bluuebunny/crossref_metadata_2025 huggingface dataset:
Power law fitting procedures: The electrical conductance of coalescing nanocluster films
Authors: Convers Pierre Y. , Sattar Abdul , Brown Simon A. , Hendy Shaun C.
Published: January 2011

The electrical conductance of bismuth nanocluster films deposited in vacuum has been observed to increase after the end of deposition. This evolution Gexp(t) can be successfully fitted with a power law. However, it is well known that interpretation of power law fits can be problematic. To investigate the physical meaning of the fitted power law exponent a percolation model with coalescence built into it was developed. In this model the evolution of the conductance of necks between neighboring occupied sites is defined as a power law with exponent β resulting in model conductance data Gmod(t). The Gmod(t) data are fitted with a power law and we show that the fitted exponent is close to the original exponent β, so long as the power law expression is chosen correctly. The fits to the synthetic Gmod(t) data provide confidence in the fitting procedure and in the power law exponents obtained from fits to the experimental data. The experimental power law exponents are found to be much smaller than expected from previous theories of micron scale particle coalescence.
Measuring lattice parameter of iron silicides using x-ray Bragg-surface diffraction
Authors: Tsai Yi-Wei , Chu Chia-Hong , Tang Mau-Tsu , Stetsko Yuriy. P. , Chou Lih-Jen , Chang Shih-Lin
Published: January 2011

We investigated the strain field of the β-FeSi2 semiconductor on a Si(001) substrate, where FeSi in a grain form coexists with β-FeSi2 during the growth of β-FeSi2. The lattice-parameter variations in silicon due to the presence of β-FeSi2, FeSi and the grain boundary between β-FeSi2 and FeSi were detected by using the x-ray three-beam, Si(002)/(1¯11), Bragg-surface diffraction, where (002) is a symmetric Bragg reflection and (1¯11) a surface diffraction. The diffraction images of (1¯11) reflection as a function of the azimuth rotation angle around the reciprocal lattice vector of (002) provide information of lattice-parameter variation in Si. The surface nature of the (1¯11) reflection makes the (1¯11) diffraction images extremely sensitive to the interfaces between Si, β-FeSi2 and FeSi. With the penetration (detection) depth calculated from the dynamical theory of x-ray diffraction, the strain field versus the depth in the Si substrate near the interfaces is determined with the resolution of 0.002 Å for lattice variation. The largest strain detected is about 0.4% up to 15–70 Å below the interfaces.
Minority carrier transport in p-ZnO nanowires
Authors: Lin Y. , Shatkhin M. , Flitsiyan E. , Chernyak L. , Dashevsky Z. , Chu S. , Liu J. L.
Published: January 2011

In this work, we explore the minority carrier diffusion length in zinc oxide nanowires, using the electron beam-induced current technique. Systematic measurements as a function of temperature were performed on p-type, Sb-doped ZnO film, containing a 4 μm thick nanowire layer. The minority carrier diffusion length exhibits a thermally activated increase with the energy of 74±5 meV. Electron beam irradiation also causes the diffusion length increase with the activation energy of 247±10 meV, likely related to SbZn–2VZn acceptor-complex.
Antiferromagnetically coupled capped bit patterned media for high-density magnetic recording
Authors: Lubarda Marko V. , Li Shaojing , Livshitz Boris , Fullerton Eric E. , Lomakin Vitaliy
Published: January 2011

We report micromagnetic modeling of a bit patterned media where a two-dimensional array of patterned composite islands is antiferromagnetically coupled to a continuous capping layer. This media allows optimization of writability, switching field distributions, and readback response. Lateral and vertical exchange introduced through the coupling with the capping layer compensates the dipolar interactions between islands and antiferromagnetic coupling is employed to modulate the high-density readback response.
Sharply tuned small force measurement with a biomimetic sensor
Authors: Kim Hyery , Song Taegeun , Ahn Kang-Hun
Published: January 2011

Hair cells in biological hearing organs transform mechanical stimuli into neuronal signals with great sensitivity, sharp frequency selectivity, and wide range of intensity. By combining principle of adaptation in hair cells with electronic engineering, we have produced a biomimetic force sensor under water showing all these features. For the nano-Newton force signal, the biomimetic sensor showed that more than an order of magnitude increases in sensitivity and frequency selectivity compared to the passive sensor. The nonlinear amplification mechanism in the hair cell is demonstrated by showing that the hair cell can precisely detect pulse signals weaker than noise.
Mechanical properties of graphene under shear deformation
Authors: Min K. , Aluru N. R.
Published: January 2011

In this letter, we investigate the mechanical properties of graphene under shear deformation. Specifically, using molecular dynamics simulations, we compute the shear modulus, shear fracture strength, and shear fracture strain of zigzag and armchair graphene structures at various temperatures. To predict shear strength and fracture shear strain, we also present an analytical theory based on the kinetic analysis. We show that wrinkling behavior of graphene under shear deformation can be significant. We compute the amplitude to wavelength ratio of wrinkles using molecular dynamics and compare it with existing theory. Our results indicate that graphene can be a promising mechanical material under shear deformation.
Room-temperature spin injection and spin loss across a GaNAs/GaAs interface
Authors: Puttisong Y. , Wang X. J. , Buyanova I. A. , Tu C. W. , Geelhaar L. , Riechert H. , Chen W. M.
Published: January 2011

