bluuebunny/crossref_metadata_2025 huggingface dataset:
Do radiologists agree on the quality of computed tomography enterography?
Authors: Ersland Kari , Kvaløy Jan Terje , Styr Bodil Margrethe , Helland Eli Berit , Espeland Ansgar
Published: July 2009

This study aimed to assess variation between radiologists evaluating the quality of multi‐detector computed tomography enterography.

For 40 consecutive examinations, three experienced radiologists independently rated the following quality variables: % length of adequately filled bowel, bowel lumen diameters, bowel wall delineation, superior mesenteric vein, and bowel wall enhancement, artefacts, and total quality. We calculated the mean difference between observers with standard deviation (SD) for continuous variables and % total agreement, exact Fleiss kappa, and P‐values (McNemar's test) for categorical variables.

Depending on bowel segment (duodenum distal to bulb, jejunum, ileum, terminal ileum), mean difference between observers ranged from two to 33 (SD from 11 to 32) for % length of adequately filled bowel judged subjectively, 0–2 (SD 0–3) mm for smallest bowel lumen diameter and 0–4 (SD 3–7) mm for largest bowel lumen diameter. Agreement on bowel wall delineation was 80%/kappa 0.50 in duodenum, 90%/kappa 0.57 in jejunum, 75%/kappa 0.14 in ileum and 88%/kappa 0.17 in terminal ileum, where ratings differed between observers (P < 0.04). Agreement was 65%/kappa 0.18 for bowel wall enhancement judged subjectively. For contrast enhancement measured in Hounsfield Units, mean difference between observers ranged from two to 11 (SD 12–15) in normal jejunum wall and zero to one (SD 4–5) in the superior mesenteric vein depending on observer pair. Agreement was 78%/kappa 0.12 for image artefacts. Rating of total examination quality (good/optimal versus poor/very poor) differed between observers (P < 0.01); agreement was 60%/kappa 0.41.

Many subjective evaluations varied between observers. We believe that measurements of bowel lumen diameters and contrast enhancement may be preferable.
T1‐weighted fluid‐attenuated inversion recovery and T1‐weighted fast spin‐echo contrast‐enhanced imaging: A comparison in 20 patients with brain lesions
Authors: Al‐Saeed O , Ismail M , Athyal RP , Rudwan M , Khafajee S
Published: July 2009

T1‐weighted fluid‐attenuated inversion recovery (FLAIR) sequence is a relatively new pulse sequence for intracranial MR imaging. This study was performed to compare the image quality of T1‐weighted FLAIR with the T1‐weighted FSE sequence. Twenty patients with brain lesions underwent T1‐weighted fast spin‐echo (FSE) and T1‐weighted FLAIR during the same imaging session. Four quantitative and three qualitative criteria were used to compare the two sequences after contrast. Two of four quantitative criteria pertained to lesion characteristics: lesion to white matter (WM) contrast‐to‐noise ratio (CNR) and lesion to cerebrospinal fluid (CSF) CNR, and two related to signals from normal tissue: grey matter to WM CNR and WM to CSF CNR. The three qualitative criteria were conspicuousness of the lesion, the presence of image artefacts and the overall image contrast. Both T1‐weighted FSE and FLAIR images were effective in demonstrating lesions. Image contrast was superior in T1‐weighted FLAIR images with significantly improved grey matter‐WM CNRs and CSF‐WM CNRs. The overall image contrast was judged to be superior on T1‐weighted FLAIR images compared with T1‐weighted FSE images by all neuroradiologists. Two of three reviewers considered that the FLAIR images had slightly increased imaging artefacts that, however, did not interfere with image interpretation. T1‐weighted FLAIR imaging provides improved lesion‐to‐background and grey to WM contrast‐to‐noise ratios. Superior conspicuity of lesions and overall image contrast is obtained in comparable acquisition times. These indicate an important role for T1‐weighted FLAIR in intracranial imaging and highlight its advantage over the more widely practiced T1‐weighted FSE sequence.
Impact of a real‐time peer review audit on patient management in a radiation oncology department
Authors: Boxer M , Forstner D , Kneebone A , Delaney G , Koh E‐S , Fuller M , Kaadan N
Published: July 2009

In September 2006, the Royal Australian and New Zealand College of Radiologists (RANZCR) endorsed the modified Peer Review Audit Tool (PRAT). We aimed to assess the feasibility of using this tool in a busy radiation oncology department using an electronic medical record (EMR) system, identify areas of compliance and assess the impact of the audit process on patient management. Fortnightly random clinical audit was undertaken by using the revised RANZCR PRAT in the departments of radiation oncology at Liverpool and Macarthur Cancer Therapy Centres (LCTC and MCTC). Following audit of the EMR, treatment plans were audited by peer review. Data were collected prospectively from June 2007 to June 2008. Audits were carried out on 208 patients. Behaviour criteria were well documented in the EMR, but scanning of histology and medical imaging reports did not occur in up to a third of cases. With electronic prescriptions, treatment prescription errors were rare. In total, 8 (3.8%) out of 208 patients had a change to management recommended. Variability in interpretation of PRAT ‘protocol/study’ criteria was identified. We found that real‐time audit is feasible and effective in detecting both issues with documentation in the EMR, and a small number of patients in whom a change to management is recommended. Recommendations have been made in order to continue to improve the audit process including documentation of any changes recommended and whether the recommended change occurred.
Centre credentialing for Trans Tasman Radiation Oncology Group trial 06.02: multicentre feasibility study of accelerated partial breast irradiation
Authors: Kron T , Willis D , Bignell F , Martland J , Donnell S , May S , Chua BH
Published: July 2009

Introduction:  Inconsistencies in contouring target volumes for partial breast irradiation (PBI) may result in geographical misses and compromise treatment outcomes. The present study aimed to (1) determine the variability of the target volumes contoured and treatment plans generated by participating centres in credentialing for participation in a multicentre PBI trial; and (2) assess dosimetric changes when standardized target volumes were used.

