bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of NBS Coal Standard Reference Materials 1632a and 1635 by Instrumental Neutron Activation Analysis
Authors: KENDRICK D.T. , KYLE P.R. , KUELLMER F.J.
Published: May 2007

NBS SRM 1635 and NBS SRM 1632a were analyzed for trace and minor element contents by instrumental neutron activation analysis. The results of these analyses show excellent agreement with NBS certified values and/or literature values.
DETERMINATION OF BROMINE AND IODINE IN FOUR MARINE SEDIMENT REFERENCE SAMPLES BY ENERGY‐DISPERSIVE X‐RAY FLUORESCENCE SPECTROMETRY
Authors: DOFF David H.
Published: May 2007

The concentrations of bromine and iodine in the USGS marine mud MAG‐1, the NRCC marine sediments BCSS‐1 and MESS‐1, and the NBS estuarine sediment SRM 1646 have been determined by energy‐dispersive x‐ray fluorescence spectrometry. Matrix and intermediate thickness effects were overcome by standard additions to constant weights of each sample. 3‐sigma detection limits are 6 ppm Br and 24 ppm I. There is a need for many more analysts to report their results before “usable values’can be established for these elements in marine sediment reference malterials.
A SENSITIVE AUTOMATED METHOD FOR DETERMINATION OF MERCURY IN GEOLOGICAL MATERIALS BY COLD VAPOR ATOMIC ABSORPTION
Authors: CHAN Chris C.Y. , BINA Sasan
Published: May 2007

An improved sensitive automated method for the determination of mercury in geological materials by cold vapor atomic absorption has been developed. Sample is digested with nitric and hydrochloric acids at low heat. Mercuric ions in the digested sample solution are reduced to elemental mercury by stannous chloride. The gaseous mercury separated from the solution is swept by a stream of argon into the absorption cell of an LDC/Milton Roy Mercury Monitor where the atomic absorption at 253.7 nm is measured. The precision of the method is 2.7% r.s.d., and the detection limit is 1 ppb. The results on 53 international geochemical reference samples are presented.
1988 Compilation of Elemental Concentration Data for CCRMP Soils SO‐1 to SO‐4
Authors: GLADNEY Ernest S. , ROELANDTS Iwan
Published: May 2007

Concentration data on 74 individual constituents in CCRMP (Canadian Certified Reference Materials Project) soils SO‐1, SO‐2, SO‐3, and SO‐4 have been collected from 83 journal articles and technical reports. These data are summarized in consensus (mean) values with uncertainties expressed as one standard deviation. Mean values are also calculated as a function of analytical procedure and all raw data are given in the tables. Recommended values are proposed based upon data criteria used by NIST (National Institute of Standards and Technology, formerly the National Bureau of Standards or NBS).
Inductively Coupled Plasma Determination Of Nine Rare‐Earth Elements In Sixty International Geochemical Reference Samples
Authors: ROELANDTS Iwan
Published: May 2007

Data for nine rare‐earth elements (REE) determined by inductively coupled plasma spectrometry (ICP‐AES) in sixty international geochemical reference samples (igneous and sedimentary rocks, soils and sediments) are presented. The method is based on acid digestion of the sample and cation‐exchange separation from matrix elements. Good agreement is generally achieved between the results of this work and the recent compilation values. The present paper includes analytical data on several reference materials for which existing data are rather scarce or even inexistent
Germanium Contents of Selected International Geostandards by Hydride Generation and ICP‐AES.
Authors: HALICZ Ludwik
Published: May 2007

Germanium in thirty‐four SRM's was determined by hydride generation and ICP‐AES after separation of germanium from the concomitant matrix into carbon tetrachloride, and finally back‐extraction into water. This procedure permits the determination of 0.1 ppm of germanium in as small as 50 mg sample. The precision and accuracy of the method was established using Basalt BCR‐1 as the most precisely determined standard available.
Instrumental Neutron Activation Analysis by Collecting Only One Spectrum: Results For International Geochemical Reference Samples
Authors: BEDARD L. Paul , BARNES Sarah‐Jane
Published: May 2007

Instrumental neutron activation analysis of rocks and minerals is currently done on basis of collecting 2 or 3 energy spectra. We have found that, by collecting one spectrum one week after irradiation, satisfactory results for the USGS and CRPG geochemical reference samples can be obtained.
Analysis of Sulfides for Gold and Associated Trace Metals by Direct Neutron Activation With a Low‐Flux Reactor
Authors: HANNINGTON M.D. , GORTON M.P.
Published: May 2007

A routine method for the direct determination of Au and associated trace metals in sulfides has been developed for use with a low‐flux nuclear reactor (SLOWPOKE II Reactor Facility, University of Toronto). Small samples (100–200 mg) are analysed simultaneously for Au, Ag, As, Sb, Mo, Co, Se, Cd, Fe, and Zn. Sulfides containing finely divided gold can be analysed with a high degree of precision and yield results which agree closely with commercial fire assay‐atomic absorption analyses for Au. Favourable comparisons with other analytical techniques (flameless atomic absorption and emission spectrometry) are also indicated for Ag, As, and Sb. Neutron activation has the advantage of providing precise and accurate results for these elements without chemical separation or preconcentration. Analyses of 10 sulfide‐bearing reference materials from CANMET, Ottawa are compared with published best values for selected trace metals including Au.
VANADIUM CONTENT OF TWENTY‐EIGHT GEOCHEMICAL REFERENCE MATERIALS DETERMINED BY A SPECTROPHOTOMETRIC PROCEDURE
Authors: REDDY G.R. , RAO B.L. , SARKAR R.C.
Published: May 2007