Recently discovered effect of spin-filtering and spin amplification in GaNAs enables us to reliably obtain detailed information on the degree of spin loss during optical spin injection across a semiconductor heterointerface at room temperature. Spin polarization of electrons injected from GaAs into GaNAs is found to be less than half of what is generated in GaNAs by optical orientation. We show that the observed reduced spin injection efficiency is not only due to spin relaxation in GaAs, but more importantly due to spin loss across the interface due to structural inversion asymmetry and probably also interfacial point defects.
Pressure induced structural transition and enhancement of superconductivity in Co doped CeFeAsO
Authors: Kumar Ravhi S. , Antonio Daniel , Kanagaraj M. , Arumugam S. , Prakash J. , Sinogeikin Stanislav , Thakur Gohil S. , Ganguli A. K. , Cornelius Andrew , Zhao Yusheng
Published: January 2011

The superconducting CeFe1−xCoxAsO (Co=0.1) oxyarsenide with a transition temperature (Tc) 11.4 K has been investigated by in situ high pressure synchrotron x-ray diffraction, magnetization, and resistivity measurements. The experiments performed at 10 K up to 6 GPa and at room temperature (RT) up to 55 GPa indicate large anisotropic lattice compression. A pressure induced structural change to a collapsed tetragonal structure is observed above 10 GPa at RT. We report here the enhancement of Tc from 11.4 to 12.3 K with a small increase in pressure up to 0.4 GPa and is first observed in an electron doped Ce-1111 system.
Magnetic vortex wall motion driven by spin waves
Authors: Seo Soo-Man , Lee Hyun-Woo , Kohno Hiroshi , Lee Kyung-Jin
Published: January 2011

A magnetic vortex wall motion driven by propagating spin waves in a nanostrip is investigated by means of micromagnetic simulation. Propagating spin waves can drive a vortex wall into a stream motion in spite of its complex internal spin structure. Compared to the transverse wall, the vortex wall moves faster and its velocity is less sensitive to the spin wave frequency. The amplitude of spin waves changes when passing through the domain wall, closely related to the domain wall velocity. This domain-wall-type-specific study provides important information for developing the theory of the interaction between domain wall and spin waves.
An intrinsically disordered C terminus allows the La protein to assist the biogenesis of diverse noncoding RNA precursors
Authors: Kucera Nathan J. , Hodsdon Michael E. , Wolin Sandra L.
Published: January 2011

The La protein binds the 3′ ends of many newly synthesized noncoding RNAs, protecting these RNAs from nucleases and influencing folding, maturation, and ribonucleoprotein assembly. Although 3′ end binding by La involves the N-terminal La domain and adjacent RNA recognition motif (RRM), the mechanisms by which La stabilizes diverse RNAs from nucleases and assists subsequent events in their biogenesis are unknown. Here we report that a conserved feature of La proteins, an intrinsically disordered C terminus, is required for the accumulation of certain noncoding RNA precursors and for the role of the
Saccharomyces cerevisiae
La protein Lhp1p in assisting formation of correctly folded pre-tRNA anticodon stems in vivo. Footprinting experiments using purified Lhp1p reveal that the C terminus is required to protect a pre-tRNA anticodon stem from chemical modification. Although the C terminus of Lhp1p is hypersensitive to proteases in vitro, it becomes protease-resistant upon binding pre-tRNAs, U6 RNA, or pre-5S rRNA. Thus, while high affinity binding to 3′ ends requires the La domain and RRM, a conformationally flexible C terminus allows La to interact productively with a diversity of noncoding RNA precursors. We propose that intrinsically disordered domains adjacent to well characterized RNA-binding motifs in other promiscuous RNA-binding proteins may similarly contribute to the ability of these proteins to influence the cellular fates of multiple distinct RNA targets.
The effect of internal and external stress on two-way shape-memory behaviour in Co49Ni21.6Ga29.4 single crystals
Authors: Liu G D , Dai X F , Luo H Z , Liu H Y , Meng F B , Li Y , Yu X , Chen J L , Wu G H
Published: January 2011

The effect of the internal stress on the two-way shape memory in Co49Ni21.6Ga29.4 single crystals has been investigated. We found that the internal stress generated natively by the solidifying process works as a tensile force along the growth direction. Applying different compressive pre-stresses along the [0 0 1] direction, the shape-memory strain can be continuously changed from +1.0% to −2.3%. In the [1 1 0] direction, the strain monotonically increases from −2.0% to −4.0% due to a strong detwinning produced by the consistent effect of the external and internal stresses.
Physical model of spherical glow discharge stratification
Authors: Belikov A E , Sakhapov S Z
Published: January 2011

A physical model of spherical glow discharge stratification is suggested where the striations represent the electric double layers, where opposite charges, initially separated in space due to fluctuations or ambipolar diffusion, are then stabilized by the specific conditions of the gas media with negative differential conductivity. These conditions appear and disappear during the discharge development owing to plasma-chemical reactions. The model has been tested using time-dependent mass-spectrometry, as well as numerical calculations of the electron transport coefficients for the observed composition.
Measurement of the body force field of plasma actuators
Authors: Kotsonis M , Ghaemi S , Veldhuis L , Scarano F
Published: January 2011

