesha; Cinar, Ayhan; Yeruva, Sunil; Riederer, Brigitte; Singh, Anurag Kumar; Li, Junhua; Bonhagen, Janina; Chen, Gang; Yun, Chris; Donowitz, Mark; Hogema, Boris; deJonge, Hugo; Seidler, Ursula

2010-01-01

Trafficking and regulation of the epithelial brush border membrane (BBM) Na+/H+ exchanger 3 (NHE3) in the intestine involves interaction with four different members of the NHERF family in a signal-dependent and possibly segment-specific fashion. The aim of this research was to study the role of NHERF2 (E3KARP) in intestinal NHE3 BBM localization and second messenger-mediated and receptor-mediated inhibition of NHE3. Immunolocalization of NHE3 in WT mice revealed predominant microvillar localization in jejunum and colon, a mixed distribution in the proximal ileum but localization near the terminal web in the distal ileum. The terminal web localization of NHE3 in the distal ileum correlated with reduced acid-activated NHE3 activity (fluorometrically assessed). NHERF2 ablation resulted in a shift of NHE3 to the microvilli and higher basal fluid absorption rates in the ileum, but no change in overall NHE3 protein or mRNA expression. Forskolin-induced NHE3 inhibition was preserved in the absence of NHERF2, whereas Ca2+ ionophore- or carbachol-mediated inhibition was abolished. Likewise, Escherichia coli heat stable enterotoxin peptide (STp) lost its inhibitory effect on intestinal NHE3. It is concluded that in native murine intestine, the NHE3 adaptor protein NHERF2 plays important roles in tethering NHE3 to a position near the terminal web and in second messenger inhibition of NHE3 in a signal- and segment-specific fashion, and is therefore an important regulator of intestinal fluid transport. PMID:20962002

C library for topological study of the electronic charge density.

PubMed

Vega, David; Aray, Yosslen; Rodríguez, Jesús

2012-12-05

The topological study of the electronic charge density is useful to obtain information about the kinds of bonds (ionic or covalent) and the atom charges on a molecule or crystal. For this study, it is necessary to calculate, at every space point, the electronic density and its electronic density derivatives values up to second order. In this work, a grid-based method for these calculations is described. The library, implemented for three dimensions, is based on a multidimensional Lagrange interpolation in a regular grid; by differentiating the resulting polynomial, the gradient vector, the Hessian matrix and the Laplacian formulas were obtained for every space point. More complex functions such as the Newton-Raphson method (to find the critical points, where the gradient is null) and the Cash-Karp Runge-Kutta method (used to make the gradient paths) were programmed. As in some crystals, the unit cell has angles different from 90°, the described library includes linear transformations to correct the gradient and Hessian when the grid is distorted (inclined). Functions were also developed to handle grid containing files (grd from DMol® program, CUBE from Gaussian® program and CHGCAR from VASP® program). Each one of these files contains the data for a molecular or crystal electronic property (such as charge density, spin density, electrostatic potential, and others) in a three-dimensional (3D) grid. The library can be adapted to make the topological study in any regular 3D grid by modifying the code of these functions. Copyright © 2012 Wiley Periodicals, Inc.

Long-read whole genome sequencing and comparative analysis of six strains of the human pathogen Orientia tsutsugamushi.

PubMed

Batty, Elizabeth M; Chaemchuen, Suwittra; Blacksell, Stuart; Richards, Allen L; Paris, Daniel; Bowden, Rory; Chan, Caroline; Lachumanan, Ramkumar; Day, Nicholas; Donnelly, Peter; Chen, Swaine; Salje, Jeanne

2018-06-01

Orientia tsutsugamushi is a clinically important but neglected obligate intracellular bacterial pathogen of the Rickettsiaceae family that causes the potentially life-threatening human disease scrub typhus. In contrast to the genome reduction seen in many obligate intracellular bacteria, early genetic studies of Orientia have revealed one of the most repetitive bacterial genomes sequenced to date. The dramatic expansion of mobile elements has hampered efforts to generate complete genome sequences using short read sequencing methodologies, and consequently there have been few studies of the comparative genomics of this neglected species. We report new high-quality genomes of O. tsutsugamushi, generated using PacBio single molecule long read sequencing, for six strains: Karp, Kato, Gilliam, TA686, UT76 and UT176. In comparative genomics analyses of these strains together with existing reference genomes from Ikeda and Boryong strains, we identify a relatively small core genome of 657 genes, grouped into core gene islands and separated by repeat regions, and use the core genes to infer the first whole-genome phylogeny of Orientia. Complete assemblies of multiple Orientia genomes verify initial suggestions that these are remarkable organisms. They have larger genomes compared with most other Rickettsiaceae, with widespread amplification of repeat elements and massive chromosomal rearrangements between strains. At the gene level, Orientia has a relatively small set of universally conserved genes, similar to other obligate intracellular bacteria, and the relative expansion in genome size can be accounted for by gene duplication and repeat amplification. Our study demonstrates the utility of long read sequencing to investigate complex bacterial genomes and characterise genomic variation.

Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis

PubMed Central

2012-01-01

Background Chaos Game Representation (CGR) is an iterated function that bijectively maps discrete sequences into a continuous domain. As a result, discrete sequences can be object of statistical and topological analyses otherwise reserved to numerical systems. Characteristically, CGR coordinates of substrings sharing an L-long suffix will be located within 2-L distance of each other. In the two decades since its original proposal, CGR has been generalized beyond its original focus on genomic sequences and has been successfully applied to a wide range of problems in bioinformatics. This report explores the possibility that it can be further extended to approach algorithms that rely on discrete, graph-based representations. Results The exploratory analysis described here consisted of selecting foundational string problems and refactoring them using CGR-based algorithms. We found that CGR can take the role of suffix trees and emulate sophisticated string algorithms, efficiently solving exact and approximate string matching problems such as finding all palindromes and tandem repeats, and matching with mismatches. The common feature of these problems is that they use longest common extension (LCE) queries as subtasks of their procedures, which we show to have a constant time solution with CGR. Additionally, we show that CGR can be used as a rolling hash function within the Rabin-Karp algorithm. Conclusions The analysis of biological sequences relies on algorithmic foundations facing mounting challenges, both logistic (performance) and analytical (lack of unifying mathematical framework). CGR is found to provide the latter and to promise the former: graph-based data structures for sequence analysis operations are entailed by numerical-based data structures produced by CGR maps, providing a unifying analytical framework for a diversity of pattern matching problems. PMID:22551152

Accelerating moderately stiff chemical kinetics in reactive-flow simulations using GPUs

NASA Astrophysics Data System (ADS)

Niemeyer, Kyle E.; Sung, Chih-Jen

2014-01-01

The chemical kinetics ODEs arising from operator-split reactive-flow simulations were solved on GPUs using explicit integration algorithms. Nonstiff chemical kinetics of a hydrogen oxidation mechanism (9 species and 38 irreversible reactions) were computed using the explicit fifth-order Runge-Kutta-Cash-Karp method, and the GPU-accelerated version performed faster than single- and six-core CPU versions by factors of 126 and 25, respectively, for 524,288 ODEs. Moderately stiff kinetics, represented with mechanisms for hydrogen/carbon-monoxide (13 species and 54 irreversible reactions) and methane (53 species and 634 irreversible reactions) oxidation, were computed using the stabilized explicit second-order Runge-Kutta-Chebyshev (RKC) algorithm. The GPU-based RKC implementation demonstrated an increase in performance of nearly 59 and 10 times, for problem sizes consisting of 262,144 ODEs and larger, than the single- and six-core CPU-based RKC algorithms using the hydrogen/carbon-monoxide mechanism. With the methane mechanism, RKC-GPU performed more than 65 and 11 times faster, for problem sizes consisting of 131,072 ODEs and larger, than the single- and six-core RKC-CPU versions, and up to 57 times faster than the six-core CPU-based implicit VODE algorithm on 65,536 ODEs. In the presence of more severe stiffness, such as ethylene oxidation (111 species and 1566 irreversible reactions), RKC-GPU performed more than 17 times faster than RKC-CPU on six cores for 32,768 ODEs and larger, and at best 4.5 times faster than VODE on six CPU cores for 65,536 ODEs. With a larger time step size, RKC-GPU performed at best 2.5 times slower than six-core VODE for 8192 ODEs and larger. Therefore, the need for developing new strategies for integrating stiff chemistry on GPUs was discussed.