Vanadium in twenty‐eight international geostandards was determined spectrophotometrically after selectively extracting vanadium as its red NBPHA complex. In general, the results compare favorably with the published values.
DETERMINATION OF MINOR AND TRACE ELEMENTS IN FOUR CANADIAN IRON FORMATION STANDARD SAMPLES FER‐1, FER‐2, FER‐3 AND FER‐4 BY INAA AND ICP‐MS
Authors: DULSKI Peter
Published: May 2007

Analytical data on samples FeR‐1, FeR‐2, FeR‐3 and FeR‐4 obtained by instrumental neutron activation analysis and by inductively coupled plasma mass spectrometry are presented. The applied methods are described, and the analytical problems associated with their use are discussed. The accuracy of the two methods is demonstrated by comparing the results with the recommended values of the iron formation reference sample, IF‐G. For the four FeR samples a set of values summarizing all data obtained by the two analytical methods is also given.
INSTRUMENTAL NEUTRON ACTIVATION ANALYSIS OF TWO NEW GEOCHEMICAL REFERENCE SAMPLES: BOTTOM SILT FROM LAKE BAIKAL, BIL‐1 AND BROWN COAL ASH, ZUK‐1
Authors: BULNAYEV A.I. , VAKHROMEYEV G.S.
Published: May 2007

Instrumental neutron activation data on 19 trace elements in two new geostandards, Bottom Silt from Lake Baikal, BIL‐1 and Brown Coal Ash, ZUK‐1 are presented.
DETERMINATION OF THIRTY‐TWO MAJOR AND TRACE ELEMENTS IN THREE NIST SOIL SRMS USING ICP‐AES AND WDXRF
Authors: WILSON S.A. , BRIGGS P.H. , MEE J.S. , SIEMS D.F.
Published: May 2007

The National Institute for Standards and Technology (NIST) has recently released three soil standard reference materials that are uncontaminated (SRM 2709), moderately contaminated (SRM 2711), and highly contaminated (SRM 2710) with metals. The SRMs were analyzed at the U.S. Geological Survey (USGS) for thirty two major, minor and trace elements using a combination of wavelength dispersive X‐ray fluorescence spectroscopy (WDXRF) and inductively coupled plasma atomic emission spectroscopy (ICP‐AES). Good agreement is observed between NIST certified values and USGS results. The wide concentration ranges for most transition metals should make these SRMs useful in assessing the accuracy of methods used in geochemical exploration and environmental studies.
MAJOR, TRACE AND RARE‐EARTH ELEMENTS IN FOURTEEN GSJ REFERENCE SAMPLES. DETERMINATION BY X‐RAY FLUORESCENCE SPECTROMETRY AND INDUCTIVELY COUPLED PLASMA OPTICAL EMISSION SPECTROMETRY
Authors: GERMANIQUE Jean‐Claude
Published: May 2007

Major and trace elements have been determined by wavelength dispersive X‐ray fluorescence and by inductively coupled plasma optical emission spectroscopy (ICP‐OES), in the Geological Survey of Japan Igneous rock series, using a routine sample preparation technique including lithium borate fusion. Samples were analysed for 10 majors elements and the following trace elements: Ba, Co, Cr, Ga, Nb, Sc, Sr, V, Y, Zn and Zr. The rare‐earth elements were determined only by ICP‐OES following separation by ion exchange. In most cases, results compared well with published values.
Neutron Activation Analysis of Nine GSJ Sedimentary Rock Reference Samples
Authors: AOTA Naomi , MIYAMOTO Yutaka , KOSANDA Sakae , OURA Yasuji , OKUI Toshiyuki , SAKAMOTO Koh
Published: May 2007

Nine rock reference samples “Sedimentary rock series” issued by the Geological Survey of Japan (GSJ) were analysed for up to 31 elements by neutron activation analysis (NAA); 14MeV‐NAA for Si and Al, fission track method for U, radiochemical and instrumental NAA for rare‐earth elements, and instrumental NAA for the remaining elements, with reactor neutrons for the latter three. The present results are compared with reported values.
DETERMINATION OF MERCURY IN ONE HUNDRED AND EIGHTEEN GEOCHEMICAL REFERENCE SAMPLES BY COLD VAPOR ATOMIC ABSORPTION SPECTROMETRY
Authors: TERASHIMA Shigeru
Published: May 2007

The mercury content of 118 geochemical reference samples have been determined by combustion followed by cold vapor atomic absorption spectrometry. The negative interference from volatile halogen and sulfur was eliminated by a packing of sodium carbonate in the combustion tube and addition of magnesium oxide to the samples. A comparison with published data show clearly the need for much more data on most reference samples.
UMATILLA COLUMBIA RIVER BASALT UMAT‐1
Authors: HOOPER P.R. , REIDEL S.P. , JOHNSON D.M. , KNAACK C.M.
Published: May 2007

A preliminary report is presented on a basalt reference sample, Umatilla Columbia River Basalt, UMAT‐1. Prepared in over 100 kg by the Columbia River Basalt Group, UMAT‐1 was, initially, tested for its homogeneity by two US laboratories for major, minor and several trace elements; mean values of these two laboratories are presented. More recent data on 50 elements by a French laboratory attest to the excellent homogeneity of the sample. UMAT‐1 is now available for further studies.
1994 REPORT ON WHIN SILL DOLERITE WS‐E FROM ENGLAND AND PITSCURRIE MICROGABBRO PM‐S FROM SCOTLAND: ASSESSMENT BY ONE HUNDRED AND FOUR INTERNATIONAL LABORATORIES
Authors: GOVINDARAJU K. , POTTS Philip J. , WEBB Peter C. , WATSON John S.
Published: May 2007