A novel technique is proposed and investigated for the estimation of the body force field resulting from the operation of a dielectric barrier discharge plasma actuator. The technique relies on the measurement of the spatio-temporal evolution of the induced velocity field using high-speed particle image velocimetry (PIV). The technique has the advantage of providing spatial distribution of the body force vector field. A full Navier–Stokes term decomposition is applied on the evolving field along with additional closure norms in order to decouple the pressure gradient and body force terms. Results are compared with load-cell measurements of the direct reaction force and also momentum balance calculations based on the PIV field. Agreement between the different methods is observed. The data can easily be incorporated in computational flow solvers and also be used for validation and calibration of numerical plasma models.
Group actions on geodesic Ptolemy spaces
Authors: Foertsch Thomas , Schroeder Viktor
Published: January 2011

In this paper we study geodesic Ptolemy metric spaces

X
X

which allow proper and cocompact isometric actions of crystallographic or, more generally, virtual polycyclic groups. We show that

X
X

is equivariantly roughly isometric to a Euclidean space.
Loggerhead turtle (Caretta caretta) movement off the coast of Taiwan: characterization of a hotspot in the East China Sea and investigation of mesoscale eddies
Authors: Kobayashi Donald R. , Cheng I-Jiunn , Parker Denise M. , Polovina Jeffrey J. , Kamezaki Naoki , Balazs George H.
Published: January 2011

Kobayashi, D. R., Cheng, I-J., Parker, D. M., Polovina, J. J., Kamezaki, N., and Balazs, G. H. 2011. Loggerhead turtle (Caretta caretta) movement off the coast of Taiwan: characterization of a hotspot in the East China Sea and investigation of mesoscale eddies. – ICES Journal of Marine Science, 68: 707–718. Satellite tags were attached to 34 non-reproductive loggerhead turtles (Caretta caretta) caught as bycatch in the Taiwanese coastal poundnet fishery from 2002 to 2008. Transmission durations ranged from 6 to 503 d (median 172 d), with 5860 d tracked in total. Horizontal track data were processed using the Bayesian state-space modelling to extract the most likely daily positions, taking into account ARGOS data quality and other forms of statistical error. A region of high occupancy in the East China Sea, covering 433 549 km2 of coastal and pelagic area next to Taiwan, China, Japan, and South Korea, was characterized from the tracking data. Various attributes of this hotspot are described using satellite tracks and remotely sensed data. The tracks were merged with oceanographic data, emphasizing a new global dataset characterizing mesoscale eddies from satellite altimetry data. A proximity-probability approach coupled with odds ratio testing was used to infer orientation to eddy features. Comparisons against random points, simulated particle tracks, and drifter buoys were used to demonstrate turtle differential responses to eddies inside and outside the hotspot, depending on eddy features (i.e. cyclonic vs. anticyclonic, edges vs. centres). Turtles inside the hotspot utilize fewer strong cyclonic eddy edges than those outside.
Effectiveness of a School-Based Deworming Campaign in Rural Kenya
Authors: Peterson Laura S. , Ondiek Michael , Oludhe Denis O. , Naul Brett A. , Vermund Sten H.
Published: January 2011

In 2007, the rate of intestinal helminth infection in primary school-aged children in a rural village in Southwestern Kenya was estimated to be at least 68%, based on direct stool smear. Since the 2007 survey, these same school children have been treated with 400-mg albendazole every 3 months. We repeated a cross-sectional stool survey in the same area in 2010 (i.e. 3 years later) to estimate the current parasite prevalence. While only 44.5% of children were infected in 2010, the decline was not as marked as one might expect from a well-managed quarterly deworming campaign. Due to the relative insensitivity of the technique utilized here—the direct smear examination of a single stool sample—we were only able to identify heavy infections, and the true rate of parasitism is likely much higher, suggesting heavy environmental contamination and rapid re-infection rates. Community education and sanitation improvements are needed for more definitive impact.
Introgression in the genus Campylobacter: generation and spread of mosaic alleles
Authors: Sheppard Samuel K. , McCarthy Noel D. , Jolley Keith A. , Maiden Martin C. J.
Published: January 2011

Horizontal genetic exchange strongly influences the evolution of many bacteria, substantially contributing to difficulties in defining their position in taxonomic groups. In particular, how clusters of related bacterial genotypes – currently classified as microbiological species – evolve and are maintained remains controversial. The nature and magnitude of gene exchange between two closely related (approx. 15 % nucleotide divergence) microbiologically defined species,Campylobacter jejuniandCampylobacter coli, was investigated by the examination of mosaic alleles, those with some ancestry from each population. A total of 1738 alleles from 2953 seven-locus housekeeping gene sequence types (STs) were probabilistically assigned to each species group with the model-based clustering algorithmstructure. Alleles with less than 75 % assignment probability to one of the populations were confirmed as mosaics using thestructurelinkage model. For each of these, the putative source of the recombinant region was determined and the allele was mapped onto aclonalframegenealogy derived from concatenated ST sequences. This enabled the direction and frequency of introgression between the two populations to be established, with 8.3 % ofC. coliclade 1 alleles having acquiredC. jejunisequence, compared to 0.5 % for the reciprocal process. Once generated, mosaic genes spread withinC. coliclade 1 by a combination of clonal expansion and lateral gene transfer, with some evidence of erosion of the mosaics by reacquisition ofC. colisequence. These observations confirm previous analyses of the exchange of complete housekeeping alleles and extend this work by describing the processes of horizontal gene transfer and subsequent spread within recipient species.
Nucleoid-associated protein HU controls three regulons that coordinate virulence, response to stress and general physiology in Salmonella enterica serovar Typhimurium
Authors: Mangan Michael W. , Lucchini Sacha , Ó Cróinín Tadhg , Fitzgerald Stephen , Hinton Jay C. D. , Dorman Charles J.
Published: January 2011