Optimal Cutoff and Accuracy of an IgM Enzyme-Linked Immunosorbent Assay for Diagnosis of Acute Scrub Typhus in Northern Thailand: an Alternative Reference Method to the IgM Immunofluorescence Assay

PubMed Central

Blacksell, Stuart D.; Tanganuchitcharnchai, Ampai; Jintaworn, Suthatip; Kantipong, Pacharee; Richards, Allen L.; Day, Nicholas P. J.

2016-01-01

The enzyme-linked immunosorbent assay (ELISA) has been proposed as an alternative serologic diagnostic test to the indirect immunofluorescence assay (IFA) for scrub typhus. Here, we systematically determine the optimal sample dilution and cutoff optical density (OD) and estimate the accuracy of IgM ELISA using Bayesian latent class models (LCMs). Data from 135 patients with undifferentiated fever were reevaluated using Bayesian LCMs. Every patient was evaluated for the presence of an eschar and tested with a blood culture for Orientia tsutsugamushi, three different PCR assays, and an IgM IFA. The IgM ELISA was performed for every sample at sample dilutions from 1:100 to 1:102,400 using crude whole-cell antigens of the Karp, Kato, and Gilliam strains of O. tsutsugamushi developed by the Naval Medical Research Center. We used Bayesian LCMs to generate unbiased receiver operating characteristic curves and found that the sample dilution of 1:400 was optimal for the IgM ELISA. With the optimal cutoff OD of 1.474 at a sample dilution of 1:400, the IgM ELISA had a sensitivity of 85.7% (95% credible interval [CrI], 77.4% to 86.7%) and a specificity of 98.1% (95% CrI, 97.2% to 100%) using paired samples. For the ELISA, the OD could be determined objectively and quickly, in contrast to the reading of IFA slides, which was both subjective and labor-intensive. The IgM ELISA for scrub typhus has high diagnostic accuracy and is less subjective than the IgM IFA. We suggest that the IgM ELISA may be used as an alternative reference test to the IgM IFA for the serological diagnosis of scrub typhus. PMID:27008880

Differential Association of the Na+/H+ Exchanger Regulatory Factor (NHERF) Family of Adaptor Proteins with the Raft-and the Non-Raft Brush Border Membrane Fractions of NHE3

PubMed Central

Sultan, Ayesha; Luo, Min; Yu, Qin; Riederer, Brigitte; Xia, Weiliang; Chen, Mingmin; Lissner, Simone; Gessner, Johannes E.; Donowitz, Mark; Yun, C. Chris; deJonge, Hugo; Lamprecht, Georg; Seidler, Ursula

2014-01-01

Background/Aims Trafficking, brush border membrane (BBM) retention, and signal-specific regulation of the Na+/H+ exchanger NHE3 is regulated by the Na+/H+ Exchanger Regulatory Factor (NHERF) family of PDZ-adaptor proteins, which enable the formation of multiprotein complexes. It is unclear, however, what determines signal specificity of these NHERFs. Thus, we studied the association of NHE3, NHERF1 (EBP50), NHERF2 (E3KARP), and NHERF3 (PDZK1) with lipid rafts in murine small intestinal BBM. Methods Detergent resistant membranes (“lipid rafts”) were isolated by floatation of Triton X-incubated small intestinal BBM from a variety of knockout mouse strains in an Optiprep step gradient. Acid-activated NHE3 activity was measured fluorometrically in BCECF-loaded microdissected villi, or by assessment of CO2/HCO3− mediated increase in fluid absorption in perfused jejunal loops of anethetized mice. Results NHE3 was found to partially associate with lipid rafts in the native BBM, and NHE3 raft association had an impact on NHE3 transport activity and regulation in vivo. NHERF1, 2 and 3 were differentially distributed to rafts and non-rafts, with NHERF2 being most raft-associated and NHERF3 entirely non-raft associated. NHERF2 expression enhanced the localization of NHE3 to membrane rafts. The use of acid sphingomyelinase-deficient mice, which have altered membrane lipid as well as lipid raft composition, allowed us to test the validity of the lipid raft concept in vivo. Conclusions The differential association of the NHERFs with the raft-associated and the non-raft fraction of NHE3 in the brush border membrane is one component of the differential and signal-specific NHE3 regulation by the different NHERFs. PMID:24297041

Differential association of the Na+/H+ Exchanger Regulatory Factor (NHERF) family of adaptor proteins with the raft- and the non-raft brush border membrane fractions of NHE3.