This compilation report describes the field location, mineralogy, preparation and homogeneity testing of two new GIT‐IWG reference materials: Whin Sill dolerite (WS‐E) from England and Pitscurrie microgabbro (PM‐S) from Scotland. The elemental composition of these two new reference materials has been established by an international cooperative analysis programme involving participation by 104 laboratories. A full assessment of these analytical results is presented, from which working values have been derived for the major elements as well as for 45 trace elements in WS‐E and 44 trace elements in PM‐S. Furthermore, isotopic ratios are presented for both samples, particularly for 87Sr/86Sr and 143Nd/144Nd.
THREE NATURAL ZIRCON STANDARDS FOR U‐TH‐PB, LU‐HF, TRACE ELEMENT AND REE ANALYSES
Authors: WIEDENBECK M. , ALLÉ P. , CORFU F. , GRIFFIN W.L. , MEIER M. , OBERLI F. , QUADT A. VON , RODDICK J.C. , SPIEGEL W.
Published: May 2007

We report here the results of a study to develop natural zircon geochemical standards for calibrating the U‐(Th)‐Pb geochronometer and Hf isotopic analyses. Additional data were also collected for the major, minor and trace element contents of the three selected sample sets. A total of five large zircon grains (masses between 0.5 and 238 g) were selected for this study, representing three different suites of zircons with ages of 1065 Ma, 2.5 Ma and 0.9 Ma. Geochemical laboratories can obtain these materials by contacting Geostandards Newsletter.
ELEVEN GOLD GEOCHEMICAL REFERENCE SAMPLES (GAU 8–18)
Authors: YAN Mingcai , WANG Chunshu , CAO Qunxian , GU Tiexin , CHI Qinghua
Published: May 2007

Eleven gold geochemical reference samples, GAu 8–18, have been prepared by the Institute of Geophysical and Geochemical Exploration, People's Republic of China. The concentration range of gold in these samples is from 0.5 ng/g to 10 μg/g. Fifteen Chinese Institutes, experienced in gold analysis of geological samples, have participated in the certification procedure using seven reliable analytical methods.
ION EXCHANGE‐FLOW INJECTION SPECTROPHOTOMETRIC SIMULTANEOUS DETERMINATION OF TRACES OF BROMIDE AND IODIDE IN SOME CHINESE STANDARD SAMPLES
Authors: LIU Guojun , LI Jinxin , ZHAO Xiumei
Published: May 2007

An ion exchange flow injection method is presented for the simultaneous determination of bromide and iodide based on the catalytic reaction during the oxidation of Pyrocatechol Violet by hydrogen peroxide in strongly acid solution. Bromide and iodide in sample solutions are concentrated when they flow through the ion exchange column; they are removed and separated with sodium nitrate eluant flowing through the column, and are monitored spectrophotometrically at 555 nm. All possible anionic interferences were studied. The procedure has been applied successfully to the determination of bromide and iodide in some Chinese standard reference samples. The limits of detection are 0.2 ppm and 0.4 ppm of bromide and iodide respectively in soils and stream sediments.
PREPARATION OF THREE CHINESE CERTIFIED REFERENCE MATERIALS: PLASTIC CLAY, POTASSIUM FELDSPAR, SODA‐LIME‐SILICA GLASS
Authors: DUNZHONG Zhao , YIFEI Mei
Published: May 2007

The preparation and homogeneity study of three certified reference materials, Plastic Clay GBW 03115, Potassium Feldspar GBW 03116 and Soda‐Lime Silica Glass GBW 03117 are briefly presented. The recommended values with their uncertainties were assigned, after a cooperative study with 18 laboratories.
DISTRIBUTION OF CCRMP, NIST, AND USGS REFERENCE MATERIAL DATA IN THE LITERATURE (1950 ‐ 1989)
Authors: GLADNEY Ernest S. , ROELANDTS Iwan
Published: May 2007

Publication patterns of CCRMP, NIST, and USGS reference materials are traced over the past 40 years by literature source, analytical method employed, and constituents measured. This is the first update to our 1987 paper which covered the period 1951 ‐ 1985.
DETERMINATION OF RARE EARTH ELEMENTS IN SIXTEEN SILICATE REFERENCE SAMPLES BY ICP‐MS AFTER TM ADDITION AND ION EXCHANGE SEPARATION
Authors: BARRAT J.A. , KELLER F. , AMOSSÉ J. , TAYLOR R.N. , NESBITT R.W. , HIRATA T.
Published: May 2007

This study reports the results of thirteen rare earth elements (REE) in sixteen geochemical reference samples. The analytical procedure involved dissolution of a whole rock or mineral separate, spiking with Tm, and separation of the REE using a simple ion‐exchange chromatography procedure. The resulting REE solutions were analysed by ICP‐MS. The results are compared with literature values. The agreement between our data and recommended or ID‐TIMS values is very favorable. The precision of the technique is better than 5% (2) for all the REE.
DATABASE ON INTERNET FOR GEOLOGICAL SURVEY OF JAPAN GEOCHEMICAL REFERENCE SAMPLES
Authors: IMAI Noboru , SAKURAMACHI Hiroshi , TERASHIMA Shigeru , ITOH Shiro , ANDO Atsushi
Published: May 2007

A database on thirty‐one Geological Survey of Japan (GSJ) geochemical reference samples has been set up on Internet which allows the retrieval of recommended or preferable values, compiled data, location, sample preparation and other relevant information. The URL location on WWW server is: http://www.aist.go.jp./RIODB/geostand/welcome.html
Ontologies for Supporting Engineering Design Optimization
Authors: Witherell Paul , Krishnamurty Sundar , Grosse Ian R.
Published: May 2007

