bluuebunny/crossref_metadata_2025 huggingface dataset:
A Case of Fatal Aconitine Poisoning by Monkshood Ingestion*
Authors: Pullela Ravi , Young Lorraine , Gallagher Barry , Avis Simon P. , Randell Edward W.
Published: February 2008

Abstract:  Accidental aconitine poisoning is extremely rare in North America. This report describes the confirmation of a case of accidental aconitine poisoning using a liquid chromatography–tandem mass spectrometry (LC‐MS/MS) method. The case involved a 25‐year‐old man who died suddenly following a recreational outing with friends where he consumed a number of wild berries and plants including one that was later identified as Monkshood (Aconitum napellus). Postmortem blood and urine samples were available for analysis. All routine urine and blood toxicology screens were negative. The LC‐MS/MS method allowed sensitive quantification of aconitine, the main toxin in A. napellus, and showed 3.6 and 149 μg/L in blood and urine, respectively. These concentrations were similar to that reported in other aconitine‐related deaths. This case illustrates the dangers of consuming unidentified plants, and documents concentrations of aconitine in blood and urine in a fatal case of A. napallus‐related poisoning.
PED is overexpressed and mediates TRAIL resistance in human non‐small cell lung cancer
Authors: Zanca Ciro , Garofalo Michela , Quintavalle Cristina , Romano Giulia , Acunzo Mario , Ragno Pia , Montuori Nunzia , Incoronato Mariarosaria , Tornillo Luigi , Baumhoer Daniel , Briguori Carlo , Terracciano Luigi , Condorelli Gerolama
Published: February 2008

PED (phosphoprotein enriched in diabetes) is a death‐effector domain (DED) family member with a broad anti‐apoptotic action. PED inhibits the assembly of the death‐inducing signalling complex (DISC) of death receptors following stimulation. Recently, we reported that the expression of PED is increased in breast cancer cells and determines the refractoriness of these cells to anticancer therapy. In the present study, we focused on the role of PED in non‐small cell lung cancer (NSCLC), a tumour frequently characterized by evasion of apoptosis and drug resistance. Immunohistochemical analysis of a tissue microarray, containing 160 lung cancer samples, indicated that PED was strongly expressed in different lung tumour types. Western blotting performed with specimens from NSCLC‐affected patients showed that PED was strongly up‐regulated (>6 fold) in the areas of tumour compared to adjacent normal tissue. Furthermore, PED expression levels in NSCLC cell lines correlated with their resistance to tumour necrosis factor related apoptosis‐inducing ligand (TRAIL)‐induced cell death. The involvement of PED in the refractoriness to TRAIL‐induced cell death was investigated by silencing PED expression in TRAIL‐resistant NSCLC cells with small interfering (si) RNAs: transfection with PED siRNA, but not with cFLIP siRNA, sensitized cells to TRAIL‐induced cell death. In conclusion, PED is specifically overexpressed in lung tumour tissue and contributes to TRAIL resistance.
Incidence of dental trauma among adolescents: a prospective cohort study
Authors: Ramos‐Jorge Maria Letícia , Peres Marco Aurélio , Traebert Jefferson , Ghisi Carolina Zanella , De Paiva Saul Martins , Pordeus Isabela Almeida , Marques Leandro Silva
Published: February 2008

Abstract –  We estimated the incidence of traumatic dental injuries (TDI) in a 2‐year follow‐up of adolescents with and without previous dental trauma and verified the hypothesis that individuals with previous trauma are more prone to recurrent TDI events. The present study was developed in three phases. First, a dental trauma cross‐sectional study was carried out with 2260 schoolchildren aged 11–13 years in Biguaçu, southern Brazil. In the second phase, a case–control study was developed to identify risk factors associated with dental trauma. The third step was a 2‐year longitudinal observational study with the participants of the second phase of the study. The exposed group of individuals with previous dental traumatism (208) and a non‐exposed group (208) of participants who had no previous signs of dental trauma were followed up for 2 years. Descriptive, univariate, simple and conditional multiple logistic regression analyses were performed. The greatest incidence of dental trauma was identified among adolescents with previous dental trauma (11.9%–11.44/1000 incisors) when compared with those without previous dental trauma (2.7%–2.45/1000 incisors) (P < 0.001). In the study period, adolescents with previous dental trauma showed a 4.85 times greater odds ratio for presenting further dental trauma when compared with adolescents without previous dental trauma (P = 0,005) after adjusting for incisal overjet, lip coverage and mother’s schooling. A notable difference was observed regarding the incidence of TDI between the case and control groups. Individuals with previous dental trauma had greater chances of developing develop further dental trauma in a 2‐year follow‐up.
Effect of a new restoration technique on fracture resistance of endodontically treated teeth
Authors: Sengun Abdulkadir , Cobankara Funda Kont , Orucoglu Hasan
Published: February 2008