PubMed

Sultan, Ayesha; Luo, Min; Yu, Qin; Riederer, Brigitte; Xia, Weiliang; Chen, Mingmin; Lissner, Simone; Gessner, Johannes E; Donowitz, Mark; Yun, C Chris; deJonge, Hugo; Lamprecht, Georg; Seidler, Ursula

2013-01-01

Trafficking, brush border membrane (BBM) retention, and signal-specific regulation of the Na+/H+ exchanger NHE3 is regulated by the Na+/H+ Exchanger Regulatory Factor (NHERF) family of PDZ-adaptor proteins, which enable the formation of multiprotein complexes. It is unclear, however, what determines signal specificity of these NHERFs. Thus, we studied the association of NHE3, NHERF1 (EBP50), NHERF2 (E3KARP), and NHERF3 (PDZK1) with lipid rafts in murine small intestinal BBM. Detergent resistant membranes ("lipid rafts") were isolated by floatation of Triton X-incubated small intestinal BBM from a variety of knockout mouse strains in an Optiprep step gradient. Acid-activated NHE3 activity was measured fluorometrically in BCECF-loaded microdissected villi, or by assessment of CO2/HCO3(-) mediated increase in fluid absorption in perfused jejunal loops of anethetized mice. NHE3 was found to partially associate with lipid rafts in the native BBM, and NHE3 raft association had an impact on NHE3 transport activity and regulation in vivo. NHERF1, 2 and 3 were differentially distributed to rafts and non-rafts, with NHERF2 being most raft-associated and NHERF3 entirely non-raft associated. NHERF2 expression enhanced the localization of NHE3 to membrane rafts. The use of acid sphingomyelinase-deficient mice, which have altered membrane lipid as well as lipid raft composition, allowed us to test the validity of the lipid raft concept in vivo. The differential association of the NHERFs with the raft-associated and the non-raft fraction of NHE3 in the brush border membrane is one component of the differential and signal-specific NHE3 regulation by the different NHERFs. © 2013 S. Karger AG, Basel.

New Genotypes of Orientia tsutsugamushi Isolated from Humans in Eastern Taiwan

PubMed Central

Lin, Chin-Hui; Chen, Tren-Yi; Chen, Li-Kuang

2012-01-01

Scrub typhus, an acute febrile illness, is caused by the obligate intracellular bacterium Orientia tsutsugamushi. In our study, O. tsutsugamushi was rapidly detected and typed by polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis of the 56-kDa type-specific antigen (TSA) gene. To investigate the genotypes of clinical variants of O. tsutsugamushi, we collected 3223 blood samples from eastern Taiwanese patients with suspected scrub typhus from 2002 to 2008. In total, 505 samples were found to be positive for scrub typhus infection by PCR, and bacteria were isolated from 282 of them. Four prototype genotype strains (Karp, Kato, Kawasaki and Gilliam) and eleven different Taiwanese genotype isolates (Taiwan-A, -B, -C, -D, -E, -G, -H, -J, -N, -O and -P) were identified by RPLF analysis. Taiwan-H, the major genotype in eastern Taiwan, exhibited prevalence and isolation rates of 47.3% (239/505) and 42.6% (120/282), respectively. We also assessed the genetic relatedness of the 56-kDa TSA gene among eight Taiwan-H isolates, thirteen other Taiwanese isolates and 104 DNA sequences deposited in the GenBank database using MEGA version 5.0 and PHYLIP version 3.66. We found that the Taiwan-H isolates formed into a new cluster, which was designated the Taiwan Gilliam-variant (TG-v) cluster to distinguish it from the Japanese Gilliam-variant (JG-v) cluster. According to Simplot analysis, TG-v is a new recombinant strain among Gilliam, Ikeda and Kato. Moreover, the Gilliam-Kawasaki cluster had the highest percentage of RFLP cases and was the most frequently isolated type in eastern Taiwan (50.1%, 253/505; 44.0%, 124/282). These findings shed light on the genetic evolution of O. tsutsugamushi into different strains and may be useful in vaccine development and epidemic disease control in the future. PMID:23071693

Warm-up Optimizes Postural Control but Requires Some Minutes of Recovery.