This paper presents an optimization ontology and its implementation into a prototype computational knowledge-based tool dubbed ONTOP (ontology for optimization). Salient feature of ONTOP include a knowledge base that incorporates both standardized optimization terminology, formal method definitions, and often unrecorded optimization details, such as any idealizations and assumptions that may be made when creating an optimization model, as well as the model developer’s rationale and justification behind these idealizations and assumptions. ONTOP was developed using Protégé, a Java-based, free open-source ontology development environment created by Stanford University. Two engineering design optimization case studies are presented. The first case study consists of the optimization of a structural beam element and demonstrates ONTOP’s ability to address the variations in an optimal solution that may arise when different techniques and approaches are used. A second case study, a more complex design problem that deals with the optimization of an impeller of a pediatric left ventricular heart assist device, demonstrates the wealth of knowledge ONTOP is able to capture. Together, these test beds help illustrate the potential value of an ontology in representing application-specific knowledge while facilitating both the sharing and exchanging of this knowledge in engineering design optimization.
Response to Comments on "Impacts of Biodiversity Loss on Ocean Ecosystem Services"
Authors: Worm Boris , Barbier Edward B. , Beaumont Nicola , Duffy J. Emmett , Folke Carl , Halpern Benjamin S. , Jackson Jeremy B. C. , Lotze Heike K. , Micheli Fiorenza , Palumbi Stephen R. , Sala Enric , Selkoe Kimberley A. , Stachowicz John J. , Watson Reg
Published: May 2007

We show that globally declining fisheries catch trends cannot be explained by random processes and are consistent with declining stock abundance trends. Future projections are inherently uncertain but may provide a benchmark against which to assess the effectiveness of conservation measures. Marine reserves and fisheries closures are among those measures and can be equally effective in tropical and temperate areas—but must be combined with catch-, effort-, and gear restrictions to meet global conservation objectives.
Comment on "Impacts of Biodiversity Loss on Ocean Ecosystem Services"
Authors: Hölker Franz , Beare Doug , Dörner Hendrik , di Natale Antonio , Rätz Hans-Joachim , Temming Axel , Casey John
Published: May 2007

Worm
et al
. (Research Articles, 3 November 2006, p. 787) investigated the importance of biodiversity to marine ecosystem services across temporal and spatial scales. In projecting the extent of future fisheries collapse, we argue that the authors inappropriately extrapolated beyond their available observations and used data on marine reserves and fishery closures that are not representative of global fisheries.
155,000 Years of West African Monsoon and Ocean Thermal Evolution
Authors: Weldeab Syee , Lea David W. , Schneider Ralph R. , Andersen Nils
Published: May 2007

A detailed reconstruction of West African monsoon hydrology over the past 155,000 years suggests a close linkage to northern high-latitude climate oscillations. Ba/Ca ratio and oxygen isotope composition of planktonic foraminifera in a marine sediment core from the Gulf of Guinea, in the eastern equatorial Atlantic (EEA), reveal centennial-scale variations of riverine freshwater input that are synchronous with northern high-latitude stadials and interstadials of the penultimate interglacial and the last deglaciation. EEA Mg/Ca-based sea surface temperatures (SSTs) were decoupled from northern high-latitude millennial-scale fluctuation and primarily responded to changes in atmospheric greenhouse gases and low-latitude solar insolation. The onset of enhanced monsoon precipitation lags behind the changes in EEA SSTs by up to 7000 years during glacial-interglacial transitions. This study demonstrates that the stadial-interstadial and deglacial climate instability of the northern high latitudes exerts dominant control on the West African monsoon dynamics through an atmospheric linkage.
Quantification of 1,3-β-
d
-Glucan Levels in Children: Preliminary Data for Diagnostic Use of the β-Glucan Assay in a Pediatric Setting
Authors: Smith P. Brian , Benjamin Daniel K. , Alexander Barbara D. , Johnson Melissa D. , Finkelman Malcolm A. , Steinbach William J.
Published: May 2007

1,3-β-
d
-Glucan serum levels have demonstrated good diagnostic sensitivity and specificity for the diagnosis of candidiasis in adult patients, but normal levels for children have not been established. We found higher 1,3-β-
d
-glucan levels in children than those previously reported in adults.
Typing of Human Enterovirus by Partial Sequencing of VP2
Authors: Nasri Dorsaf , Bouslama Lamjed , Omar Shabir , Saoudin Henia , Bourlet Thomas , Aouni Mahjoub , Pozzetto Bruno , Pillet Sylvie
Published: May 2007

The sequencing of the VP1 hypervariable region of the human enterovirus (HEV) genome has become the reference test for typing field isolates. This study describes a new strategy for typing HEV at the serotype level that uses a reverse transcription-PCR assay targeting the central part of the VP2 capsid protein. Two pairs of primers were used to amplify a fragment of 584 bp (with reference to the PV-1 sequence) or a part of it (368 bp) for typing. For a few strains not amplified by the first PCR, seminested primers enhanced the sensitivity (which was found to be approximately 10
−1
and 10
−4
50% tissue culture infective dose per reaction tube for the first and seminested assay, respectively). The typing method was then applied to 116 clinical and environmental strains of HEV. Sixty-one typeable isolates were correctly identified at the serotype level by comparison to seroneutralization. Forty-eight of 55 “untypeable” strains (87.3%) exhibited the same serotype using VP1 and VP2 sequencing methods. For six strains (four identified as EV-71, one as E-9, and one as E-30 by the VP2 method), no amplification was obtained by the VP1 method. The last strain, typed as CV-B4 by VP1 and CV-B3 by VP2 and monovalent antiserum, could exhibit recombination within the capsid region. Although the VP2 method was tested on only 36 of the 68 HEV serotypes, it appears to be a promising strategy for typing HEV strains isolated on a routine basis. The good sensitivity of the seminested technique could avoid cell culture and allow HEV typing directly from PCR products.
Sensitive Detection of
Mycoplasma pneumoniae
in Human Respiratory Tract Samples by Optimized Real-Time PCR Approach
Authors: Dumke Roger , Schurwanz Nicol , Lenz Matthias , Schuppler Markus , Lück Christian , Jacobs Enno
Published: May 2007