The role of the HU nucleoid-associated proteins in gene regulation was examined inSalmonella entericaserovar Typhimurium. The dimeric HU protein consists of different combinations of itsαandβsubunits. Transcriptomic analysis was performed with cultures growing at 37 °C at 1, 4 and 6 h after inoculation with mutants that lack combinations of HUαand HUβ. Distinct but overlapping patterns of gene expression were detected at each time point for each of the three mutants, revealing not one but three regulons of genes controlled by the HU proteins. Mutations in thehupgenes altered the expression of regulatory and structural genes in both the SPI1 and SPI2 pathogenicity islands. ThehupA hupBdouble mutant was defective in invasion of epithelial cell lines and in its ability to survive in macrophages. The double mutant also had defective swarming activity and a competitive fitness disadvantage compared with the wild-type. In contrast, inactivation of just thehupBgene resulted in increased fitness and correlated with the upregulation of members of the RpoS regulon in exponential-phase cultures. Our data show that HU coordinates the expression of genes involved in central metabolism and virulence and contributes to the success ofS. entericaas a pathogen.
A unique Coxiella burnetii lipoprotein involved in metal binding (LimB)
Authors: Battisti James M. , Hicks Linda D. , Minnick Michael F.
Published: January 2011

Coxiella burnetii is the bacterial agent of Q fever in humans. Here, we describe a unique, ∼7.2 kDa, surface-exposed lipoprotein involved in metal binding which we have termed LimB. LimB was initially identified as a potential metal-binding protein on far-Western (FW) blots containing whole-cell lysate proteins when probed with nickel-coated horseradish peroxidase (Ni-HRP) and developed with a chemiluminescent HRP substrate. The corresponding identity of LimB as CBU1224a was established by matrix-assisted laser desorption ionization-tandem time-of-flight mass spectrometry. blast analyses with CBU1224a showed no significant similarity to sequences outside strains of C. burnetii. Additional in silico analyses revealed a putative 20 residue signal sequence with the carboxyl end demarcated by a potential lipobox (LSGC) whose Cys residue is predicted to serve as the N-terminal, lipidated Cys of mature LimB. The second residue of mature LimB is predicted to be Ala, an uncharged envelope localization residue. These features suggest that CBU1224a is synthesized as a prolipoprotein which is subsequently lipidated, secreted and anchored in the outer membrane. Mature LimB is predicted to contain 45 aa, of which there are 10 His and 5 Cys; both amino acids are frequently involved in binding transition metal cations. Recombinant LimB (rLimB) was generated and its Ni-HRP-binding activity demonstrated on FW blots. Ni-HRP binding by rLimB was inhibited by >95 % on FW blots done in the presence of EDTA, imidazole, Ni2+ or Zn2+, and roughly halved in the presence of Co2+ or Fe3+. The limB gene was maximally expressed at 3–7 days post-infection in Coxiella-infected Vero cells, coinciding with exponential phase growth. Two isoforms of LimB were detected on FW and Western blots, including a smaller (∼7.2 kDa) species that was the predominant form in small cell variants and a larger isoform (∼8.7 kDa) in large cell variants. LimB is Sarkosyl-insoluble, like many omps. The predicted surface location of LimB was verified by immunoelectron and immunofluorescence microscopy using anti-rLimB antibodies. Overall, the results suggest that LimB is a unique Coxiella lipoprotein that serves as a surface receptor for divalent metal cations and may play a role in acquiring at least one of these metals during intracellular growth.
Phenotypic and molecular characterization of Salmonella enterica serovar Sofia, an avirulent species in Australian poultry
Authors: Gan Emily , Baird Fiona J. , Coloe Peter J. , Smooker Peter M.
Published: January 2011

Salmonella enterica serovar Sofia (S. Sofia) is often isolated from chickens in Australia. However, despite its high frequency of isolation from chicken and chicken meat products, S. Sofia is rarely associated with animal or human salmonellosis, presumably because this serovar is avirulent in nature. The objective of this work was to investigate the phenotypic and molecular properties of S. Sofia in order to assess its pathogenic potential. Our in vivo studies support the observation that this serovar can colonize tissues, but does not cause disease in chickens. This was further confirmed with tissue culture assays, which showed that the ability of S. Sofia to adhere, invade and survive intracellularly is significantly diminished compared with the pathogenic Salmonella enterica serovar Typhimurium (S. Typhimurium) 82/6915. Molecular analysis of Salmonella pathogenicity islands (SPIs) showed that most of the differences observed in SPI1 to SPI5 of S. Sofia could be attributed to minor changes in the sequences, as indicated by a loss or gain of restriction cleavage sites within these regions. Sequence analysis demonstrated that the majority of virulence genes identified were predicted to encode proteins sharing a high identity (75–100 %) with corresponding proteins from S. Typhimurium. However, a number of virulence genes in S. Sofia have accumulated mutations predicted to affect transcription and/or translation. The avirulence of this serovar is probably not the result of a single genetic change but rather of a series of alterations in a large number of virulence-associated genes. The acquisition of any single virulence gene will almost certainly not be sufficient to restore S. Sofia virulence.
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons
Authors: Haas Brian J. , Gevers Dirk , Earl Ashlee M. , Feldgarden Mike , Ward Doyle V. , Giannoukos Georgia , Ciulla Dawn , Tabbaa Diana , Highlander Sarah K. , Sodergren Erica , Methé Barbara , DeSantis Todd Z. ,   The Human Microbiome Consortium, Petrosino Joseph F. , Knight Rob , Birren Bruce W.
Published: January 2011