PubMed

Paillard, Thierry; Kadri, Mohamed Abdelhafid; Nouar, Merbouha Boulahbel; Noé, Frederic

2018-05-02

Paillard, T, Kadri, MA, Nouar, MB, and Noé, F. Warm-up optimizes postural control but requires some minutes of recovery. J Strength Cond Res XX(X): 000-000, 2018-The aim was to compare monopedal postural control between the dominant leg (D-Leg) and the nondominant leg (ND-Leg) in pre- and post-warm-up conditions. Thirty healthy male sports science students were evaluated before and after a warm-up exercise (12 minutes of pedaling with an incremental effort on a cycle ergometer with a controlled workload). Monopodal postural control was assessed for the D- and ND-Legs before and immediately, 2, 5, 10, and 15 minutes after the warm-up exercise, using a force platform and calculating the displacement velocity of the center of foot pressure on the mediolateral (COPML velocity) and anteroposterior (COPAP velocity) axes. No significant difference was observed between the D-Leg and ND-Leg for both COPML and COPAP velocity in all the periods. In comparison with pre-warm-up, COPML decreased after 15-minute and 10-minute recovery periods for the D-Leg and the ND-Leg, respectively (p < 0.05), whereas COPAP decreased after 10-minute and 15-minute recovery periods (p < 0.001; p < 0.01, respectively) for the D-Leg, and after a 10-minute recovery period for the ND-Leg (p < 0.001). The warm-up optimized monopedal postural control but did not make it possible to distinguish a difference between the D-Leg and the ND-Leg. Some minutes of recovery are required between the end of the whole-body warm-up exercise and the beginning of the postural test to optimize postural control. The optimal duration of recovery turns out to be about 10-15 minutes.

Comparison of the Ultrastructure of Several Rickettsiae, Ornithosis Virus, and Mycoplasma in Tissue Culture

PubMed Central

Anderson, Douglas R.; Hopps, Hope E.; Barile, Michael F.; Bernheim, Barbara C.

1965-01-01

Anderson, Douglas R. (National Cancer Institute, Bethesda, Md.), Hope E. Hopps, Michael F. Barile, and Barbara C. Bernheim. Comparison of the ultrastructure of several rickettsiae, ornithosis virus, and Mycoplasma in tissue culture. J. Bacteriol. 90:1387–1404. 1965.—In an effort to make a valid comparison of the ultrastructure of several intracellular parasites, selected agents were propagated under identical conditions in a single type of tissue culture cell; such infected preparations were processed for examination by electron microscopy by use of a standardized procedure for fixation and embedding. The organisms studied were: the Breinl and E strains of epidemic typhus, Rickettsia prowazeki; the Bitterroot strain of R. rickettsii; the Karp strain of R. tsutsugamushi (R. orientalis); R. sennetsu; the P-4 strain of ornithosis virus; and the HEp-2 strain of Mycoplasma hominis type I. Each of the rickettsial species examined had a cell wall and a plasma membrane, and contained ribosomes and deoxyribonucleic acid (DNA) in a ground substance. However, certain differences were noted. Both strains of R. prowazeki contained numerous intracytoplasmic electron-lucent spherical structures (4 to 10 mμ), not previously described. R. sennetsu, unlike the other rickettsiae, was not free in the host cytoplasm but was always enclosed in a vacuole. R. rickettsii was observed intranuclearly and in digestive organelles of the host cell as well as in the cytoplasm. Cells infected with ornithosis virus contained several forms representing the stages in its life cycle. The “initial bodies,” made up of ribosomes and DNA strands, were morphologically similar to the rickettsiae. In cultures infected with M. hominis, most of the cells became large and multinucleate. Although the Mycoplasma organisms were readily cultivated from these cultures, only a few could be found in the electron microscope preparations. These organisms were extracellular and lacked a cell wall, being bound

"European" race-specific metacentrics in East Siberian common shrews (Sorex araneus): a description of two new chromosomal races, Irkutsk and Zima.