Methods:  The CT image sets of two de‐identified patients post‐breast conserving surgery were used. Contouring of the target volumes for the two cases was performed and a treatment plan as per protocol specifications was generated for each case by the seven participating centres. Planning of both cases was repeated by five centres using a set of standardized target volumes to evaluate resulting dosimetric changes in the treatment plans.

Results:  The surgical cavity, the part of the planning target volume used for dose evaluation and ipsilateral whole breast volumes contoured by the centres varied by 25%, 16% and 21% (1 standard deviation), respectively. The dosimetric variations found when the standardized target volumes were used were smaller than those noted when centre‐specific volumes were used. The volumes of the ipsilateral lungs receiving 30% of the prescribed dose and the volumes of the ipsilateral whole breasts receiving 95% and 50% of the prescribed dose were reduced in the treatment plans developed using the standardized target volumes.

Conclusions:  Given the impact of contouring on dose distributions, quality assurance procedures in clinical trials of PBI need to take into account both the technical approaches and the contouring.
A ‘Catch Up’ Plan for radiotherapy in New South Wales to 2012
Authors: Morgan Graeme , Barton Michael , Crossing Sally , Bull Colin , Penman Andrew
Published: July 2009

In New South Wales (NSW) from 1996 to 2006, only 34–37% of newly diagnosed cancer patients were treated with radiotherapy instead of the 50% proposed by NSW Health in Radiotherapy Plans released in 1991, 1995 and 2003. As a consequence, over 50 000 cancer patients were not treated and has resulted in the estimated premature death of over 8000 patients and over 40 000 years of life lost. In 2008, there were 42 linear accelerators in NSW rather than the 62 recommended. Based on cancer incidence projections, NSW will require 69 linear accelerators in 2012 – a shortfall of 27 linear accelerators. Already 15 linear accelerators have been approved. NSW Health has funding for seven extra linear accelerators, and eight extra linear accelerators are to be funded by the private sector. To make up the shortfall, a ‘Catch Up’ Plan is proposed for an additional 12 linear accelerators by the end of fiscal year 2012. This is estimated to cost $200 million over 4 years for one‐off establishment costs for buildings and equipment plus $50 million per year for recurrent operating costs such as staff salaries. The ‘Catch Up’ Plan will create five new departments of radiation oncology in country hospitals and three new departments in metropolitan hospitals. These will be in addition to those already approved by NSW Health and will markedly improve access for treatment and result in an improvement in cancer survival. This significant increase in departments and equipment can only be achieved by the creation of an NSW Radiotherapy Taskforce similar to that proposed in the Baume report of 2002, ‘A vision for radiotherapy’. Even if the ‘Catch Up’ Plan bridges the gap in service provision, forward planning beyond 2012 should commence immediately as 76 linear accelerators will be required for NSW in 2015 and 81 linear accelerators in 2017.
The spiritual commons: Some immaterial aspects of community economies in eastern Indonesia
Authors: McWilliam Andrew
Published: July 2009

Informed by anthropologist Stephen Gudeman’s dialect between the interacting realms of community and market economies, I seek in this article to focus on aspects of the commons and the shared values of a community that might be referred to as the ‘spiritual commons’. The phrase speaks specifically to the ideas and practices that guide the ritual and spiritual elements of social life. I argue that the spiritual commons is not a realm set apart from economic life but integral to its reproduction. Gift exchange, sacrifice and commensality enacted as expressions of religious sociality represent economies of symbolic goods that serve both material and ideational ends. The article draws upon ethnographies of eastern Indonesia and the comparative possibilities expressed in case studies from Islamic southeast Sulawesi and Catholic Flores.
Speaking for itself: Art, meaning and power in New Ireland, Papua New Guinea
Authors: Eves Richard
Published: July 2009

Taking the example of thetubuanmasked figure, an art form of New Ireland, I explore recent theoretical debates on the question of meaning in art. Challenging approaches that privilege the semiotic, I argue that this form of art is more appropriately seen as a revelation of power. The tubuan brings forth the concealed efficacy, capacities and intentionality of the producer, which elicit responses from, or act upon, the audience in various negative or positive ways. This art object is a form of disclosure in itself, and thus speaks for itself. The appreciation of this art is not a matter of cerebral contemplation, the unearthing of ideas and the translation of images into verbal form, but in an embodied form that is experienced directly as affect. I take seriously the embodied nature of social action, of which the production of art is one form.
The Islam of anthropology
Authors: Houston Christopher
Published: July 2009