To enhance the sensitivity of the available real-time PCR systems for the detection of
Mycoplasma pneumoniae
, we established a method to amplify copies of the repetitive element repMp1. In a study of respiratory tract samples, we found that, compared to the use of the conserved part of the P1 adhesin gene as a monocopy target, the use of the repMp1-PCR showed an increase in the detected genome equivalents by a factor of 22.
Mycobacterium simiae
Complex Infection in an Immunocompetent Child
Authors: Cruz Andrea T. , Goytia Veronica K. , Starke Jeffrey R.
Published: May 2007

Nontuberculous mycobacteria are ubiquitous in the environment but rarely infect immunocompetent patients. We describe a pediatric case of
Mycobacterium simiae
complex lymphadenitis in an immunocompetent child and review the natural history, clinical manifestations, diagnosis, and current management of the disease.
Nonsporulating Clinical Isolate Identified as
Petromyces alliaceus
(Anamorph
Aspergillus alliaceus
) by Morphological and Sequence-Based Methods
Authors: Balajee S. Arunmozhi , Lindsley Mark D. , Iqbal Naureen , Ito James , Pappas Peter G. , Brandt Mary E.
Published: May 2007

Concerted morphological and sequencing-based strategies revealed the identity of a nonsporulating clinical isolate as
Petromyces alliaceus
(anamorph
Aspergillus alliaceus
). This rare
Aspergillus
sp. was recovered as the etiological agent of invasive pulmonary aspergillosis and had reduced in vitro susceptibilities to amphotericin B and caspofungin, which correlated with clinical failure of therapy.
Simplified and Reliable Scheme for Species-Level Identification of
Staphylococcus
Clinical Isolates
Authors: Iorio Natalia Lopes Pontes , Ferreira Rosana Barreto Rocha , Schuenck Ricardo Pinto , Malvar Karoline Lourenço , Brilhante Anike Pereira , Nunes Ana Paula Ferreira , Bastos Carla Callegário Reis , dos Santos Kátia Regina Netto
Published: May 2007

Reliable and rapid identification of staphylococcal strains continues to be a problem faced by many microbiology laboratories. This study evaluates a simplified method that uses a flowchart to assist in the identification of 12 clinical species of
Staphylococcus
, including eight subspecies. A total of 198 isolates and 11 control strains were identified by the reference method, which employed 22 tests. The results were compared with those obtained by two other methods: an automated system (MicroScan WalkAway) and a simplified method composed of nine tests. The simplified scheme showed an accuracy of 98.5%, while the automated method showed an accuracy of 79.3% (
P
< 0.001), in identifying staphylococcal species. Atypical phenotypic profiles were detected by both the reference (55.6%) and the simplified (19.7%) methods. The simplified method proposed here was shown to be reliable, with the advantage of being more practical and economic than the reference method.
Puumala Hantavirus Viremia Diagnosed by Real-Time Reverse Transcriptase PCR Using Samples from Patients with Hemorrhagic Fever and Renal Syndrome
Authors: Evander Magnus , Eriksson Irene , Pettersson Lisa , Juto Per , Ahlm Clas , Olsson Gert E. , Bucht Göran , Allard Annika
Published: May 2007

Puumala virus (PUUV) is the endemic hantavirus in northern Sweden and causes nephropathia epidemica (NE), a milder form of hemorrhagic fever with renal syndrome. There is a need for fast and reliable diagnostics to differentiate the disease from other infections. By aligning virus RNA sequences isolated from 11 different bank voles and one human patient, we designed a real-time reverse transcriptase (RT) PCR method for detection of PUUV RNA. The real-time RT-PCR assay showed linearity from 20 to 2 × 10
6
virus copies with a correlation coefficient above 0.98 to 0.99 for all experiments. The detection threshold for PUUV cDNA was two copies per reaction. A two-step qualitative RT-PCR to detect PUUV RNA showed 100% concordance with the real-time RT-PCR assay. PUUV RNA viremia was detected in 33 of 34 PUUV immunoglobulin M (IgM)-positive patients with typical clinical NE disease from the region of endemicity. One PUUV IgM-negative sample had PUUV RNA, and 4 days later, the patient was IgM positive. Of samples with indeterminate IgM, 43% were PUUV RNA positive. The kinetics of antibody titers and PUUV viremia were studied, and five of six NE patients displayed a decrease in PUUV viremia a few days after disease outbreak coupled with an increase in PUUV IgM and IgG. In one patient with continuously high PUUV RNA levels but low IgM and no IgG response, the infection was lethal. These findings demonstrated that real-time RT-PCR is a useful method for diagnosis of PUUV viremia and for detecting PUUV RNA at early time points, before the appearance of IgM antibodies.
New Highly Divergent rRNA Sequence among Biodiverse Genotypes ofEnterocytozoon bieneusiStrains Isolated from Humans in Gabon and Cameroon
Authors: Breton Jacques , Bart-Delabesse Emmanuelle , Biligui Sylvestre , Carbone Alessandra , Seiller Xavier , Okome-Nkoumou Madeleine , Nzamba Chantal , Kombila Maryvonne , Accoceberry Isabelle , Thellier Marc
Published: May 2007