Abstract –  The aim of the study was to investigate the effect of a new fiber‐reinforced composite restoration technique on fracture resistance in endodontically treated premolars. Eighty sound extracted human mandibular premolars were assigned to four groups (n = 20). Group 1 did not receive any treatment. In groups 2, 3 and 4, the teeth received root canal treatment and a mesio‐occluso‐distal cavity preparation. Group 2 was kept unrestored. Group 3 was restored with a dentin bonding system and composite resin. In group 4, a piece of polyethylene ribbon fiber was inserted into the groove in a buccal to lingual direction during the restoration of teeth with dentin bonding system and composite resin. After finishing and polishing, the specimens were stored in 100% humidity at 37°C for 24 h and placed at an angle of 45° to the long axis of the tooth and subjected to compressive loading in a universal testing machine at a crosshead speed of 0.5 mm min−1. The load necessary to fracture the samples was recorded in Newton (N) and submitted to Kruskal–Wallis anova and Mann–Whitney U‐test. The fracture strength of the teeth reinforced with a combination of polyethylene fiber and composite resin were not significantly different than those that were restored with only composite resin (P > 0.05). However, most of the failure modes of the reinforced teeth were limited to the level of the enamel, while the other three groups showed fractures generally at the level of the dentin, cemento‐enamel junction or more below (P < 0.05). Therefore, polyethylene ribbon fiber‐reinforced composite resin restorations seemed a more reliable restorative technique than traditional composite restorations for extensive cavities.
Fabricating a better mouthguard. Part II: The effect of color on adaptation and fit
Authors: Del Rossi Gianluca , Lisman Peter , Signorile Joseph
Published: February 2008

Abstract –  The thermoforming process involves the heating of plastic sheets to a critical temperature followed by the shaping of the heated material into a three‐dimensional structure. Given that custom‐fabricated mouthguards are produced using the thermoforming process, the adaptation of plastic sheets to a stone model of the dentition is likely to be affected by the ability of the mouthguard material to be heated. The purpose of this study was to establish if material color affected the adaptation and fit of custom‐made mouthguards. Twelve stone models were used in this investigation. Five mouthguards were produced using each model. These mouthguards were made using clear‐, white‐, black‐, blue‐ and green‐colored ethyl vinyl acetate. The force required to remove the various colored mouthguards from the corresponding stone models was determined using a strain gauge housed within a specially designed apparatus. Each of the mouthguards were tested three times at two different angles of pull −45° and 90°. Statistical tests performed using the average amount of force required for mouthguard removal revealed an angle by color interaction. Post hoc analyses revealed that the mean force required to remove the clear‐colored mouthguards from their respective stone models was significantly less than the force required to pull away blue‐, black‐ and green‐colored mouthguards. This difference between clear‐ and dark‐colored mouthguards was observed at both angles tested with the exception of the black mouthguard which differed from the clear‐colored mouthguard only when removed at an angle of 90°. The results of the present study indicate that by using dark‐colored mouthguard material, one can achieve superior adaptation and thus produce a more firmly fitting mouthguard.
A simplified caries risk test in stimulated saliva from elderly patients
Authors: Sánchez‐García Sergio , Gutiérrez‐Venegas Gloria , Juárez‐Cedillo Teresa , Reyes‐Morales Hortensia , Solórzano‐Santos Fortino , García‐Peña Carmen
Published: February 2008

Objectives:  To evaluate and compare lactobacilli species (LB) and mutans streptococci (MS) caries risk identification by means of a Caries Risk Test Bacteria (CRT Bacteria test), with a conventional laboratory test (CLT), as well as their correlation with the dental caries experience [(decayed‐missing‐filled teeth (DMFT index)] in subjects 60 years of age and older.

Design:  Cross‐sectional study.

Setting:  Epidemiologic and Health Service Research Unit, Aging Area. XXI Century National Medical Center; Mexican Institute of Social Security (IMSS).

Subjects:  A total of 696 elderly subjects residing in southwestern Mexico City.

Methods:  The DMFT index was determined in 696 subjects and saliva collected by stimulation. This was processed with a CRT Bacteria test and a CLT (the gold standard) test. Subjects with high [≥105 colony forming units (CFU)/ml] and low caries risk (<105 CFU/ml) were assessed.

Results:  The CRT Bacteria test sensitivity (Sen) and specificity (Spe) were 0.97 and 0.86 for LB, respectively, with positive and negative predictor values of 0.92 and 0.95 respectively. For MS, Sen and Spe was 0.92 and 0.90, and 0.96 and 0.81 respectively. The receiver operating characteristic area under the curve (ROC area) in LB and MS was 0.94 and 0.89, respectively; thus, a correlation existed between the caries experience and the LB and MS caries risk, similar to that present with the CLT test.

Conclusion:  The CRT Bacteria test shows similar results to those of the CLT test in subjects 60 years of age and over.
Arabic version of the geriatric oral health assessment Index
Authors: Atieh Momen A.
Published: February 2008

Objectives:  The purpose of this study was to translate the original English version of the Geriatric Oral Health Assessment Index (GOHAI) into an Arabic version, and to test the validity and reliability of the translated instrument (GOHAI‐Ar) for use among the elderly in Saudi Arabia.

Methods:  The 12‐item GOHAI was translated into Arabic using the back‐translation technique and performing a preliminary test to determine the comprehensibility and readability of the Arabic language version. A total of 156 elderly patients answered the questionnaire, and underwent a clinical examination by one calibrated dentist. Information on subjects’ socio‐demographic background and oral health conditions was collected. Convergent validity was evaluated by identifying the associations between perceived oral health status, general health status, perceived need for dental care and GOHAI‐Ar scores. Discriminant validity was examined by comparing the GOHAI‐Ar scores and six oral health parameters. Internal consistency was measured by Cronbach’s alpha. Test–retest reliability was assessed by intra‐class correlation coefficient (ICC) and weighted kappa. Factor structure of GOHAI‐Ar was evaluated using principal component factor analysis.