Research on ‘Muslim societies’ is a controversial topic in the present, particularly given the US army’s current employment of anthropological experts in war zones under military occupation. In 2006 the UK Foreign Office, too, sought to include anthropologists in its worldwide research project entitled ‘Combating Terrorism by Countering Radicalization’, with grants given outside the normal process of research funding and differently assessed. In this article, I immodestly argue for how the discipline of anthropology should apprehend and analyse Islam in the present political context. The paper claims that anthropological research provides an antidote to the Islamophobia of much talk about Islam in the Australian public sphere, an Islamophobia originating not only from the right but from some leftists and feminists as well.
Of crustacean blood and ant infection: Life in the migration exclusion zone, Christmas Island, Australia
Authors: Dennis Simone
Published: July 2009

This paper is framed by the cultural politics of nationhood in contemporary Australia and particularly by the ways in which the nation has sought to produce borders that have manifested themselves as altered cartographic boundaries and exclusion zones. The paper itself is concerned with life on Christmas Island, and is focused on the ways in which multiethnic Christmas Island locals use blood metaphors drawn from the Island’s native Christmas Island red crabs and alien, predatory yellow ants, to articulate patterns of human movement and migration into island space. The metaphors reveal coalescences between the body of the self, the other, nature, and the island place. I explore these coalescences to present a picture of migration and movement from the perspective of those who live within the migration exclusion zone.
Seeking healing transnationally: Australians, John of God and Brazilian Spiritism
Authors: Rocha Cristina
Published: July 2009

João de Deus (John of God) is a Brazilian faith healer who has become increasingly well‐known outside Brazil. In 2006 alone he was invited to conduct healing events in Germany, the United States of America and New Zealand. He returned to the United States of America and New Zealand in 2007, and in 2008 was once again in the United States of America. There are plans for him to come to Australia in the near future. This article is based on ethnographic research conducted in Brazil, New Zealand and Australia and on interviews with Australians in Sydney. Here, I explore the stories of Australian followers of John of God and their reasons for seeking his healing system. I argue that Western New Age and alternative medicine concepts of healing produce a disposition (Bourdieu 1972) towards ‘traditional’ healing from exotic lands. I show that the reinstatement of a connection between healing and religion, the construction of context that gives meaning to illness, and empowerment through surrendering to a higher power are three important factors that help to explain why people shun Western medicine in favour of alternative practices.
In
0.53
Ga
0.47
As
n-metal-oxide-semiconductor field effect transistors with atomic layer deposited Al2O3, HfO2, and LaAlO3 gate dielectrics
Authors: Zhao Han , Yum Jung Hwan , Chen Yen-Ting , Lee Jack C.
Published: July 2009

The authors have fabricated In0.53Ga0.47As metal-oxide-semiconductor transistors and studied the effects of different atomic layer deposited (ALD) gate dielectrics (Al2O3, HfO2, and LaAlO3) on device performance including the equivalent oxide thickness (EOT) scalability, the current driving capability, and the interface quality. ALD Al2O3 shows the best interface quality with InGaAs substrates, but it can only obtain EOT of about 2.4 nm due to its comparably low dielectric constant (κ=8.1). LaAlO3 has higher dielectric constant (κ=12.1) than Al2O3 and achieves subthreshold swing of 84 mV/decade for 1.3 nm EOT. HfO2 (κ=17.0) demonstrates the minimum EOT of 1 nm with high drive current of 133.3 mA/mm (L=5 μm).
Plasmonic behavior of Ag/dielectric nanowires and the effect of geometry
Authors: Prokes S. M. , Alexson D. , Glembocki O. J. , Park H. D. , Rendell R. W.
Published: July 2009

Recently, the authors have shown that dielectric/metal composite nanowires exhibit very strong surface enhanced Raman (SERS) signals when arranged in a random three-dimensional geometry. Since they believe that the intersections of nanowires are critical in generating the high electric fields necessary for this enhancement, they have investigated the effect of crossing geometry under more controlled conditions. Thus, they will discuss the formation of nanowire arrays by in situ growth achieved by the control of nanowire material/substrate combination, as well as ex situ nanowire array formation involving e-beam lithography. They have examined the plasmonic effects, both longitudinal and transverse, due to changes in crossing geometry by specific placements of dielectric/metal nanowires on the fabricated arrays. The effects of nanowire geometry and the resulting SERS behavior show the importance of the dielectric/metal configuration, as well as the importance of nanowire angular geometry in the SERS enhancement.
Hot electron transport studies of the Cu/Si(001) interface using ballistic electron emission microscopy
Authors: Garramone J. J. , Abel J. R. , Sitnitsky I. L. , Moore R. L. , LaBella V. P.
Published: July 2009

The hot electron transport properties of the Cu/Si(001) interface have been studied using ballistic electron emission microscopy (BEEM). The Schottky barrier height was measured to be 0.64±0.02 eV. The scanning tunneling microscopy images provide evidence of Volmer–Weber growth of the metal, while Rutherford backscattering spectrometry data corroborated with Auger depth profiling indicate distinct Cu and Si regions with little intermixing. Comparison with Au/Si(001) BEEM data provides some insight into the hot electron transport and scattering properties of the Cu/Si(001) interface.
Diffraction studies of submonolayer Sr structures on the Si (001) surface
Authors: Reiner J. W. , Segal Y. , Garrity K. F. , Hong H. , Ismail-Beigi S. , Ahn C. H. , Walker F. J.
Published: July 2009