Intestinal microsporidiosis due toEnterocytozoon bieneusiis a leading cause of chronic diarrhea in severely immunocompromised human immunodeficiency virus (HIV)-positive patients. It may be a public health problem in Africa due to the magnitude of the HIV pandemic and to poor sanitary conditions. We designed two prevalence studies ofE. bieneusiin Central Africa, the first with HIV-positive patients from an urban setting in Gabon and the second with a nonselected rural population in Cameroon. Stool samples were analyzed by an immunofluorescence antibody test and PCR. Twenty-five out of 822 HIV-positive patients from Gabon and 22 out of 758 villagers from Cameroon were found to be positive forE. bieneusi. The prevalence rates of the two studies were surprisingly similar (3.0% and 2.9%). Genotypic analysis of the internal transcribed spacer region of the rRNA gene showed a high degree of diversity in samples from both countries. In Gabon, 15 isolates showed seven different genotypes: the previously reported genotypes A, D, and K along with four new genotypes, referred to as CAF1, CAF2, CAF3, and CAF4. In Cameroon, five genotypes were found in 20 isolates: the known genotypes A, B, D, and K and the new genotype CAF4. Genotypes A and CAF4 predominated in Cameroon, whereas K, CAF4, and CAF1 were more frequent in Gabon, suggesting that different genotypes present differing risks of infection associated with immune status and living conditions. Phylogenetic analysis of the new genotype CAF4, identified in both HIV-negative and HIV-positive subjects, indicates that it represents a highly divergent strain.
Coreceptor Switch in R5-Tropic Simian/Human Immunodeficiency Virus-Infected Macaques
Authors: Ho Siu-hong , Tasca Silvana , Shek Lili , Li Amy , Gettie Agegnehu , Blanchard James , Boden Daniel , Cheng-Mayer Cecilia
Published: May 2007

The basis for the switch from CCR5 to CXCR4 coreceptor usage seen in ∼50% of human immunodeficiency virus type 1 (HIV-1) subtype B-infected individuals as disease advances is not well understood. Among the reasons proposed are target cell limitation and better immune recognition of the CXCR4 (X4)-tropic compared to the CCR5 (R5)-tropic virus. We document here X4 virus emergence in a rhesus macaque (RM) infected with R5-tropic simian/human immunodeficiency virus, demonstrating that coreceptor switch can happen in a nonhuman primate model of HIV/AIDS. The switch to CXCR4 usage in RM requires envelope sequence changes in the V3 loop that are similar to those found in humans, suggesting that the R5-to-X4 evolution pathways in the two hosts overlap. Interestingly, compared to the inoculating R5 virus, the emerging CXCR4-using virus is highly neutralization sensitive. This finding, coupled with the observation of X4 evolution and appearance in an animal with undetectable circulating virus-specific antibody and low cellular immune responses, lends further support to an inhibitory role of antiviral immunity in HIV-1 coreceptor switch.
Low Immune Activation despite High Levels of Pathogenic Human Immunodeficiency Virus Type 1 Results in Long-Term Asymptomatic Disease
Authors: Choudhary Shailesh K. , Vrisekoop Nienke , Jansen Christine A. , Otto Sigrid A. , Schuitemaker Hanneke , Miedema Frank , Camerini David
Published: May 2007

Long-term asymptomatic human immunodeficiency virus (HIV)-infected individuals (LTA) usually have low viral load and low immune activation. To discern whether viral load or immune activation is dominant in determining progression to AIDS, we studied three exceptional LTA with high viral loads. HIV type 1 isolates from these LTA were as pathogenic as viruses from progressors in organ culture. Despite high viral loads, these LTA had low levels of proliferating and activated T cells compared to progressors, like other LTA. In contrast to those in progressors, HIV-specific CD4
+
T-cell responses in these LTA were maintained. Thus, low immune activation despite a high viral load preserved HIV-specific T-cell responses and resulted in a long-term asymptomatic phenotype.
Reconstruction and Function of Ancestral Center-of-Tree Human Immunodeficiency Virus Type 1 Proteins
Authors: Rolland Morgane , Jensen Mark A. , Nickle David C. , Yan Jian , Learn Gerald H. , Heath Laura , Weiner David , Mullins James I.
Published: May 2007

The extensive diversity of human immunodeficiency virus type 1 (HIV-1) and its capacity to mutate and escape host immune responses are major challenges for AIDS vaccine development. Ancestral sequences, which minimize the genetic distance to circulating strains, provide an opportunity to design immunogens with the potential to elicit broad recognition of HIV epitopes. We developed a phylogenetics-informed algorithm to reconstruct ancestral HIV sequences, called Center of Tree (COT). COT sequences have potentially significant benefits over isolate-based strategies, as they minimize the evolutionary distances to circulating strains. COT sequences are designed to surmount the potential pitfalls stemming from sampling bias with the consensus method and outlier bias with the most-recent-common-ancestor approach. We computationally derived COT sequences from circulating HIV-1 subtype B sequences for the genes encoding the major viral structural protein (Gag) and two regulatory proteins, Tat and Nef. COT genes were synthesized de novo and expressed in mammalian cells, and the proteins were characterized. COT Gag was shown to generate virus-like particles, while COT Tat transactivated gene expression from the HIV-1 long terminal repeat and COT Nef mediated downregulation of cell surface major histocompatibility complex class I. Thus, retrodicted ancestral COT proteins can retain the biological functions of extant HIV-1 proteins. Additionally, COT proteins were immunogenic, as they elicited antigen-specific cytotoxic T-lymphocyte responses in mice. These data support the utility of the COT approach to create novel and biologically active ancestral proteins as a starting point for studies of the structure, function, and biological fitness of highly variable genes, as well as for the rational design of globally relevant vaccine candidates.
Identification of molecular markers associated with mite resistance in coconut (Cocos nucifera L.)
Authors: Shalini K.V. , Manjunatha S. , Lebrun P. , Berger A. , Baudouin L. , Pirany N. , Ranganath R.M. , Prasad D. Theertha
Published: May 2007