Bacterial diversity among environmental samples is commonly assessed with PCR-amplified 16S rRNA gene (16S) sequences. Perceived diversity, however, can be influenced by sample preparation, primer selection, and formation of chimeric 16S amplification products. Chimeras are hybrid products between multiple parent sequences that can be falsely interpreted as novel organisms, thus inflating apparent diversity. We developed a new chimera detection tool called Chimera Slayer (CS). CS detects chimeras with greater sensitivity than previous methods, performs well on short sequences such as those produced by the 454 Life Sciences (Roche) Genome Sequencer, and can scale to large data sets. By benchmarking CS performance against sequences derived from a controlled DNA mixture of known organisms and a simulated chimera set, we provide insights into the factors that affect chimera formation such as sequence abundance, the extent of similarity between 16S genes, and PCR conditions. Chimeras were found to reproducibly form among independent amplifications and contributed to false perceptions of sample diversity and the false identification of novel taxa, with less-abundant species exhibiting chimera rates exceeding 70%. Shotgun metagenomic sequences of our mock community appear to be devoid of 16S chimeras, supporting a role for shotgun metagenomics in validating novel organisms discovered in targeted sequence surveys.
You are what you eat, whenever or wherever you eat it: an integrative analysis of fish food habits in Canadian and U.S.A. waters
Authors: Bundy A. , Link J. S. , Smith B. E. , Cook A. M.
Published: January 2011

The degree to which fish diet differs by season and area, particularly over broad scales, was examined for the first time in temperate, contiguous north‐west Atlantic Ocean waters by comparing food habit data for 10 species of fishes collected concurrently during the spring and autumn surveys in the U.S.A. (Gulf of Maine proper and Georges Bank) and in the summer survey in Canada (western Scotian Shelf and Bay of Fundy). For most species, there was a general concurrence among the three seasons and four areas: summer diets had the same dominant prey items as spring and autumn diets. Although a suite of multivariate analyses did elucidate some differences in specific proportions of the diet for these species across seasons and areas, the main prey did not substantially change for most of these species. These results suggest that there are (1) minimal differences in diet across season for these species at these taxonomic resolutions, (2) there are minimal differences in diet geographically for these species and (3) differences across species, as expected, are important. Many fisheries ecosystem and multispecies models are dependent on food habit data, where resolving seasonal and spatial differences in diet remains an important consideration; however, the present work implies that amalgamated estimates of diet from seasonal surveys may be a reasonable approach when no finer seasonal resolution exists, as long as due diligence is exercised.
The incidence and outcomes of fetomaternal alloimmune thrombocytopenia: a UK national study using three data sources
Authors: Knight Marian , Pierce Matthias , Allen Dave , Kurinczuk Jennifer J , Spark Patsy , Roberts David J , Murphy Michael F
Published: January 2011

Fetomaternal alloimmune thrombocytopenia (FMAIT) is the most common cause of severe neonatal thrombocytopenia in otherwise well, term infants. First pregnancies are often severely affected. This descriptive, population‐based national study was undertaken in order to inform the case for antenatal screening. Cases were identified using three sources and capture‐recapture techniques used to generate a robust incidence estimate. One hundred and seventy three cases were identified between October 2006 and September 2008. An extra 20 cases were estimated from capture‐recapture analysis, giving an estimated incidence of clinically detected FMAIT of 12·4 cases per 100 000 total births (95%confidence interval: 10·7, 14·3). Fifty‐two cases (30%) were known at the start of pregnancy; 120 (70%) were unknown (n = 115) or unrecognized (n = 5). Unknown cases were more likely to experience a haemorrhagic complication (67% vs. 5%) (P < 0·001) and more likely to have an intracranial haemorrhage (20% vs. 4%) (P = 0·014) than known cases receiving antenatal management. In view of the incidence of severe disease identified, further assessment of the case for antenatal screening is important. There were a number of cases in which the significance of a history of FMAIT in a previous sibling was not recognized and there is a need to raise awareness of the importance of this diagnosis.
Morphological analysis of circulating tumour cells in patients undergoing surgery for non‐small cell lung carcinoma using the isolation by size of epithelial tumour cell (ISET) method
Authors: Hofman V. , Long E. , Ilie M. , Bonnetaud C. , Vignaud J. M. , Fléjou J. F. , Lantuejoul S. , Piaton E. , Mourad N. , Butori C. , Selva E. , Marquette C. H. , Poudenx M. , Sibon S. , Kelhef S. , Vénissac N. , Jais J. P. , Mouroux J. , Molina T. J. , Vielh P. , Hofman P.
Published: January 2011