Using electron and synchrotron x-ray diffraction, the authors investigate the reconstructions induced on the Si (001) surface by the presence of a submonolayer of Sr atoms. These Sr surface phases on Si (001) are the first steps in the synthesis of crystalline oxide on silicon heterostructures. Through the use of in situ reflection high energy electron diffraction, the authors observe 2×1→2×3→1×2 transitions in the surface symmetry as 12 monolayer Sr is deposited at 650 °C. Anomalous synchrotron x-ray diffraction studies of the 2×3 structure are consistent with a model where each Sr atom replaces two silicon dimers, resulting in a change in the surface Si stoichiometry. X-ray diffraction from the surface formed when the Sr deposition occurs at room temperature shows a different dependence on x-ray energy and is consistent with a surface phase consisting of Sr adsorbed onto a stoichiometric Si surface.
Current collapse transient behavior and its mechanism in submicron-gate AlGaN∕GaN heterostructure transistors
Authors: Hasegawa Hideki , Akazawa Masamichi
Published: July 2009

The current collapse transient behavior of a practical submicron AlGaN∕GaN heterostructure field effect transistor (HFET) is investigated, and its mechanism is proposed. First, the steady-state and transient characteristics of the Schottky diode obtained by connecting the source and drain electrodes of the transistor have been investigated. The steady-state characteristics can be explained by the thin surface barrier model, indicating the presence of tunneling injection of electrons. Turn-on and turn-off transient characteristics of the reverse current of Schottky diode showed very slow nonexponential transients covering six orders of magnitude of time scale from milliseconds to thousands of seconds. They are very similar to those of a large planar Schottky diode studied recently by the authors. The HFET device showed a clear current collapse behavior after a gate stress beyond pinch off. Pulsed gate stress visualized drain current transients which again included very slow nonexponential transients covering six orders of magnitude of time scale. The whole experimental results are explained consistently by a model in which the current collapse is due to surface state charging near the source side and drain side of the gate edge where its rate limiting process is not the usual Shockley–Read–Hall capture-emission process but the dispersive electron transport through the surface states by time-continual hopping, which is triggered by the tunneling injection process at the gate edge.
Anisotropic half-metallic ground state of Mn atomic wire on GaAs(110)
Authors: Hirayama Motoi , Natori Akiko , Nakamura Jun
Published: July 2009

The authors have investigated magnetic properties of Ga-substituted Mn atomic wires on the GaAs(110) surface, using first-principles calculations based on the spin-density functional theory. The Mn atomic wires are assumed to align in the ⟨110⟩- and ⟨001⟩-directions. The ⟨110⟩-oriented wire is more stable than the ⟨001⟩-oriented one and has the ferromagnetic ground state with the magnetic moment of 4.0μB per Mn atom. The band structure has a large dispersion along the wire and exhibits a half-metallic state. The ferromagnetic character of the Mn wire results from the double exchange interaction through the p-d hybridization between the Mn-3d and the GaAs surface states.
Theory and measurements of room temperature transport in graphene using SiO2 backgate and electrochemical gate
Authors: Shishir R. S. , Chen F. , Xia J. , Tao N. J. , Ferry D. K.
Published: July 2009

Room temperature transport measurements of a gated graphene monolayer, whose field effect is tuned by an oxide backgate and an electrochemical gate, are presented. The graphene samples are obtained by mechanical exfoliation, and conductance as a function of gate voltage and molarity of the electrochemical solution is measured. The experimental data are then explained and fit by a transport theory using Rode’s method and incorporating several scattering mechanisms such as acoustic phonon, optical phonon, remote impurity, and surface roughness scattering. The calculation shows impurity scattering and roughness scattering to be very important scattering mechanisms for room temperature graphene transport. Moreover, the disorder in graphene raises the value of minimum conductivity from the reported theoretical minimum.
Capacitance-voltage and photoluminescence study of high-k∕GaAs interfaces controlled by Si interface control layer
Authors: Akazawa Masamichi , Domanowska Alina , Adamowicz Boguslawa , Hasegawa Hideki
Published: July 2009

The authors performed a detailed capacitance-voltage (C-V) and photoluminescence (PL) study of the high-k dielectric/GaAs interface controlled by the Si interface control layer (Si ICL) grown by molecular beam epitaxy to investigate the feasibility of a PL method for interface characterization and to find out the optimum thickness of the Si ICL. The sample had a HfO2∕SiNx∕Si ICL/n-GaAs structure where the ultrathin SiNx buffer layer was formed by in situ partial nitridation of the Si ICL itself. For this structure, they measured the quantum efficiency of photoluminescence as a function of the excitation photon flux density and carried out a computer analysis to determine the most likely distribution of the interface state density Dit. Remarkably good agreements were obtained between the high-frequency C-V method and the PL method, indicating that the present PL method may serve as a powerful contactless and nondestructive tool for developing an optimal surface passivation structure and its processing technology. Using C-V and PL methods, they found the optimum initial thickness of Si ICL before partial nitridation to be 5–6 ML. With this thickness, a Dit minimum value of (1–2)×1011cm−2eV−1 was achieved in the HfO2∕SiNx∕Si ICL/n-GaAs structure. When the thickness was too large, it led to the generation of misfit dislocations, whereas a too thin Si ICL led to subcutaneous nitridation of GaAs during partial nitridation of the Si ICL, leading to interface disorder.
Ultralow resistance, nonalloyed Ohmic contacts to n-InGaAs
Authors: Baraskar Ashish K. , Wistey Mark A. , Jain Vibhor , Singisetti Uttam , Burek Greg , Thibeault Brian J. , Lee Yong Ju , Gossard Arthur C. , Rodwell Mark J. W.
Published: July 2009