Results:  The mean GOHAI‐Ar was 32.1 (SD 12.2; range 11–59). Mean GOHAI‐Ar scores were higher for the elderly who rated their oral and general health as good. Subjects with perceived dental treatment needs had a lower mean GOHAI‐Ar score than those without any such needs. The caries experience, number of missing teeth, OHI‐S score, number of pathologically mobile teeth and number of oral lesions were negatively correlated with the GOHAI‐Ar score. The Cronbach’s alpha (0.93) indicated a high degree of internal consistency and homogeneity between items. The ICC for GOHAI‐Ar was 0.95, the weighted kappa coefficient for individual items varied between 0.42 and 0.71, and the correlation coefficients for the 12 items were above 0.70. Factor analysis didn’t support the expected dimensions of the index, and only one factor was found at eigenvalue greater than 1.

Conclusions:  The findings suggest an excellent reliability and validity of GOHAI‐Ar. Further research is needed to assess the value of this instrument in oral health‐related quality of life studies in Arabic elderly population.
Transgender and Transsexual Studies: Sociology's Influence and Future Steps
Authors: Vidal‐Ortiz Salvador
Published: February 2008

This article provides a general sense of transgender studies in sociology. It does so by looking at the definitions and relationship between the terms transgender and transsexual, the history of transsexual studies, sociology's place in this development, and the active production (by trans people) of transsexual and transgender studies. This review primarily focuses on US sociological writing, including ethnomethodology, labeling, feminist, and symbolic interactionist frameworks, while incorporating critical theory, queer theory, and other interdisciplinary influences. The article explores various movements in the recent history of this scholarship: for instance, while transsexual studies were mostly developed with a male‐to‐female transsexual perspective, recent scholarship place female‐to‐male transsexual and transgender identity centrally. I present current trends and future steps of sociological inquiry in the area of transgender studies as a way of closing the discussion of sociology's potential contributions in the near future.
Phosphatidylinositol‐4,5‐bisphosphate (PIP2) regulation of strong inward rectifier Kir2.1 channels: multilevel positive cooperativity
Authors: Xie Lai‐Hua , John Scott A. , Ribalet Bernard , Weiss James N.
Published: February 2008

Inwardly rectifying potassium (Kir) channels are gated by the interaction of their cytoplasmic regions with membrane‐bound phosphatidylinositol‐4,5‐bisphosphate (PIP2). In the present study, we examined how PIP2 interaction regulates channel availability and channel openings to various subconductance levels (sublevels) as well as the fully open state in the strong inward rectifier Kir2.1 channel. Various Kir2.1 channel constructs were expressed in Xenopus oocytes and single channel or macroscopic currents were recorded from inside‐out patches. The wild‐type (WT) channel rarely visited the subconductance levels under control conditions. However, upon reducing Kir2.1 channel interaction with PIP2 by a variety of interventions, including PIP2 antibodies, screening PIP2 with neomycin, or mutating PIP2 binding sites (e.g. K188Q), visitation to the sublevels was markedly increased before channels were converted to an unavailable mode in which they did not open. No channel activity was detected in channels with the double mutation K188A/R189A, a mutant which exhibits extremely weak interaction with PIP2. By linking subunits together in tandem dimers or tetramers containing mixtures of WT and K188A/R189A subunits, we demonstrate that one functional PIP2‐interacting WT subunit is sufficient to convert channels from the unavailable to the available mode with a high open probability dominated by the fully open state, with similar kinetics as tetrameric WT channels. Occasional openings to sublevels become progressively less frequent as the number of WT subunits increases. Quantitative analysis reveals that the interaction of PIP2 with WT subunits exerts strong positive cooperativity in both converting the channels from the unavailable to the available mode, and in promoting the fully open state over sublevels. We conclude that the interaction of PIP2 with only one Kir2.1 subunit is sufficient for the channel to become available and to open to its full conductance state. Interaction with additional subunits exerts positive cooperativity at multiple levels to further enhance channel availability and promote the fully open state.
Bragg diffraction, synchrotron x-ray reflectance, and x-ray photoelectron spectroscopy studies of low temperature plasma oxidation of native SiO2 on silicon on insulator
Authors: Bhargava M. , Donner W. , Srivastava A. K. , Wolfe J. C.
Published: February 2008

The authors present the application of synchrotron Bragg diffraction, x-ray reflectance (XRR), and x-ray photoelectron spectroscopy (XPS) to study silicon loss in the low temperature plasma oxidation of silicon-on-insulator (SOI) wafers. The Laue oscillations of the Si(004) Bragg peak provide a direct measure of the number of lattice planes that are consumed in the silicon device layer during processing, while the Fourier transform of the XRR data provides a model-independent determination of the increase in the combined thickness of the silicon and surface oxide. XPS measurements provide complementary information concerning changes in thickness, chemical composition, and the bonding of the surface oxide. These methods were applied to samples processed in an oxidizing plasma system at temperatures below 250°C. The authors find that 2.7±1Å of silicon, corresponding to two lattice planes, is consumed while the combined thickness increases by 2.7±0.8Å, corresponding to a net increase in the oxide thickness of 5.4±1.3Å. Thus, the ratio of oxide growth to silicon loss is about 2.0±0.9, somewhat lower than the bulk ratio of 2.2, but within experimental error. The XPS measurements show the increase to be 5.5Å. Additionally, XPS shows clearly the consumption of silicon to form Si2O and SiO2 and the net oxidation of Si2O3 to SiO2.
P implantation into preamorphized germanium and subsequent annealing: Solid phase epitaxial regrowth, P diffusion, and activation
Authors: Posselt M. , Schmidt B. , Anwand W. , Grötzschel R. , Heera V. , Mücklich A. , Wündisch C. , Skorupa W. , Hortenbach H. , Gennaro S. , Bersani M. , Giubertoni D. , Möller A. , Bracht H.
Published: February 2008