V. Hofman, E. Long, M. Ilie, C. Bonnetaud, J. M. Vignaud, J. F. Fléjou, S. Lantuejoul, E. Piaton, N. Mourad, C. Butori, E. Selva, C. H. Marquette, M. Poudenx, S. Sibon, S. Kelhef, N. Vénissac, J. P. Jais, J. Mouroux, T. J. Molina, P. Vielh and P. Hofman  Morphological analysis of circulating tumour cells in patients undergoing surgery for non‐small cell lung carcinoma using the isolation by size of epithelial tumour cell (ISET) method

Background and objective:  Recurrence rates after surgery for non‐small cell lung cancer (NSCLC) range from 25 to 50% and 5‐year survival is only 60–70%. Because no biomarkers are predictive of recurrence or the onset of metastasis, pathological TNM (pTNM) staging is currently the best prognostic factor. Consequently, the preoperative detection of circulating tumour cells (CTCs) might be useful in tailoring therapy. The aim of this study was to characterize morphologically any circulating non‐haematological cells (CNHCs) in patients undergoing surgery for NSCLC using the isolation by size of epithelial tumour cell (ISET) method.

Methods:  Of 299 blood samples tested, 250 were from patients with resectable NSCLC and 59 from healthy controls. The presence of CNHCs was assessed blindly and independently by 10 cytopathologists on May‐Grünwald–Giemsa stained filters and the cells classified into three groups: (i) malignant cells, (ii) uncertain malignant cells, and (iii) benign cells. We assessed interobserver agreement using Kappa (κ) analysis as the measure of agreement.

Results:  A total of 123 out of 250 (49%) patients showed CNHCs corresponding to malignant, uncertain malignant and benign cells, in 102/250 (41%), 15/250 (6%) and 6/250 (2%) cases, respectively. No CNHCs were detected in the blood of healthy subjects. Interobserver diagnostic variability was absent for CNHCs, low for malignant cells and limited for uncertain malignant and benign cells.

Conclusion:  Identification of CTCs in resectable NSCLC patients, using ISET technology and according to cytopathological criteria of malignancy, appears to be a new and promising field of cytopathology with potential relevance to lung oncology.
Addressing challenges when studying mobile or episodic species: hierarchical Bayes estimation of occupancy and use
Authors: Mordecai Rua S. , Mattsson Brady J. , Tzilkowski Caleb J. , Cooper Robert J.
Published: January 2011

1. Understanding the distribution and ecology of episodic or mobile species requires us to address multiple potential biases, including spatial clustering of survey locations, imperfect detectability and partial availability for detection. These challenges have been addressed individually by previous modelling approaches, but there is currently no extension of the occupancy modelling framework that accounts for all three problems while estimating occupancy (ψ), availability for detection (i.e. use; θ) and detectability (P).

2. We describe a hierarchical Bayes multi‐scale occupancy model that simultaneously estimates site occupancy, use, and detectability, while accounting for spatial dependence through a state‐space approach based on repeated samples at multiple spatial or temporal scales. As an example application, we analyse the spatiotemporal distribution of the Louisiana waterthrush Seiurus motacilla with respect to catchment size and availability of potential prey based on data collected along Appalachian streams of southern West Virginia, USA. In spring 2009, single observers recorded detections of Louisiana waterthrush (henceforth, waterthrush) within 75 m of point‐count stations (i.e. sites) during four 5‐min surveys per site, with each survey broken into 1‐min intervals.

3. Waterthrushes were widely distributed (ψ range: 0·6–1·0) and were regularly using (θ range: 0·4–0·6) count circles along forested mountain streams. While accounting for detection biases and spatial dependence among nearby sampling sites, waterthrushes became more common as catchment area increased, and they became more available for detection as the per cent of the benthic macroinvertebrates that were of the orders Ephemeroptera, Plecoptera or Trichoptera (EPT) increased. These results lend some support to the hypothesis that waterthrushes are influenced by instream conditions as mediated by watershed size and benthic macroinvertebrate community composition.

4.
 Synthesis and applications. Although several available modelling techniques provide estimates of occupancy at one scale, hierarchical Bayes multi‐scale occupancy modelling provides estimates of distribution at two scales simultaneously while accounting for detection biases and spatial dependencies. Hierarchical Bayes multi‐scale occupancy models therefore hold significant potential for addressing complex conservation threats that operate at a landscape scale (e.g. climate change) and probably influence species distributions over multiple scales.
Isometric biomass partitioning pattern in forest ecosystems: evidence from temporal observations during stand development
Authors: Yang Yuanhe , Luo Yiqi
Published: January 2011

1. Knowledge of biomass partitioning is essential for estimating spatial patterns and temporal dynamics of root biomass in terrestrial ecosystems. The isometric hypothesis predicts that aboveground biomass scales isometrically with belowground biomass across both individual plants and community types (i.e. the slope of the log–log relationship between above‐ and belowground biomass is not significantly different from 1.0), and that the isometric pattern is independent of variation in environmental conditions. However, current evidence primarily comes from observations over space. It is still unknown whether biomass partitioning patterns occurring over time are similar to those observed over space.

2. In this study, we explored biomass partitioning patterns in forest ecosystems over space and time by synthesizing biomass measurements made in 112 stands extracted from 16 age sequences around the world. We characterized biomass partitioning patterns in forest ecosystems using both root: shoot ratio and the relationship between above‐ and belowground biomass. Data across various individual studies were organized to reflect biomass partitioning patterns over space, while data within each individual study were used to illustrate biomass allocation patterns over time.