The authors report ultralow specific contact resistivity (ρc) in nonalloyed, in situ Ohmic contacts to heavily doped n-type In0.53Ga0.47As:Si layers with 6×1019cm−3 active carrier concentration, lattice matched to InP. The contacts were formed by depositing molybdenum (Mo) immediately after the In0.53Ga0.47As growth without breaking vacuum. Transmission line model measurements showed a contact resistivity of (1.1±0.6)×10−8Ωcm2 for the Mo∕InGaAs interface. The contacts show no observable degradation in resistivity after annealing at 300 and 400°C for 1min duration.
Response to Comment on “Remeasuring the Double Helix”
Authors: Mathew-Fenn Rebecca S. , Das Rhiju , Fenn Timothy D. , Schneiders Michael , Harbury Pehr A. B.
Published: July 2009

We measured the mean and variance of end-to-end length in short DNA fragments in solution and reported evidence of DNA stretching that is cooperative over more than two turns of the double helix. Becker and Everaers suggest that the structural fluctuations we observed arise from bending motions of the DNA, rather than stretching. We present three experimental tests of this bending-based explanation.
Probing Spin-Charge Separation in a Tomonaga-Luttinger Liquid
Authors: Jompol Y. , Ford C. J. B. , Griffiths J. P. , Farrer I. , Jones G. A. C. , Anderson D. , Ritchie D. A. , Silk T. W. , Schofield A. J.
Published: July 2009

Electron Breakdown

An electron possesses charge and spin. In general, these properties are confined to the electron. However, in strongly interacting many-body electronic systems, such as one-dimensional wires, it has long been theorized that the charge and spin should separate. There have been tantalizing glimpses of this separation experimentally, but questions remain.

Jompol
et al.

(p.
597
) looked at the tunneling current between an array of one-dimensional wires and a two-dimensional electron gas and argue that the results reveal a clear signature of spin-charge separation.
The cAMP Sensor Epac2 Is a Direct Target of Antidiabetic Sulfonylurea Drugs
Authors: Zhang Chang-Liang , Katoh Megumi , Shibasaki Tadao , Minami Kohtaro , Sunaga Yasuhiro , Takahashi Harumi , Yokoi Norihide , Iwasaki Masahiro , Miki Takashi , Seino Susumu
Published: July 2009

Expanding Sulfonylurea Mechanisms

Sulfonylureas are important drugs used for treatment of diabetes that act through adenosine triphosphate–sensitive potassium channels to promote secretion of insulin from the pancreas.

Zhang
et al.

(p.
607
) present another mechanism by which the beneficial effects of sulfonylureas may also be obtained. Sulfonylureas were identified in a screen for substances that modify the activity of Epac2, a guanine nucleotide exchange factor for the small guanosine triphosphatase Rap1. Mice lacking Epac2 were less responsive to sulfonylureas, which may suggest that Epac2 would be a useful target for development of drugs for treatment of diabetes.
Nucleosomal Fluctuations Govern the Transcription Dynamics of RNA Polymerase II
Authors: Hodges Courtney , Bintu Lacramioara , Lubkowska Lucyna , Kashlev Mikhail , Bustamante Carlos
Published: July 2009

Gradual Unpacking

Eukaryotic DNA is packaged onto nucleosomes, which form the main constituent of chromatin. This packaging material presents a barrier to accessing the genome by the various machineries that need to deal with the DNA: replication, recombination, repair, and transcription complexes, for example.

Hodges
et al.

(p.
626
; see the Perspective by

Otterstrom and van Oijen

) use single-molecule techniques to analyze how a yeast RNA polymerase II ternary elongation complex copes when it encounters a single nucleosome directly in its path. The polymerase does not actively peel the DNA from the nucleosome's surface but, instead, waits patiently until the DNA fluctuates off the nucleosome and then advances, increment by increment, until the nucleosome is destabilized. Under certain conditions the destabilized nucleosome, rather than being lost entirely from the DNA, can be passed back to the DNA behind the polymerase.
Soil Microbial Communities and Restoration Ecology: Facilitators or Followers?
Authors: Harris Jim
Published: July 2009

Microorganisms have critical roles in the functioning of soil in nutrient cycling, structural formation, and plant interactions, both positive and negative. These roles are important in reestablishing function and biodiversity in ecosystem restoration. Measurement of the community indicates the status of the system in relation to restoration targets and the effectiveness of management interventions, and manipulation of the community shows promise in the enhancement of the rate of recovery of degraded systems.
Rebuilding Global Fisheries
Authors: Worm Boris , Hilborn Ray , Baum Julia K. , Branch Trevor A. , Collie Jeremy S. , Costello Christopher , Fogarty Michael J. , Fulton Elizabeth A. , Hutchings Jeffrey A. , Jennings Simon , Jensen Olaf P. , Lotze Heike K. , Mace Pamela M. , McClanahan Tim R. , Minto Cóilín , Palumbi Stephen R. , Parma Ana M. , Ricard Daniel , Rosenberg Andrew A. , Watson Reg , Zeller Dirk
Published: July 2009

Fighting for Fisheries

In the debate concerning the future of the world's fisheries, some have forecasted complete collapse but others have challenged this view. The protagonists in this debate have now joined forces to present a thorough quantitative review of current trends in world fisheries.