Phosphorus implantation (30 keV, 3×1015 cm−2) into preamorphized Ge and subsequent rapid thermal or flash lamp annealing is investigated. During annealing a significant P diffusion in amorphous Ge is not observed. However, the fast solid phase epitaxial regrowth causes a rapid redistribution of P. After completion of the regrowth and at temperatures above 500 °C, a concentration-dependent diffusion of P in crystalline Ge takes place and leads to considerable loss of P toward the surface. An appreciable influence of implantation defects on the diffusion coefficient of P is not detected. For 60 s rapid thermal annealing at 600 °C and for 20 ms flash lamp annealing at 900 °C, the junction depth and the sheet resistance vary between 140 and 200 nm and between 50 and 100 Ω, respectively, and the maximum electrical activation of P is about 3–7×1019 cm−3.
Insights in junction photovoltage based sheet resistance measurements for advanced complementary metal-oxide semiconductor
Authors: Clarysse Trudo , Moussa Alain , Zangerle Thomas , Schaus Frederic , Vandervorst Wilfried , Faifer Vladimir , Current Michael
Published: February 2008

Earlier work has clearly shown that only a very few tools are able to measure reliably sheet resistances on advanced complementary metal-oxide semiconductor (CMOS) structures. One of these promising techniques is the junction photovoltage based technique, which uses a modulated light emitting diode to generate, in a millimeter size area of a single junction isolated structure, excess carriers which are separated by the underlying electrical field, and subsequently outdiffuse laterally. From the lateral variation in junction photovoltage, one can extract in a noncontact way the sheet resistance (Rs) of the top layer and the junction leakage (L) of the junction. First, a simplified theoretical solution of the underlying diffusion equations will be presented. Next, a recently developed simulation framework will be discussed, combining the SCILAB environment with SYNOPSIS∕MEDICI device simulations, allowing for the detailed study of both ideal (in agreement with the theoretical solution) and less ideal advanced CMOS structures. Using this simulation framework, new insights will be proposed relating to the capability of RsL to characterize the impact of the presence of oxide charges on the accuracy of the measurements, and the relevance of the RsL leakage value for the actual diode (device) reverse bias characteristics in the presence of an underlying halo∕well implant.
Doping fin field-effect transistor sidewalls: Impurity dose retention in silicon due to high angle incident ion implants and the impact on device performance
Authors: Duffy R. , Curatola G. , Pawlak B. J. , Doornbos G. , van der Tak K. , Breimer P. , van Berkum J. G. M. , Roozeboom F.
Published: February 2008

The three dimensional (3D) nature of a fin field-effect transistor (FinFET) structure creates new challenges for an impurity doped region formation. For the triple gate FinFET, both top and side surfaces require high levels of dopant incorporation to minimize access resistance. In this work, we investigate the use of conventional ion implantation for the introduction of impurities in this 3D silicon structure. Specifically, we evaluate sidewall impurity dose retention at various angles of incidence. The retention of dose is determined by (i) trigonometry of the implant angle in the 3D fin system, (ii) backscattering, and (iii) material properties of the target surface. Dose retention is most sensitive to the implant angle. For a fixed implant projected range, lighter ions are more likely to be ejected from the target. Thus, heavier ions are better for dose retention. The influence of sidewall dose retention on the electrical performance of fully depleted FinFETs was investigated by means of 3D device simulation. Drive current and short channel effect control are more sensitive to dose retention on sidewalls than to dopant conformality.
Enhanced local oxidation of silicon using a conducting atomic force microscope in water
Authors: Hilton A. M. , Jacobson K. W. , Lynch B. P. , Simpson G. J.
Published: February 2008

A new mechanism for direct-write surface scanning probe lithography is considered based on electrodynamic cavitation in a true liquid environment. Oxide layers grown on Si∕SiO2∕H2O and Si∕SiO2∕Au∕H2O interfaces reached maximum heights of 130 and 690nm, respectively. These structures represent a full order of magnitude increase in height over oxides grown in air under similar voltages and time durations, suggesting a unique reaction mechanism. Time-dependent studies indicated that oxide structures generated in water grew by discrete intervals and occasionally grew at a significant distance from the tip, effects that have not been previously reported. The possibility of electrodynamic cavitation-assisting silicon oxide growth under aqueous conditions is considered, potentially opening up opportunities for formation of nanoscale surface structures based on largely underutilized cavitation-induced (e.g., sonochemical) reactions.
Optical properties of n-doped Ga1−xMnxN epitaxial layers grown by metal-organic chemical-vapor deposition in mid and far (5−50 μm) IR range
Authors: Weerasekara A. B. , Hu Z. G. , Dietz N. , Perera A. G. U. , Asghar A. , Kane M. H. , Strassburg M. , Ferguson I. T.
Published: February 2008

Optical properties of n-doped (Si) hexagonal Ga1−xMnxN films (x=0.015) grown by metal-organic chemical-vapor deposition (MOCVD) on c-plane sapphire substrates have been studied by infrared reflectance spectroscopy. The effect of free carriers on GaMnN optical phonons, namely E1(LO) and E1(TO), is explored. It is found that the frequency of E1(LO) increases with increasing free carrier concentration. The absorption coefficient (α) is calculated for the 200−2000 cm−1 range and the maximum value of α is found to be ∼105 cm−1 at a frequency of 560 cm−1. With increasing free carrier concentration, the FWHM of the absorption peak increased by 35%−40% as compared to an unintentionally doped (<1×1016 cm−3) film.
Nanostructuring GaN using microsphere lithography
Authors: Ng W. N. , Leung C. H. , Lai P. T. , Choi H. W.
Published: February 2008