PubMed

Pavlova, Svetlana V; Borisov, Sergei A; Timoshenko, Alexander F; Sheftel, Boris I

2017-01-01

Karyotype studies of common shrews in the vicinity of Lake Baikal (Irkutsk Region, Eastern Siberia) resulted in the description of two new chromosomal races of Sorex araneus Linnaeus, 1758 (Lypotyphla, Mammalia), additional to 5 races formerly found in Siberia. In the karyotypes of 12 specimens from 3 locations, the polymorphism of metacentric and acrocentric chromosomes of the Robertsonian type was recorded and two distinct groups of karyotypes interpreted as the chromosomal races were revealed. They are geographically distant and described under the racial names Irkutsk (Ir) and Zima (Zi). Karyotypes of both races were characterized by species-specific (the same for all 74 races known so far) metacentric autosomes af, bc, tu and jl , and the typical sex chromosome system - XX/XY 1 Y 2 . The race-specific arm chromosome combinations include three metacentrics and four acrocentrics in the Irkutsk race ( gk, hi, nq, m, o, p, r ) and four metacentrics and two acrocentrics in the Zima race ( gm, hi, ko, nq, p, r ). Within the races, individuals with polymorphic chromosomes were detected ( g/m, k/o, n/q, p/r ). The presence of the specific metacentric gk allowed us to include the Irkutsk race into the Siberian Karyotypic Group (SKG), distributed in surrounding regions. The Zima race karyotype contained two metacentrics, gm and ko , which have been never found in the Siberian part of the species range, but appear as the common feature of chromosomal races belonging to the West European Karyotypic Group (WEKG). Moreover, the metacentrics of that karyotype are almost identical to the Åkarp race (except the heterozygous pair p/r ) locally found in the southern Sweden. One of two Siberian races described here for the first time, the Zima race, occurs in an area considerably distant from Europe and shares the common metacentrics ( gm, hi, ko ) with races included in WEKG. This fact may support a hypothesis of independent formation of identical arm chromosome combinations

Detection of Orientia tsutsugamushi (Rickettsiales: rickettsiaceae) in unengorged chiggers (Acari: Trombiculidae) from Oita Prefecture, Japan, by nested polymerase chain reaction.

PubMed

Pham, X D; Otsuka, Y; Suzuki, H; Takaoka, H

2001-03-01

The current study surveyed the 56-kDa type-specific antigen (TSA) gene DNAs of Orientia tsutsugamushi (Hayashi) in approximately 4.000 unengorged chiggers obtained from the soil or ground surface in an endemic and a nonendemic area of the Tsutsugamushi disease in Oita Prefecture, southwestern Japan, by nested polymerase chain reaction (PCR). Serotypes of O. tsutsugamushi were identified by restriction fragment-length polymorphism (RFLP) analysis. In the endemic area, 242 pools from five species [234 pools of Leptotrombidium scutellare (Nagayo, Miyagawa, Mitamura, Tamiya and Tenjin), two L. pallidum (Nagayo, Miyagawa, Mitamura and Tamiya), four L. kitasatoi (Fukuzumi & Obata), one L. fuji (Kuwata, Berge and Philip), and one Neotrombicula japonica (Tanaka, Kaiwa, Teramura and Kagaya)] were tested, and eight (seven pools of L. scutellare and one N. japonica) were positive for O. tsutsugamushi. Among the seven positive pools of L. scutellare, the distribution of serotypes was as follows: Kuroki (4), Gilliam (1), Karp (1), and Kawasaki (1). The first two serotypes (Kuroki and Gilliam) were identified for the first time in this species. In the nonendemic area, 128 pools from eight species were tested, and 13 were positive for O. tsutsugamushi. The positive rate was as follows: L. pallidum (4/41). L. kitasatoi (1/18), Gahrliepia saduski Womersley (2/10), L. fuji (4/50), L. himizu (Sasa, Kumada, Hayashi, Enomoto, Fukuzumi and Obata) (1/2), and Miyatrombicula kochiensis (Sasa, Kawashima and Egashira) (1/3). The latter three species were shown for the first time to harbor O. tsutsugamushi. All ofthe positive pools were Kuroki, except for two pools (one L. pallidum and one L. fuji), which were Gilliam (this serotype was also detected for the first time in L. pallidum). Further analysis revealed no differences in the nucleotide sequences (125 bp of variable domain 1 of TSA gene) of the same serotypes (i.e., Kuroki and Gilliam) among the positive samples. These data indicate

Triad Resonance in the Gravity-Acoustic Family

NASA Astrophysics Data System (ADS)

Kadri, U.