3. Our results showed that root:shoot ratio did not exhibit any significant trend with stand age over space. Similarly, root:shoot ratio remained relatively constant over time in 10 out of 16 age sequences.

4. Reduced major axis analysis indicated that the slope of the log–log relationship between above‐ and belowground biomass did not reveal a significant difference from 1.0 over space, supporting the isometric hypothesis. Likewise, the slope was not statistically different from 1.0 in 10 out of 16 age sequences, nor did it show any significant change with climatic factors and stand age. Thus, the isometric hypothesis also most probably holds true during forest stand development.

5. Synthesis. Our results demonstrate that biomass partitioning patterns occurring over time are consistent with those observed over space, suggesting that belowground biomass dynamics in forest ecosystems may be reliably estimated from aboveground biomass using biomass partitioning patterns generated over space.
Misprescription of antibiotics in primary care: a critical systematic review of its determinants
Authors: Lopez‐Vazquez Paula , Vazquez‐Lago Juan M. , Figueiras Adolfo
Published: January 2011

Background  Antibiotic resistance is one of the principal public health problems worldwide. Currently, inappropriate use of antibiotics is regarded as the principal determinant of resistance, with most of these drugs being prescribed outside a hospital setting. This systematic review sought to identify the factors, attitudes and knowledge linked to misprescription of antibiotics.

Methods  A systematic review was conducted using the MEDLINE‐PubMed and EMBASE databases. The selection criteria required that papers: (1) be published in English or Spanish; (2) designate their objective as that of addressing attitudes/knowledge or other factors related with the prescribing of antibiotics; and (3) use quality and/or quantity indicators to define misprescription. The following were excluded: any paper that used qualitative methodology and any paper that included descriptive analysis only.

Results  A total of 46 papers that met the inclusion criteria were included in the review. They were very heterogeneous and displayed major methodological limitations. Doctors' socio‐demographic and personal factors did not appear to exert much influence. Complacency (fulfilling what professionals perceived as being patients'/parents' expectations) and, to a lesser extent, fear (fear of possible complications in the patient) were the attitudes associated with misprescription of antibiotics.

Conclusions  Before designing interventions aimed at improving the prescription and use of antibiotics, studies are needed to identify precisely which factors influence prescribing.
Incidence and preventability of adverse events requiring intensive care admission: a systematic review
Authors: Vlayen Annemie , Verelst Sandra , Bekkering Geertruida E , Schrooten Ward , Hellings Johan , Claes Neree
Published: January 2011

Rationale, aims and objectives Adverse events are unintended patient injuries or complications that arise from health care management resulting in death, disability or prolonged hospital stay. Adverse events that require critical care are a considerable financial burden to the health care system, but also their global impact on patients and society is probably underestimated. The objectives of this systematic review were to synthesize the best available evidence regarding the estimates of the incidence and preventability of adverse events that necessitate intensive care admission, to determine the type and consequences [mortality, length of intensive care unit (ICU) stay and costs] of these adverse events.

Methods MEDLINE (from 1966 to present), EMBASE (from 1974 to present) and CENTRAL (version 1‐2010) were searched for studies reporting on unplanned admissions on ICUs. Several other sources were searched for additional studies. Only quantitative studies that used chart review for the detection of adverse events requiring intensive care admission were considered for eligibility. For the purposes of this systematic review, ICUs were defined as specialized hospital facilities which provide continuous monitoring and intensive care for acutely ill patients. Studies that were published in the English, Dutch, German, French or Spanish language were eligible for inclusion. Two reviewers independently extracted data and assessed the methodological quality of the included studies.

Results A total of 27 studies were reviewed. Meta‐analysis of the data was not appropriate because of methodological and statistical heterogeneity between studies; therefore, results are presented in a descriptive way. The percentage of surgical and medical adverse events that required ICU admission ranged from 1.1% to 37.2%. ICU readmissions varied from 0% to 18.3%. Preventability of the adverse events varied from 17% to 76.5%. Preventable adverse events are further synthesized by type of event. Consequences of the adverse events included a mean length of ICU stay that ranged from 1.5 days to 10.4 days for the patient's first stay in ICU and mortality percentages between 0% and 58%.

Conclusions Adverse events are an important reason for (re)admission to the ICU and a considerable proportion of these are preventable. It was not possible to estimate an overall incidence and preventability rate of these events as we found considerable heterogeneity. To decrease adverse events that necessitate ICU admission, several systems are recommended such as early detection of patients with clinical instability on general wards and the implementation of rapid response teams. Step‐down or intermediate care units could be a useful strategy for patients who require monitoring to avoid ICU readmissions. However, the effectiveness of such systems needs to be investigated.
Quality of care for individuals with osteoarthritis: a longitudinal study
Authors: McHugh Gretl A. , Campbell Malcolm , Luker Karen A.
Published: January 2011

Objectives  The objectives of this paper were to investigate quality of care for individuals with osteoarthritis (OA) and to determine if those most in need had the outcome of a total joint replacement (TJR). Key quality indicators were involvement in treatment decisions, appropriate information provision and outcomes of care.