The authors report on the fabrication and characterization of nanopillar arrays on GaN substrates using the technique of microsphere lithography. Self-assembled hexagonally packed silica microsphere arrays were formed on GaN wafers by spin coating and tilting. By precision control of process parameters, a monolayer can be formed over a wide region. The silica microspheres act as a hard mask for pattern transfer of the nanostructures. After dry etching, arrays of nanopillars were formed on the surface of the wafer. The ordered nanostructures can be clearly seen in the scanning electron microscopy images, while photoluminescence measurements revealed a twofold enhancement of light emission intensity.
Surface structure characterization of nanodiamond thin film for electronic field emission applications
Authors: Xie F. Y. , Xie W. G. , Chen J. , Liu X. , Lu D. Y. , Zhang W. H.
Published: February 2008

The nanodiamond thin film is deposited on a single crystal silicon substrate by a dip-coating technique from the pretreated nanodiamond suspension. The surface structures of the as-prepared thin film and the annealed sample have been investigated by x-ray photoelectron spectroscopy and nuclear magnetic resonance. The change of surface elements of O, N, and a different hybridized carbon is derived. Initiation of graphitization is observed at an annealing temperature of 900 °C and the dangling bonds from the internal diamond phase are confirmed. The electron field emission property of this annealed sample is better than the as-prepared thin film. The enhancement of electron emission is discussed with the change of surface structure and the surface states.
Low energy electron-excited nanoscale luminescence spectroscopy studies of intrinsic defects in HfO2 and SiO2–HfO2–SiO2–Si stacks
Authors: Strzhemechny Y. M. , Bataiev M. , Tumakha S. P. , Goss S. H. , Hinkle C. L. , Fulton C. C. , Lucovsky G. , Brillson L. J.
Published: February 2008

Low energy electron-excited nanoscale (LEEN) luminescence spectroscopy and secondary ion mass spectrometry have been used to probe the defect states and chemical composition in as-deposited relatively thick (∼100nm) HfO2 films and in SiO2∕HfO2∕SiO2∕Si (5nm∕15nm∕5nm) heterojunction stacks grown by plasma enhanced chemical vapor deposition including as well changes in bonding and defects after high temperature (900°C) annealing. LEEN measurements of optical transitions in the thicker HfO2 films are assigned to defect-associated radiative transitions centered at approximately 2.7, 3.4, 4.2 and 5.5eV. These spectra exhibited significant changes in as-deposited films (300°C) and after a 900°C anneal in forming gas (N2∕H2). Qualitative differences in LEEN spectra of stacked films are correlated with (i) formation of Hf silicate during deposition of the HfO2 film onto the SiO2 substrates in the as-deposited films, and (ii) a chemical phase separation of these Hf silicates into a heterogeneous mixture SiO2 and HfO2 nanocrystallites after the 900°C anneal.
Optimum activation and diffusion with a combination of spike and flash annealing
Authors: Paul S. , Lerch W. , Chan J. , McCoy S. , Gelpey J. , Cristiano F. , Severac F. , Fazzini P. F. , Bolze D.
Published: February 2008

Different shallow n-type and p-type dopants were annealed with spike, flash, and a combination of spike+flash or vice versa to find the optimum annealing condition for both activation and diffusion. The implant conditions investigated during this study were Ge+74 with B+11 as well as B+11, B49F2+, and As+75. The wafers were characterized regarding sheet resistance, junction depth, and chemical dose. An electrically active dose was derived from the Hall-effect measurement. Transmission electron microscopy analysis for the characterization of defects was done on selected samples. Boron implanted into crystalline as well as preamorphized silicon shows a similarly low sheet resistance which is independent of whether they are annealed with spike+flash, flash, or flash+spike. For arsenic by far the lowest sheet resistance is seen with a combination of spike+flash anneal. The main advantage when using a spike+flash anneal combination is that similar sheet resistance values for arsenic and boron implant can be achieved with the same anneal sequence.
Characterization of the Archaeal Community in a Minerotrophic Fen and Terminal Restriction Fragment Length Polymorphism-Directed Isolation of a Novel Hydrogenotrophic Methanogen
Authors: Cadillo-Quiroz Hinsby , Yashiro Erica , Yavitt Joseph B. , Zinder Stephen H.
Published: February 2008

Minerotrophic fen peatlands are widely distributed in northern latitudes and, because of their rapid turnover of organic matter, are potentially larger sources of atmospheric methane than bog peatlands per unit area. However, studies of the archaeal community composition in fens are scarce particularly in minerotrophic sites. Several 16S rRNA-based primer sets were used to obtain a broad characterization of the archaeal community in a minerotrophic fen in central New York State. A wide archaeal diversity was observed in the site: 11 euryarchaeal and 2 crenarchaeal groups, most of which were uncultured. The E1 group, a novel cluster in the order
Methanomicrobiales
, and
Methanosaetaceae
were the codominant groups in all libraries and results of terminal restriction fragment length polymorphism (T-RFLP) analysis. Given its abundance and potential hydrogenotrophic methane contribution, the E1 group was targeted for culture attempts with a low-ionic-strength medium (PM1). Initial attempts yielded
Methanospirillum
-dominated cultures. However, by incorporating a T-RFLP analysis as a quick selection tool for treatments and replicates, we were able to select an enrichment dominated by E1. Further dilutions to 10
−9
and tracking with T-RFLP yielded a strain named E1-9c. E1-9c is a novel coccoid hydrogenotrophic, mesophilic, slightly acidophilic methanogen and is highly sensitive to Na
2
S concentrations (requires <0.12 mM for growth). We propose E1-9c as the first representative of a novel genus in the
Methanomicrobiales
order.
Development of a Strain-Specific Molecular Method for Quantitating Individual
Campylobacter
Strains in Mixed Populations
Authors: Elvers Karen T. , Helps Christopher R. , Wassenaar Trudy M. , Allen Vivien M. , Newell Diane G.
Published: February 2008