2015-12-01

Resonance interactions of waves play a prominent role in energy share among the different wave types involved. Such interactions may significantly contribute, among others, to the evolution of the ocean energy spectrum by exchanging energy between surface-gravity waves; surface and internal gravity waves; or even surface and compression-type waves, that can transfer energy from the upper ocean through the whole water column reaching down to the seafloor. A resonant triad occurs among a triplet of waves, usually involving interaction of nonlinear terms of second order perturbed equations. Until recently, it has been believed that in a homogeneous fluid a resonant triad is possible only when tension forces are included, or at the limit of a shallow water, and that when the compressibility of water is considered, no resonant triads can occur within the family of gravity-acoustic waves. However, more recently it has been proved that, under some circumstances, resonant triads comprising two opposing surface-gravity waves of similar periods (though not identical) and a much longer acoustic-gravity wave, of almost double the frequency, exist [Kadri and Stiassnie 2013, J. Fluid Mech.735 R6]. Here, I report on a new resonant triad involving a gravity wave and two acoustic waves of almost double the length. Interestingly, the two acoustic waves propagate in the same direction with similar wavelengths, that are almost double of that of the gravity wave. The evolution of the wave triad amplitudes is periodic and it is derived analytically, in terms of Jacobian elliptic functions and elliptic integrals. The physical importance of this type of triad interactions is the modulation of pertinent acoustic signals, leading to inaccurate signal perceptions. Enclosed figure: presents an example spatio-temporal evolution of the wave triad amplitudes. The gravity wave (top) remains almost unaltered, while the envelope slowly displaces to the left. However, the prescribed acoustic

Strong interferon-gamma mediated cellular immunity to scrub typhus demonstrated using a novel whole cell antigen ELISpot assay in rhesus macaques and humans.

PubMed

Sumonwiriya, Manutsanun; Paris, Daniel H; Sunyakumthorn, Piyanate; Anantatat, Tippawan; Jenjaroen, Kemajittra; Chumseng, Suchintana; Im-Erbsin, Rawiwan; Tanganuchitcharnchai, Ampai; Jintaworn, Suthatip; Blacksell, Stuart D; Chowdhury, Fazle R; Kronsteiner, Barbara; Teparrukkul, Prapit; Burke, Robin L; Lombardini, Eric D; Richards, Allen L; Mason, Carl J; Jones, James W; Day, Nicholas P J; Dunachie, Susanna J

2017-09-01

Scrub typhus is a febrile infection caused by the obligate intracellular bacterium Orientia tsutsugamushi, which causes significant morbidity and mortality across the Asia-Pacific region. The control of this vector-borne disease is challenging due to humans being dead-end hosts, vertical maintenance of the pathogen in the vector itself, and a potentially large rodent reservoir of unclear significance, coupled with a lack of accurate diagnostic tests. Development of an effective vaccine is highly desirable. This however requires better characterization of the natural immune response of this neglected but important disease. Here we implement a novel IFN-γ ELISpot assay as a tool for studying O. tsutsugamushi induced cellular immune responses in an experimental scrub typhus rhesus macaque model and human populations. Whole cell antigen for O. tsutsugamushi (OT-WCA) was prepared by heat inactivation of Karp-strain bacteria. Rhesus macaques were infected intradermally with O. tsutsugamushi. Freshly isolated peripheral blood mononuclear cells (PBMC) from infected (n = 10) and uninfected animals (n = 5) were stimulated with OT-WCA, and IFN-γ secreting cells quantitated by ELISpot assay at five time points over 28 days. PBMC were then assayed from people in a scrub typhus-endemic region of Thailand (n = 105) and responses compared to those from a partially exposed population in a non-endemic region (n = 14), and to a naïve population in UK (n = 12). Mean results at Day 0 prior to O. tsutsugamushi infection were 12 (95% CI 0-25) and 15 (2-27) spot-forming cells (SFC)/106 PBMC for infected and control macaques respectively. Strong O. tsutsugamushi-specific IFN-γ responses were seen post infection, with ELISpot responses 20-fold higher than baseline at Day 7 (mean 235, 95% CI 200-270 SFC/106 PBMC), 105-fold higher at Day 14 (mean 1261, 95% CI 1,097-1,425 SFC/106 PBMC), 125-fold higher at Day 21 (mean 1,498, 95% CI 1,496-1,500 SFC/106 PBMC) and 118-fold higher at Day 28

Algorithms in Discrepancy Theory and Lattices

NASA Astrophysics Data System (ADS)

Ramadas, Harishchandra

n). Finding the minimum, however, is NP-hard. In polynomial time, the differencing algorithm by Karmarkar and Karp from 1982 can produce a solution with difference at most n-theta(log n), but no further improvement has been made since then. We show a relationship between NBP and Minkowski's Theorem. First we show that an approximate oracle for Minkowski's Theorem gives an approximate NBP oracle. Perhaps more surprisingly, we show that an approximate NBP oracle gives an approximate Minkowski oracle. In particular, we prove that any polynomial time algorithm that guarantees a solution of difference at most 2√n/2 n would give a polynomial approximation for Minkowski as well as a polynomial factor approximation algorithm for the Shortest Vector Problem.