Methods  A longitudinal study was conducted on individuals newly referred to an orthopaedic specialist at one hospital in North West England. A total of 268 participants were recruited consecutively and followed up at 3, 6 and 12 months. Validated measurement tools such as, a Visual Analogue Scale for pain and the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) assessed pain and physical functioning. Mean scores on the outcome measures were estimated and plotted over time by joint affected and whether or not the participant had a TJR by 12 months.

Results  Most participants (82%) felt that they were involved in the decision about their care, although 21% reported that they had not received a diagnosis of OA. Information was not provided on OA, pain management and exercise to 58%, 65% and 57% of participants, respectively. However, 98% of the 109 having a TJR reported receiving information about the procedure. Among the 118 known not to have had a TJR, pain and physical functioning remained relatively stable over time.

Conclusion  It appears that patients with the most severe symptoms of pain and physical functioning were selected for TJR. However, care for individuals with OA could be improved by providing standard information on OA in general and pain management and exercise. In particular, effective strategies for the implementation of the research evidence and guidelines are required to improve quality of care.
‘How do you know what Aunt Martha looks like?’ A video elicitation study exploring tacit clues in doctor–patient interactions
Authors: Henry Stephen G. , Forman Jane H. , Fetters Michael D.
Published: January 2011

Rationale and objectives  Theory suggests that tacit clues inform clinical judgements, but the prevalence and role of tacit clues during clinical interactions is unknown. This study explored whether doctors and patients identify information likely to be tacit clues or judgements based on tacit clues during health maintenance examinations.

Methods  Qualitative analysis of video elicitation interview transcripts involving 18 community‐based primary care doctors and 36 patients. Outcomes were description and analysis of tacit clues and judgements based on tacit clues mentioned by participants.

Results  A total of 57 references to tacit clues and 53 references to judgements based on tacit clues were identified from patient and doctor transcripts. Non‐verbal behaviours comprised the most common category of tacit clues (53% of doctor comments; 42% of patient comments). Patients mostly discussed judgements based on tacit clues that related to the doctor–patient relationship. Doctors discussed actively using non‐verbal behaviours to provide patients with tacit clues about the doctor–patient relationship. They also mentioned tacit clues that informed medical judgements and decision making. Gestalt judgements based on tacit clues were common (33% of doctor comments). Several participants identified instances in which they had difficulty articulating their rationale for specific judgements. Doctors varied widely in how frequently they mentioned tacit clues.

Conclusion  During video elicitation interviews, patients and doctors identified tacit clues and judgements based on these clues as playing a role during health maintenance examinations. Future research should further elucidate the role of tacit clues in medical judgements and doctor–patient relationships.
Incidence and risk factors of hospital falls on long‐term care wards in Japan
Authors: Tanaka Buichi , Sakuma Mio , Ohtani Masae , Toshiro Jinichi , Matsumura Tadashi , Morimoto Takeshi
Published: January 2011

Rationale, aims and objective  Falls among hospitalized patients are an important patient safety issue. In particular, the incidence of falls and risk of related injuries among the elderly are particularly high. Because the epidemiology of falls is not well scrutinized in Japanese long‐term care wards, we evaluated the incidence and risk factors of falls in this setting.

Methods  A prospective cohort study was conducted on long‐term care wards with 160 beds in a general hospital in Japan. All patients admitted to the wards over 25 months were enrolled and followed until discharge. The baseline characteristics and incidences of falls were measured.

Results  We enrolled 2973 patients with a mean age of 74 years, and median length of stay was 36 days. During the study period, 657 falls occurred in 411 (14%) patients. The incidence of falls was 3.8 per 1000 patient‐days, and by 15 and 30 days after admission to the ward, 7.3% and 11.4% of patients, respectively, had fallen. Independent risk factors related to falls during hospitalization were advanced age [≥70 years, hazard ratio (HR) 1.5, 95% confidence interval (CI) 1.2–2.0], history of falls (HR 1.2, 95% CI 1.0–1.5), frequent urination (HR 1.4, 95% CI 1.0–1.8) and requirement for toileting assistance (HR 1.4, 95% CI 1.1–1.8). Among patients who fell during the study period, 23% sustained an injury.

Conclusions  Many patients on long‐term care wards in Japan were elderly and experienced falls during their hospital stay, with consequent injuries. Taking into account the risk factors identified, we need to devise effective strategies to prevent falls and related injuries.
Design and validation of a multiplex specific primer‐directed polymerase chain reaction assay for killer‐cell immunoglobulin‐like receptor genetic profiling
Authors: Abalos A. T. , Eggers R. , Hogan M. , Nielson C. M. , Giuliano A. R. , Harris R. B. , Thompson P. A.
Published: January 2011

Current methodologies for the analysis of the killer‐cell immunoglobulin‐like receptor (KIR) locus utilize specific primer‐directed polymerase chain reaction (SSP‐PCR), which require a wide range of DNA input, multiple reaction conditions, and up to 16 individual reactions. We have developed and validated a multiplex SSP‐PCR method for the genetic analysis of the KIR locus. Design and optimization of four multiplex groups targeting 14 genes and their alleles on the KIR locus has been completed. Each multiplex group contains PCR products that differ in size by a minimum of 15 bp to allow sufficient fragment length resolution for size discrimination by gel electrophoresis. This assay allows for efficient genotyping of the KIR locus while requiring a minimum amount of DNA input, utilizing the simplicity of SSP‐PCR.