Coconut mite ( Aceria guerreronis ‘Keifer’) has become a major threat to Indian coconut ( Coçcos nucifera L.) cultivators and the processing industry. Chemical and biological control measures have proved to be costly, ineffective, and ecologically undesirable. Planting mite-resistant coconut cultivars is the most effective method of preventing yield loss and should form a major component of any integrated pest management stratagem. Coconut genotypes, and mite-resistant and -susceptible accessions were collected from different parts of South India. Thirty-two simple sequence repeat (SSR) and 7 RAPD primers were used for molecular analyses. In single-marker analysis, 9 SSR and 4 RAPD markers associated with mite resistance were identified. In stepwise multiple regression analysis of SSRs, a combination of 6 markers showed 100% association with mite infestation. Stepwise multiple regression analysis for RAPD data revealed that a combination of 3 markers accounted for 83.86% of mite resistance in the selected materials. Combined stepwise multiple regression analysis of RAPD and SSR data showed that a combination of 5 markers explained 100% of the association with mite resistance in coconut. Markers associated with mite resistance are important in coconut breeding programs and will facilitate the selection of mite-resistant plants at an early stage as well as mother plants for breeding programs.
AFLP analysis of genetic relationships in the genus Fosterella L.B. Smith (Pitcairnioideae, Bromeliaceae)
Authors: Rex Martina , Patzolt Kerstin , Schulte Katharina , Zizka Georg , Vásquez Roberto , Ibisch Pierre L. , Weising Kurt
Published: May 2007

The neotropical genus Fosterella L.B. Smith (Pitcairnioideae, Bromeliaceae) comprises about 30 species, with a centre of diversity in semiarid to humid habitats of the Andean slopes and valleys of Bolivia. Morphologic differentiation of species is difficult because of a paucity of diagnostic characters, and little is known about the infrageneric phylogeny. Here, we present the results of an amplified fragment length polymorphism (AFLP) analysis of 77 Fosterella specimens, covering 18 recognized species and 9 as-yet undescribed morphospecies. Eight primer combinations produced 310 bands, which were scored as presence/absence characters. Neighbour-joining tree reconstruction revealed 12 clusters (A–L) with various levels of support. Well-supported species groups were also recovered by a principal coordinates analysis. With few exceptions, morphologically defined species boundaries were confirmed by the molecular data. Phylogenetic relationships between species groups remained ambiguous, however, because of short internal branch lengths. The AFLP data were complemented by a survey of the leaf anatomy of 19 Fosterella species. Species concepts and assemblages are discussed in the context of molecular, morphologic, anatomic, ecologic, and biogeographic data. The data suggest that accidental long-distance dispersal and founder events have been important for Fosterella speciation.
Mitochondrial genomic comparisons of the subterranean termites from the Genus Reticulitermes (Insecta: Isoptera: Rhinotermitidae)
Authors: Cameron Stephen L. , Whiting Michael F.
Published: May 2007

Termites of the genus Reticulitermes are some of the most significant pests of structural timber and tree farming in the northern hemisphere, causing losses in the billions of dollars annually because of direct damage and termite control costs. This group has been frequently targeted for population genetic, phylogenetic, and species limit studies, most of which use mitochondrial (mt) genes; however, only a small fraction of the genome has been sequenced. The entire mt genome was sequenced for the eastern North American members of Reticulitermes: R. flavipes, R. santonensis, R. virginicus, and R. hageni. The mt genome has the same gene content and organization as that found in most insect species; however, the nucleotide composition and skew are highly biased (AT% low, strong A- and C-skew). Both the protein-coding and transfer RNA genes show high absolute levels of nucleotide substitution, suggesting that the high rates of mutation within Reticulitermes inferred from analyses of single mt genes are a general characteristic of the entire mt genome. The AT-rich or control region has a remarkable structure not previously observed in insect mt genomes. The majority of the control region is made up of 2 sets of repeat units, typically with 2 full and 1 partial copies of both the A (or small; 186 bp) and B (or large; 552 bp) repeats. The partial repeat units overlap by 36 bp. The size, location, and degree of overlap for the partial repeat units correspond to highly conserved stem/loop structures within the repeat units, suggesting that these structures are involved in the replication-mediated processes that govern repeat-unit evolution within mt genomes. Finally, molecular variation within the mt gene regions was compared with previous regions used in molecular diagnostics or phylogenetics of Reticulitermes. High numbers of single nucleotide polymorphisms were found in each of the mt genes, and some of the highest variability was found in gene regions that have not previously been investigated in this group. The whole mt genome sequence can thus be used to predict useful regions for future investigation.
Detecting the fracture process zone in concrete using scanning electron microscopy and numerical modelling using the nonlocal isotropic damage model
Authors: Hadjab-Souag H , Thimus J.-F. , Chabaat M
Published: May 2007

This paper deals with two aspects of the characterization of the fracture process zone (FPZ) in quasi-brittle materials such as concrete. An overview is given of the possibility of using a destructive technique, such as the scanning electron microscope, and a numerical model, such as the nonlocal isotropic damage model (NLIDM), to detect FPZ characteristics, e.g., length and width of the FPZ. The fracture of concrete requires the consideration of progressive damage, which is usually modelled by a constitutive law and can be studied by a numerical method. The object-oriented finite element method (OOFEM) has recently been used in damage studies, and thus the FPZ is calculated on the basis of one of the damage models (the NLIDM). The results obtained from the experimental investigation are similar to those obtained using the NLIDM, which has proven to be a useful tool for analysis of the cracking process.Key words: object-oriented finite element method, nonlocal isotropic damage model, fracture process zone, scanning electron microscope.
The analysis of design wind speed estimates specified in the National Building Code of Canada
Authors: Pandey M D , An Y
Published: May 2007