The identification of sites resulting in cross-contamination of poultry flocks in the abattoir and determination of the survival and persistence of campylobacters at these sites are essential for the development of intervention strategies aimed at reducing the microbial burden on poultry at retail. A novel molecule-based method, using strain- and genus-specific oligonucleotide probes, was developed to detect and enumerate specific campylobacter strains in mixed populations. Strain-specific oligonucleotide probes were designed for the short variable regions (SVR) of the
flaA
gene in individual
Campylobacter jejuni
strains. A 16S rRNA
Campylobacter
genus-specific probe was also used. Both types of probes were used to investigate populations of campylobacters by colony lift hybridization. The specificity and proof of principle of the method were tested using strains with closely related SVR sequences and mixtures of these strains. Colony lifts of campylobacters were hybridized sequentially with up to two labeled strain-specific probes, followed by the generic 16S rRNA probe. SVR probes were highly specific, differentiating down to 1 nucleotide in the target sequence, and were sufficiently sensitive to detect colonies of a single strain in a mixed population. The 16S rRNA probe detected all
Campylobacter
spp. tested but not closely related species, such as
Arcobacter skirrowi
and
Helicobacter pullorum
. Preliminary field studies demonstrated the application of this technique to target strains isolated from poultry transport crate wash tank water. This method is quantitative, sensitive, and highly specific and allows the identification and enumeration of selected strains among all of the campylobacters in environmental samples.
Interactions of
Cryptosporidium parvum
,
Giardia lamblia
, Vaccinal Poliovirus Type 1, and Bacteriophages φX174 and MS2 with a Drinking Water Biofilm and a Wastewater Biofilm
Authors: Helmi Karim , Skraber Sylvain , Gantzer Christophe , Willame Raphaël , Hoffmann Lucien , Cauchie Henry-Michel
Published: February 2008

Biofilms colonizing surfaces inside drinking water distribution networks may provide a habitat and shelter to pathogenic viruses and parasites. If released from biofilms, these pathogens may disseminate in the water distribution system and cause waterborne diseases. Our study aimed to investigate the interactions of protozoan parasites (
Cryptosporidium parvum
and
Giardia lamblia
[oo]cysts) and viruses (vaccinal poliovirus type 1, φX174, and MS2) with two contrasting biofilms. First, attachment, persistence, and detachment of the protozoan parasites and the viruses were assessed with a drinking water biofilm. This biofilm was allowed to develop inside a rotating annular reactor fed with tap water for 7 months prior to the inoculation. Our results show that viable parasites and infectious viruses attached to the drinking water biofilm within 1 h and persisted within the biofilm. Indeed, infectious viruses were detected in the drinking water biofilm up to 6 days after the inoculation, while viral genome and viable parasites were still detected at day 34, corresponding to the last day of the monitoring period. Since viral genome was detected much longer than infectious particles, our results raise the question of the significance of detecting viral genomes in biofilms. A transfer of viable parasites and viruses from the biofilm to the water phase was observed after the flow velocity was increased but also with a constant laminar flow rate. Similar results regarding parasite and virus attachment and detachment were obtained using a treated wastewater biofilm, suggesting that our observations might be extrapolated to a wide range of environmental biofilms and confirming that biofilms can be considered a potential secondary source of contamination.
Evolution of the
iss
Gene in
Escherichia coli
Authors: Johnson Timothy J. , Wannemuehler Yvonne M. , Nolan Lisa K.
Published: February 2008

The increased serum survival gene
iss
has long been recognized for its role in extraintestinal pathogenic
Escherichia coli
(ExPEC) virulence.
iss
has been identified as a distinguishing trait of avian ExPEC but not of human ExPEC. This gene has been localized to large virulence plasmids and shares strong similarities with the
bor
gene from bacteriophage λ. Here, we demonstrate that three alleles of
iss
occur among
E. coli
isolates that appear to have evolved from a common λ
bor
precursor. In addition to the occurrence of
iss
on the ColV/BM virulence plasmids, at least two
iss
alleles occur within the
E. coli
chromosome. One of these alleles (designated type 3) was found to occur in the genomes of all currently sequenced ExPEC strains on a similar prophage element that also harbors the Sit iron and manganese transport system. When the prevalence of the three
iss
types was examined among 487
E. coli
isolates, the
iss
type 3 gene was found to occur at a high frequency among ExPEC isolates, irrespective of the host source. The plasmid-borne
iss
allele (designated type 1) was highly prevalent among avian pathogenic
E. coli
and neonatal meningitis-associated
E. coli
isolates but not among uropathogenic
E. coli
isolates. This study demonstrates the evolution of
iss
in
E. coli
and provides an additional tool for discriminating among
E. coli
pathotypes through the differentiation of the three
iss
allele types and
bor
.
Carnitine-Dependent Transport of Acetyl Coenzyme A in
Candida albicans
Is Essential for Growth on Nonfermentable Carbon Sources and Contributes to Biofilm Formation
Authors: Strijbis Karin , van Roermund Carlo W. T. , Visser Wouter F. , Mol Els C. , van den Burg Janny , MacCallum Donna M. , Odds Frank C. , Paramonova Ekaterina , Krom Bastiaan P. , Distel Ben
Published: February 2008