Worm
et al.

(p.
578
) evaluate the evidence for a global rebuilding of marine capture fisheries and their supporting ecosystems. Contrasting regions that have been managed for rebuilding with those that have not, reveals trajectories of decline and recovery from individual stocks to species, communities, and large marine ecosystems. The management solutions that have been most successful for rebuilding fisheries and ecosystems, include both large- and small-scale fisheries around the world.
Identification of Splenic Reservoir Monocytes and Their Deployment to Inflammatory Sites
Authors: Swirski Filip K. , Nahrendorf Matthias , Etzrodt Martin , Wildgruber Moritz , Cortez-Retamozo Virna , Panizzi Peter , Figueiredo Jose-Luiz , Kohler Rainer H. , Chudnovskiy Aleksey , Waterman Peter , Aikawa Elena , Mempel Thorsten R. , Libby Peter , Weissleder Ralph , Pittet Mikael J.
Published: July 2009

Monitoring Monocyte Reservoirs

Monocytes are cells of the immune system that are recruited to sites of tissue injury and inflammation where they help to resolve the infection and are important for tissue repair. The bone marrow and blood are believed to be the primary reservoirs from which monocytes are mobilized after injury.Swirskiet al.(p.612; see the Perspective byJia and Pamer) now demonstrate that the spleen also serves as a critical reservoir of monocytes that are recruited during ischemic myocardial injury. Monocytes in the spleen are very similar in phenotype to blood-derived monocytes and are mobilized to the injured heart, where they represent a large fraction of the total monocytes that are recruited. The chemoattractant, angiotensin II, is required for optimal monocyte mobilization from the spleen and emigration into injured tissue.
Mathematical Biology Education: Beyond Calculus
Authors: Robeva Raina , Laubenbacher Reinhard
Published: July 2009

Training in developing algebraic models is often overlooked but can be valuable to biologists and mathematicians.
Nudging Through a Nucleosome
Authors: Otterstrom Jason J. , M. van Oijen Antoine
Published: July 2009

Single-molecule data suggest that RNA polymerase II moves a small step forward only when its DNA template briefly unwraps from the histone core.
Brain Wiring by Presorting Axons
Authors: Miyamichi Kazunari , Luo Liqun
Published: July 2009

Specific molecular interactions among axons of mammalian olfactory neurons ensure their orderly arrival along the path from the nose to the brain.
Dispensable But Not Irrelevant
Authors: Jia Ting , Pamer Eric G.
Published: July 2009

Heart injury triggers the release of monocytes from an unexpected reservoir, the spleen.
More Bad Connections May Limit LHC Energy or Delay Restart
Authors: Cho Adrian
Published: July 2009

Researchers have found flaws in electrical connections in the world's highest-energy particle smasher—the Large Hadron Collider—that will limit the LHC's energy. The problem could delay the planned November restart of the gargantuan accelerator.
Fix Funding Agency's 'Original Sin,' ERC Review Panel Demands
Authors: Enserink Martin
Published: July 2009

A panel reviewing the European Research Council opined in a report presented last week that despite a successful start, the ERC's structure is "a source of great frustration and ongoing low-level conflict" among its managers.
Universities Begin to Rethink First-Year Biology Courses
Authors: Mervis Jeffrey
Published: July 2009

Efforts to improve undergraduate introductory biology courses are seen as a critical step toward raising the nation's scientific literacy. Correcting the problem, speakers at a recent conference agreed, will require changing a deep-rooted academic culture that values research over teaching and makes little provision for doing a good job in the classroom.
Reshuffling Graduate Training
Authors: Mervis Jeffrey
Published: July 2009

Nobelist Roald Hoffmann believes that taking graduate students off grants and giving them fellowships would be good for U.S. science. But others say such a radical change isn't in the cards.
A Quest for Cosmic Karma
Authors: Bhattacharjee Yudhijit
Published: July 2009

Inexplicably hot bubbles in space have put researchers on the trail of feedback loops that slap weight limits on galaxies and stifle the birth of stars.
Help Wanted: 2000 Leading Lights To Inject a Spirit of Innovation
Authors: Xin Hao
Published: July 2009

Reform-minded Chinese scientists hope a new program,
Qianren Jihua
, will reel in the sort of comrades who can help raise the nation's scientific game.
Immunogenicity and Protective Efficacy of a Recombinant Subunit West Nile Virus Vaccine in Rhesus Monkeys
Authors: Lieberman Michael M. , Nerurkar Vivek R. , Luo Haiyan , Cropp Bruce , Carrion Ricardo , de la Garza Melissa , Coller Beth-Ann , Clements David , Ogata Steven , Wong Teri , Martyak Tim , Weeks-Levy Carolyn
Published: July 2009