Bin Packing, Number Balancing, and Rescaling Linear Programs

NASA Astrophysics Data System (ADS)

Hoberg, Rebecca

is the problem of minimizing | 〈a,x〉 | over x ∈ {-1,0,1}n \\ { 0}, given a ∈ [0,1]n. While an application of the pigeonhole principle shows that there always exists x with | 〈a,x〉| ≤ O(√ n/2n), the best known algorithm only guarantees |〈a,x〉| ≤ 2-ntheta(log n). We show that an oracle for Minkowski's Theorem with approximation factor rho would give an algorithm for NBP that guarantees | 〈a,x〉 | ≤ 2-ntheta(1/rho). In particular, this would beat the bound of Karmarkar and Karp provided rho ≤ O(logn/loglogn). In the other direction, we prove that any polynomial time algorithm for NBP that guarantees a solution of difference at most 2√n/2 n would give a polynomial approximation for Minkowski as well as a polynomial factor approximation algorithm for the Shortest Vector Problem.

Final Technical Report for Project "Improving the Simulation of Arctic Clouds in CCSM3"

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

Stephen J. Vavrus

2008-11-15

greenhouse warming and the extent to which models adequately represent Arctic clouds in the modern climate. This site was used extensively in the IARC summer school projects. This work has also led to a collaboration this year during a 4-month visit I made to NCAR through its Faculty Fellowship Program. I worked with scientists Marika Holland, David Bailey, Andrew Gettleman, and Jen Kay, who are researching polar climate and/or clouds. I met with this group frequently during my visit, leading to some fruitful interactions. This work led to the discovery of a tightly coupled response of clouds and sea ice during intervals of rapid sea ice loss in greenhouse simulations, as well as advising on the evolving CCSM3.5 to CCSM4 model development. This involvement with NCAR also led to a longer-term connection, as I have recently begun a two-year stint on the SSC for CCSM.« less

Thymic commitment of regulatory T cells is a pathway of TCR-dependent selection that isolates repertoires undergoing positive or negative selection.

PubMed

Coutinho, A; Caramalho, I; Seixas, E; Demengeot, J

2005-01-01

. 2001). In turn, such natural regulation of Treg by immune responses to non-self may well explain the alarming epidemiology of allergic and AID in wealthy societies (Wills-Karp et al. 2001; Bach 2002; Yazdanbakhsh et al. 2002), where a variety of childhood infections have become rare or absent. Thus, it is plausible that Treg were evolutionarily set by a given density of infectious agents in the environment. With hindsight, it is not too surprising that natural Treg performance falls once hygiene, vaccination, and antibiotics suddenly (i.e., 100 years) plunged infectious density to below some critical physiological threshold. As the immune system is not adapted to modern clean conditions of postnatal development, clinical immunologists must now deal with frequent Treg deficiencies (allergies and AID) for which they have no curative or rational treatments. It is essential, therefore, that basic immunologists concentrate on strategies to selectively stimulate the production, survival, and activity of this set of lymphocytes that is instrumental in preventing immune pathology. We have argued that the culprit of this inability of basic research to solve major clinical problems has been the self-righteousness of recessive tolerance champions, from Ehrlich to some of our contemporaries. It is ironical, however, that none of us--including the heretic opponents of horror autotoxicus--had understood that self-tolerance, or its robustness at least, is in part determined by the frequency and intensity of the responses to non-self. In the evolution of ideas on immunological tolerance, the time might be ripe for some kinds of synthesis. First, conventional theory reduced self-tolerance to negative selection and microbial defense to positive selection, while the MM96 solution was the precise opposite: positive selection of autoreactivities for self-tolerance (Treg) and negative selection (of Treg) for ridding responses. In contrast, it would now appear that positive and negative