The design wind pressures specified in the 2005 National Building Code of Canada (NBCC) have been derived from the Gumbel distribution fitted to annual maximum wind speed data collected up to early 1990s. The statistical estimates of the annual maxima method are affected by a relatively large sampling variability, since the method considers a fairly small subset of available wind speed records. Advanced statistical methods have emerged in recent years with the purpose of reducing both sampling and model uncertainties associated with extreme quantile estimates. The two most notable methods are the peaks-over-threshold (POT) and annually r largest order statistics (r-LOS), which extend the data set by including additional maxima observed in wind speed time series. The objective of the paper is to explore the use of advanced extreme value theory for updating the design wind speed estimates specified in the Canadian building design code. The paper re-examines the NBCC method for design wind speed estimation and presents the analysis of the latest Canadian wind speed data by POT, r-LOS, and annual maxima methods. The paper concludes that r-LOS method is an effective alternative for the estimation of extreme design wind speed.Key words: wind speed, extreme value theory, order statistics, return period, maximum likelihood method, peaks-over-threshold method, generalized extreme value distribution, Gumbel distribution, generalized Pareto distribution.
Collimated beam tests: their limitations for assessing wastewater disinfectability by UV, and a proposal for an additional evaluation parameter
Authors: Gehr R
Published: May 2007

This study examines the effects of the liquid matrix on the disinfectability of waters and wastewaters by ultraviolet (UV) light. Collimated beam (CB) curves, which are routinely used to assess disinfectability, and to provide the average fluence (in microjoules per square centimetre) necessary to reach a target effluent microbial count, eliminate the effect of UV transmission (UVT), using the Morowitz equation. However, this calculation has the consequence of masking the differences between samples of differing UVT, which may indeed require the same average UV fluence to reach the target, but require considerably different energy input and number of lamps in the full-scale system. An additional parameter, called herein an "energy factor'', is proposed in addition to the CB curve to evaluate disinfectability. The energy factor is the applied UV energy per unit volume divided by the average fluence experienced by the microbes in the liquid matrix. Synthetic data and actual CB curves from various types of samples are used to assess the effects of UVT, the depth of sample in the petri dish, the slope of the CB curve, the target microbial count, and, finally, the original microbial count on the energy factor. Key words: ultraviolet disinfection, collimated beam, energy factor.
Simple physical treatment for the reuse of wastewater from textile industry in the Middle East
Authors: Arafat Hassan A
Published: May 2007

In this work, different treatment methods for wastewater from textile washing operations in the Palestinian territories were studied. The goal of the treatment process was to enable the textile industry to reuse the wastewater in textile washing through simple, efficient, and cost-effective methodologies. Actual textile wastewater samples from local textile factories were used and were found to be highly polluted. The study focused on three main processes; sedimentation, coagulation, and adsorption. While sedimentation was found to reduce the total suspended solids (TSS) of the wastewater, coagulation had the additional advantages of lowering the chemical oxygen demand (COD) and achieving higher filtration rates. Four coagulants were tested, ferric chloride, ferrous sulfate plus lime, aluminum sulfate, and aluminum sulfate plus lime. While ferric chloride failed to perform effectively as a coagulant, the other three coagulants were fairly effective. Finally, to further lower the COD of post-coagulation treated water, adsorption using activated carbon was studied. It was found that carbon was effective in reducing the COD of the wastewater using reasonable quantities, where up to 98% COD reduction was achieved using 6 g carbon/L.Key words: textile, wastewater, treatment, coagulation, sedimentation, adsorption.
An evaluation of autothermal thermophilic aerobic digestion (ATAD) of municipal sludge in Ireland
Authors: Layden Noreen M
Published: May 2007

Autothermal thermophilic aerobic digestion (ATAD) is an exothermic process where sludge is subjected to temperatures greater than 55 °C and a hydraulic retention time of 6–15 days. Organic solids are degraded and the heat released during the microbial degradation maintains thermophilic temperatures. Autothermal thermophilic aerobic digestion can produce a biologically stable product while reducing both sludge mass and volume. The full-scale ATAD facility in Killarney, Ireland, is unique because the feed sludge is blended from three different secondary treatments and there are seasonal fluctuations in hydraulic load. An assessment of the on-site operational and solids data showed that the process operation has improved since commissioning. Total solids reduction increased from 13.7% in 2001 to 39.1% in 2004. Also, despite some operational problems the regulatory target of 38% reduction in volatile solids was achieved. The data fluctuated but the percent reduction in volatile solids increased from 35.6% in 2001 to 49.8% in 2004. This paper compares the process data obtained from the Killarney site with other ATAD facilities operated in Europe and North America. It discusses some of the operational changes employed to deal with process control issues and it presents recommendations for enhanced ATAD process improvement.Key words: autothermal, thermophilic, aerobic, digestion, sludge, biosolids.
Computational fluid dynamics for predicting performance of ultraviolet disinfection  sensitivity to particle tracking inputs
Authors: Munoz Alex , Craik Stephen , Kresta Suzanne
Published: May 2007

A three-dimensional (3-D) computational fluid dynamic model that predicts the performance of a full-scale medium-pressure lamp ultraviolet (UV) reactor for disinfection of drinking water is described. The model integrates velocity field, fluence rate distribution, and particle trajectory calculations with a microorganism inactivation kinetic model to arrive at predictions of reduction equivalent dose and microorganism inactivation for MS2 coliphage. A rational approach to determining an appropriate number of fluid particles that would generate the required computational precision is presented. Predictions of inactivation and equivalent dose were found to be sensitive to computational mesh geometry (hexahedral versus tetrahedral) but were less sensitive to the value of the Lagrangian empirical constant used in the random walk model and to choice of turbulence model (κ – εε versus Reynolds stress). Non-steady-state (dynamic) simulations produced results that were similar to those of steady-state simulations. Utility of the model for evaluating different lamp operating modes and alternative physical arrangements of the baffles and lamps was demonstrated.Key words: ultraviolet, UV reactor, disinfection, water, computational fluid dynamics, modeling.