The immunogenicity and protective efficacy of a recombinant subunit West Nile virus (WNV) vaccine was evaluated in rhesus macaques (
Macaca mulatta
). The vaccine consisted of a recombinant envelope (E) protein truncated at the C-terminal end, resulting in a polypeptide containing 80% of the N-terminal amino acids of the native WNV protein (WN-80E), mixed with an adjuvant (GPI-0100). WN-80E was produced in a
Drosophila melanogaster
expression system with high yield and purified by immunoaffinity chromatography using a monoclonal antibody specific for flavivirus E proteins. Groups of monkeys were vaccinated with formulations containing 1 or 25 μg of WN-80E antigen, and both humoral and cellular immunity were assessed after vaccination. The results demonstrated potent antibody responses to vaccination, as determined by both enzyme-linked immunosorbent assay and virus-neutralizing antibody assays. All vaccinated animals responded favorably, and there was little difference in response between animals immunized with 1 or 25 μg of WN-80E. Cellular immunity was determined by lymphocyte proliferation and cytokine production assays using peripheral blood mononuclear cells from vaccinated animals stimulated in vitro with WN-80E. Cell-mediated immune responses varied from animal to animal within each group. About half of the animals responded with lymphoproliferation, cytokine production, or both. Again, there was little difference in response between animals immunized with a 1- or 25-μg dose of WN-80E in the vaccine formulations. In a separate experiment, groups of monkeys were immunized with the WN-80E/GPI-0100 vaccine or an adjuvant-only control formulation. Animals were then challenged by inoculation of wild-type WNV, and the level of viremia in each animal was monitored daily for 10 days. The results showed that whereas all animals in the control group had detectable viremia for at least 3 days after challenge, all of the vaccinated animals were negative on all days after challenge. Thus, the WN-80E vaccine was 100% efficacious in protecting monkeys against infection with WNV.
Development and Evaluation of an Enzyme-Linked Immunosorbent Assay Based on Recombinant VP2 Capsids for the Detection of Antibodies to Aleutian Mink Disease Virus
Authors: Knuuttila Anna , Aronen Pirjo , Saarinen Auli , Vapalahti Olli
Published: July 2009

Aleutian disease (AD), a common infectious disease in farmed minks worldwide, is caused by Aleutian mink disease virus (AMDV). Serodiagnosis of AD in minks has been based on detection of AMDV antibodies by counterimmunoelectrophoresis (CIE) since the 1980s. The aim of this study was to develop and evaluate an enzyme-linked immunosorbent assay (ELISA) based on recombinant virus-like particles (VLPs) for identifying AMDV antibodies from mink sera. AMDV capsid protein (VP2) of a Finnish wild-type strain was expressed by the baculovirus system inSpodoptera frugiperda9 insect cells and was shown to self-assemble to VLPs (with an ultrastructure similar to that of the actual virion). A direct immunoglobulin G ELISA was established using purified recombinant AMDV VP2 VLPs as an antigen. Sera from farmed minks were collected to evaluate the AMDV VP2 ELISA (n= 316) and CIE (n= 209) based on AMDV VP2 recombinant antigen in parallel with CIE performed using a commercially available traditional antigen. CIE performed with the recombinant antigen had a sensitivity and specificity of 100% and ELISA a sensitivity of 99% and a specificity of 97%, with reference to CIE performed with the commercial antigen. The results show that the recombinant AMDV VP2 VLPs are antigenic and that AMDV VP2 ELISA is sensitive and specific and encourage further development of the method for high-throughput diagnostics, involving hundreds of thousands of samples in Finland annually.
Adjuvants Induce Distinct Immunological Phenotypes in a Bovine Tuberculosis Vaccine Model
Authors: Vordermeier H. Martin , Dean Gillian S. , Rosenkrands Ida , Agger Else M. , Andersen Peter , Kaveh Daryan A. , Hewinson R. Glyn , Hogarth Philip J.
Published: July 2009

Tuberculosis (TB) remains one of the most important infectious diseases of humans and animals.Mycobacterium bovisBCG, the only currently available TB vaccine, demonstrates variable levels of efficacy; therefore, a replacement or supplement to BCG is required. Protein subunit vaccines have shown promise but require the use of adjuvants to enhance their immunogenicity. Using the protective mycobacterial antigen Rv3019c, we have evaluated the induction of relevant immune responses by adjuvant formulations directly in the target species for bovine TB vaccines and compared these to responses induced by BCG. We demonstrate that two classes of adjuvant induce distinct immune phenotypes in cattle, a fact not previously reported for mice. A water/oil emulsion induced both an effector cell and a central memory response. A cationic-liposome adjuvant induced a central memory response alone, similar to that induced by BCG. This suggests that water/oil emulsions may be the most promising formulations. These results demonstrate the importance of testing adjuvant formulations directly in the target species and the necessity of measuring different types of immune response when evaluating immune responses.
Detection of
Enterobacter sakazakii
and Other Pathogens Associated with Infant Formula Powder by Use of a DNA Microarray
Authors: Wang Min , Cao Boyang , Gao Qili , Sun Yamin , Liu Pei , Feng Lu , Wang Lei
Published: July 2009