In eukaryotes, acetyl coenzyme A (acetyl-CoA) produced during peroxisomal fatty acid β-oxidation needs to be transported to mitochondria for further metabolism. Two parallel pathways for acetyl-CoA transport have been identified in
Saccharomyces cerevisiae
; one is dependent on peroxisomal citrate synthase (Cit), while the other requires peroxisomal and mitochondrial carnitine acetyltransferase (Cat) activities. Here we show that the human fungal pathogen
Candida albicans
lacks peroxisomal Cit, relying exclusively on Cat activity for transport of acetyl units. Deletion of the
CAT2
gene encoding the major Cat enzyme in
C. albicans
resulted in a strain that had lost both peroxisomal and mitochondrion-associated Cat activities, could not grow on fatty acids or C
2
carbon sources (acetate or ethanol), accumulated intracellular acetyl-CoA, and showed greatly reduced fatty acid β-oxidation activity. The
cat2
null mutant was, however, not attenuated in virulence in a mouse model of systemic candidiasis. These observations support our previous results showing that peroxisomal fatty acid β-oxidation activity is not essential for
C. albicans
virulence. Biofilm formation by the
cat2
mutant on glucose was slightly reduced compared to that by the wild type, although both strains grew at the same rate on this carbon source. Our data show that
C. albicans
has diverged considerably from
S. cerevisiae
with respect to the mechanism of intracellular acetyl-CoA transport and imply that carnitine dependence may be an important trait of this human fungal pathogen.
Aspergillus calidoustus
sp. nov., Causative Agent of Human Infections Previously Assigned to
Aspergillus ustus
Authors: Varga János , Houbraken Jos , Van Der Lee Henrich A. L. , Verweij Paul E. , Samson Robert A.
Published: February 2008

Aspergillus ustus
is a relatively rare human pathogen causing invasive infections in immunocompromised hosts. In this study isolates originating from clinical and other sources have been examined using molecular, morphological, and physiological approaches to clarify their species assignment. Phylogenetic analysis of partial β-tubulin, calmodulin, actin, and intergenic transcribed spacer sequences indicated that none of the clinical isolates recognized previously as
A. ustus
belongs to this species. All but two of these isolates formed a well-defined clade related to
A. pseudodeflectus
based on sequence analysis of protein-coding regions. Morphological and physiological examination of these isolates indicated that they are able to grow above 37°C, in contrast with
A. ustus
isolates, and give a positive Ehrlich reaction, in contrast with related species including
A. granulosus, A. ustus
, and
A. pseudodeflectus
. These isolates are proposed as a new species,
A. calidoustus
. Antifungal susceptibility testing showed that this species has decreased susceptibilities to several antifungal drugs. The triazoles are inactive in vitro, including the new azole posaconazole.
Late-Stage Polyribitol Phosphate Wall Teichoic Acid Biosynthesis in
Staphylococcus aureus
Authors: Meredith Timothy C. , Swoboda Jonathan G. , Walker Suzanne
Published: February 2008

Wall teichoic acids are cell wall polymers that maintain the integrity of the cellular envelope and contribute to the virulence of
Staphylococcus aureus
. Despite the central role of wall teichoic acid in
S. aureus
virulence, details concerning the biosynthetic pathway of the predominant wall teichoic acid polymer are lacking, and workers have relied on a presumed similarity to the putative polyribitol phosphate wall teichoic acid pathway in
Bacillus subtilis
. Using high-resolution polyacrylamide gel electrophoresis for analysis of wall teichoic acid extracted from gene deletion mutants, a revised assembly pathway for the late-stage ribitol phosphate-utilizing enzymes is proposed. Complementation studies show that a putative ribitol phosphate polymerase, TarL, catalyzes both the addition of the priming ribitol phosphate onto the linkage unit and the subsequent polymerization of the polyribitol chain. It is known that the putative ribitol primase, TarK, is also a bifunctional enzyme that catalyzes both ribitol phosphate priming and polymerization. TarK directs the synthesis of a second, electrophoretically distinct polyribitol-containing teichoic acid that we designate K-WTA. The biosynthesis of K-WTA in
S. aureus
strain NCTC8325 is repressed by the accessory gene regulator (
agr
) system. The demonstration of regulated wall teichoic acid biosynthesis has implications for cell envelope remodeling in relation to
S. aureus
adhesion and pathogenesis.
Sinorhizobium melilotiMutants Lacking Phosphotransferase System Enzyme HPr or EIIA Are Altered in Diverse Processes, Including Carbon Metabolism, Cobalt Requirements, and Succinoglycan Production
Authors: Pinedo Catalina Arango , Bringhurst Ryan M. , Gage Daniel J.
Published: February 2008