Pathogen detection is critical to the process of generating and testing powdered infant formula (PIF). An obstacle associated with PIF microbial surveillance is that most current procedures are time-consuming and labor-intensive. We have developed a rapid, DNA microarray-based detection technique to identify 10 different pathogenic bacteria associated with PIF contamination based on the 16S-23S rRNA gene internal transcribed spacer (ITS) sequences and
wzy
(O antigen polymerase) gene. Using this procedure,
Enterobacter sakazakii
,
Salmonella enterica
,
Klebsiella pneumoniae
,
Klebsiella oxytoca
,
Serratia marcescens
,
Acinetobacter baumannii
,
Bacillus cereus
,
Listeria monocytogenes
,
Staphylococcus aureus
, and
Escherichia coli
O157 were identified. One hundred eighty-five strains were used to validate the microarray assay (including 134 target pathogen strains and 51 closely related bacteria). Twenty-seven probes reproducibly detected multiple pathogens with high specificity and sensitivity (0.100 ng genomic DNA or 10
4
CFU/ml). Twenty-one real PIF samples were tested by the microarray with 100% accuracy. The data presented reveal that the designed oligonucleotide microarray is a promising method for basic microbiology, clinical diagnosis, food safety, and epidemiological surveillance.
Prospective Comparison of Eubacterial PCR and Measurement of Procalcitonin Levels with Blood Culture for Diagnosing Septicemia in Intensive Care Unit Patients
Authors: Rowther Farjana B. , Rodrigues Camilla S. , Deshmukh Minal S. , Kapadia Farhad N. , Hegde Ashit , Mehta Ajita P. , Joshi Vinay R.
Published: July 2009

Rapid identification of infection has a major impact on the clinical course, management, and outcome of critically ill intensive care unit (ICU) patients. We compared the results of PCR and procalcitonin with blood culture for ICU patients suspected of having septicemia. Ninety patients (60 patients meeting the criteria for sepsis and 30 patients not meeting the criteria for sepsis) were evaluated. Compared with blood culture as the gold standard, the sensitivity, specificity, and positive and negative predictive values for PCR were 100%, 43.33%, 46.87%, and 100%, respectively, and for procalcitonin were 100%, 61.66%, 56.6%, and 100%, respectively. The average times required to produce a final result were as follows: PCR, 10 h; blood culture, 33 h; procalcitonin, 45 min. Both PCR and procalcitonin may be useful as rapid tests for detecting septicemia but compared with blood cultures lacked specificity.
Site and Clinical Significance ofAlloscardovia omnicolensandBifidobacteriumSpecies Isolated in the Clinical Laboratory
Authors: Mahlen Steven D. , Clarridge Jill E.
Published: July 2009

Most of the members of the genusBifidobacterium, including the related organismAlloscardovia omnicolens, are inhabitants of the gastrointestinal tract and oral cavity of humans and animals and have been considered nonpathogenic for humans. However, the actual site of isolation and the clinical significance ofA. omnicolensand ofBifidobacteriumspecies are unclear. This may be due in part to the difficulties in distinguishing these organisms from other genera such asActinomyces. To determine the potential disease-causing role of these organisms, we analyzed the clinical significance of 15A. omnicolensandBifidobacteriumisolates identified by 16S rRNA gene sequencing from a clinical laboratory. All of the organisms in this study were isolated from sterile sites or in significant numbers by standard clinical microbiological culture methods. Our 15 clinical strains fit into only four species:A. omnicolens(five isolates),Bifidobacterium scardovii(four isolates),B. longum(two isolates), andB. breve(four isolates). All fiveA. omnicolensisolates, one of theB. breveisolates, and three of the fourB. scardoviiisolates were cultured from urine at 105CFU/ml. OneB. scardoviiisolate was from a patient with a genitourinary tract wound infection, twoB. longumisolates were from abdominal wounds, and threeB. breveisolates were from blood cultures. This study enlarges the spectrum of diseases and clinical sources associated withA. omnicolensandBifidobacteriumspecies and addresses identification problems.
Identification of Performance Problems in a Commercial Human Immunodeficiency Virus Type 1 Enzyme Immunoassay by Multiuser External Quality Control Monitoring and Real-Time Data Analysis
Authors: Kim J. , Swantee C. , Lee B. , Gunning H. , Chow A. , Sidaway F. , Sherlock C. , Garceau R. , Dimech W. , Malloch L.
Published: July 2009

In June 2005, a pilot program was implemented in Canadian laboratories to monitor the performance of the Abbott human immunodeficiency virus types 1 and 2 (HIV-1/2) gO enzyme immunoassay (EIA). Two different external quality control (QC) reagents and a “real-time” software analysis program were evaluated. In November 2005, higher-than-expected calibrator rate values in these kits were first reported at the Ontario Ministry of Health (Etobicoke), followed by the Alberta Provincial Public Health Laboratory (Edmonton and Calgary) and others. These aberrations were easily and readily tracked in “real time” using the external QC reagents and the software program. These high calibrator values were confirmed in Delkenheim, Germany, by Abbott, and a manufacturing change was initiated beginning with lot 38299LU00, which was distributed to laboratories in Canada in April 2006. However, widespread reports of calibrator failure by laboratories outside Canada were made in March 2006. In April 2006, Abbott Diagnostics initiated a level III investigation to identify the root cause, which was prolonged storage, under uncontrolled storage conditions, of the raw material used in the manufacture of the matrix cells. To the best of our knowledge, this is the first example of a program in Canada for serological testing that combines a common external QC reagent and a “real-time” software program to allow laboratories to monitor kit performance. In this case, external QC monitoring helped identify and confirm performance problems in the Abbott HIV-1/2 gO EIA kit, further highlighting the benefit of implementing such a program in a national or multilaboratory setting for laboratories performing diagnostic and clinical monitoring testing.