Sinorhizobium melilotiis a member of theAlphaproteobacteriathat fixes nitrogen when it is in a symbiotic relationship. Genes for an incomplete phosphotransferase system (PTS) have been found in the genome ofS. meliloti. The genes present code for Hpr and ManX (an EIIAMan-type enzyme). HPr and EIIA regulate carbon utilization in other bacteria.hprandmanXin-frame deletion mutants exhibited altered carbon metabolism and other phenotypes. Loss of HPr resulted in partial relief of succinate-mediated catabolite repression, extreme sensitivity to cobalt limitation, rapid die-off during stationary phase, and altered succinoglycan production. Loss of ManX decreased expression ofmelA-agpandlac, the operons needed for utilization of α- and β-galactosides, slowed growth on diverse carbon sources, and enhanced accumulation of high-molecular-weight succinoglycan. A strain with bothhprandmanXdeletions exhibited phenotypes similar to those of the strain with a singlehprdeletion. Despite these strong phenotypes, deletion mutants exhibited wild-type nodulation and nitrogen fixation when they were inoculated ontoMedicago sativa. The results show that HPr and ManX (EIIAMan) are involved in more than carbon regulation inS. melilotiand suggest that the phenotypes observed occur due to activity of HPr or one of its phosphorylated forms.
Interactions between CdsD, CdsQ, and CdsL, Three PutativeChlamydophila pneumoniaeType III Secretion Proteins
Authors: Johnson Dustin L. , Stone Chris B. , Mahony James B.
Published: February 2008

Chlamydophila pneumoniaeis a gram-negative obligate intracellular bacterial pathogen that causes pneumonia and bronchitis and may contribute to atherosclerosis. The developmental cycle ofC. pneumoniaeincludes a morphological transition from an infectious extracellular elementary body (EB) to a noninfectious intracellular reticulate body (RB) that divides by binary fission. TheC. pneumoniaegenome encodes a type III secretion (T3S) apparatus that may be used to infect eukaryotic cells and to evade the host immune response. In the present study, Cpn0712 (CdsD), Cpn0704 (CdsQ), and Cpn0826 (CdsL), threeC. pneumoniaegenes encoding yersiniae T3S YscD, YscQ, and YscL homologs, respectively, were cloned and expressed as histidine- and glutathioneS-transferase (GST)-tagged proteins inEscherichia coli. Purified recombinant proteins were used to raise hyper-immune polyclonal antiserum and were used in GST pull-down and copurification assays to identify protein-protein interactions. CdsD was detected in both EB and RB lysates by Western blot analyses, and immunofluorescent staining demonstrated the presence of CdsD within inclusions. Triton X-114 solubilization and phase separation of chlamydial EB proteins indicated that CdsD partitions with cytoplasmic proteins, suggesting it is not an integral membrane protein. GST pull-down assays indicated that recombinant CdsD interacts with CdsQ and CdsL, and copurification assays with chlamydial lysates confirmed that native CdsD interacts with CdsQ and CdsL. To the best of our knowledge, this is the first report demonstrating interactions between YscD, YscQ, and YscL homologs of bacterial T3S systems. These novel protein interactions may play important roles in the assembly or function of the chlamydial T3S apparatus.
ROLE OF THE ROOT IN THE TRANSLOCATION OF PRODUCTS OF PHOTOSYNTHESIS IN SUGAR BEET, SOYBEAN, AND PUMPKIN
Authors: Winter H. , Mortimer D. C.
Published: February 2008

The influence of root function on the export of 14C-labelled products from leaves of sugar beet, soybean, and pumpkin plants was examined with reference to the concept of a circulatory mechanism for translocation. When roots were placed on demineralized water for periods up to 10 days, oxygen uptake rates were reduced. In sugar beet, this was accompanied by an apparent stimulation of about 21% in the quantity of labelled sugar exported from the leaf. In soybean and pumpkin the quantity of export was not altered, but the distribution of exported 14C in the plant was modified to favor a decrease in the proportion recovered from the young parts and an increase in that from the stem and root. The absence of nutrient in the root medium did not result in any significant changes in the pattern of slow metabolism of the sugar translocated to the roots of sugar beet or soybean. In the pumpkin, the proportion of radioactivity recovered in the amino acids was lower, and glyceric acid accumulated in the fed leaf. When portions of the sugar beet root were excised 30 min before assimilation of 14CO2 by a leaf, the quantity of labelled sucrose exported during a 30-min interval was reduced to about 25% of normal, but the apparent velocity of translocation was not altered and the reduction in quantity could be eliminated by extending the time allowed for export. These results led to the conclusion that the root does not exert a controlling influence on translocation, but that it can contribute to the efficiency of the process.
ASCORBIC ACID AND CAROTENE VALUES OF NATIVE EASTERN ARCTIC PLANTS
Authors: Hoffman I. , Nowosad F. S. , Cody W. J.
Published: February 2008

Leaves, stems, roots, and berries of a number of native plants which were collected in the Ungava Bay region of northern Quebec were analyzed for ascorbic acid (vitamin C) and β-carotene (vitamin A) in a laboratory set up near Fort Chimo.The results indicated that some plants from the Eastern Arctic were remarkably vitamin-rich. These findings demonstrated that wild plants represent a valuable natural resource which might be utilized under survival conditions or as required to ensure proper nutrition in the far North.
Histological study of organogenesis in vitro from callus cultures of two Nicotiana species
Authors: Ronchi V. Nuti
Published: February 2008

The histological events leading to shoot formation in Nicotiana glauca and in the nontumorous Nicotiana glauca × Nicotiana langsdorffii hybrid have been studied. Organized development begins from a single vacuolated parenchyma cell which divides and precociously differentiates tracheidal cells, forming a growth center with nodular structures with xylem in the center and phloem outside. The vascular tissue is precociously separated from the surrounding callus by a layer of cells which are shown to be endodermal by position and by histochemical reactions. Further growth leads to the formation of a mound of meristematic tissue which later forms shoot apical meristems. The sequences of events are discussed in relation to other known systems of regeneration in calluses.The system described could be suitable for evaluating the effects of various physical and chemical agents on the different steps of differentiation.