bluuebunny/crossref_metadata_2025 huggingface dataset:
Application of the Predicted Heat Strain Model in Development of Localized, Threshold-based Heat Stress Management Guidelines for the Construction Industry
Authors: Rowlinson Steve , Jia Yunyan Andrea
Published: December 2013

Existing heat stress risk management guidelines recommended by international standards are not practical for the construction industry which needs site supervision staff to make instant managerial decisions to mitigate heat risks. The ability of the predicted heat strain (PHS) model [ISO 7933 (2004). Ergonomics of the thermal environment analytical determination and interpretation of heat stress using calculation of the predicted heat strain. Geneva: International Standard Organisation] to predict maximum allowable exposure time (D  lim) has now enabled development of localized, action-triggering and threshold-based guidelines for implementation by lay frontline staff on construction sites. This article presents a protocol for development of two heat stress management tools by applying the PHS model to its full potential. One of the tools is developed to facilitate managerial decisions on an optimized work-rest regimen for paced work. The other tool is developed to enable workers’ self-regulation during self-paced work.
SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes
Authors: Jaron Kamil S. , Moravec Jiří C. , Martínková Natália
Published: December 2013

Motivation: Genomic islands (GIs) are DNA fragments incorporated into a genome through horizontal gene transfer (also called lateral gene transfer), often with functions novel for a given organism. While methods for their detection are well researched in prokaryotes, the complexity of eukaryotic genomes makes direct utilization of these methods unreliable, and so labour-intensive phylogenetic searches are used instead.

Results: We present a surrogate method that investigates nucleotide base composition of the DNA sequence in a eukaryotic genome and identifies putative GIs. We calculate a genomic signature as a vector of tetranucleotide (4-mer) frequencies using a sliding window approach. Extending the neighbourhood of the sliding window, we establish a local kernel density estimate of the 4-mer frequency. We score the number of 4-mer frequencies in the sliding window that deviate from the credibility interval of their local genomic density using a newly developed discrete interval accumulative score (DIAS). To further improve the effectiveness of DIAS, we select informative 4-mers in a range of organisms using the tetranucleotide quality score developed herein. We show that the SigHunt method is computationally efficient and able to detect GIs in eukaryotic genomes that represent non-ameliorated integration. Thus, it is suited to scanning for change in organisms with different DNA composition.

Availability and implementation: Source code and scripts freely available for download at http://www.iba.muni.cz/index-en.php?pg=research–data-analysis-tools–sighunt are implemented in C and R and are platform-independent.

Contact:  376090@mail.muni.cz or martinkova@ivb.cz
ALEA: a toolbox for allele-specific epigenomics analysis
Authors: Younesy Hamid , Möller Torsten , Heravi-Moussavi Alireza , Cheng Jeffrey B. , Costello Joseph F. , Lorincz Matthew C. , Karimi Mohammad M. , Jones Steven J. M.
Published: December 2013

The assessment of expression and epigenomic status using sequencing based methods provides an unprecedented opportunity to identify and correlate allelic differences with epigenomic status. We present ALEA, a computational toolbox for allele-specific epigenomics analysis, which incorporates allelic variation data within existing resources, allowing for the identification of significant associations between epigenetic modifications and specific allelic variants in human and mouse cells. ALEA provides a customizable pipeline of command line tools for allele-specific analysis of next-generation sequencing data (ChIP-seq, RNA-seq, etc.) that takes the raw sequencing data and produces separate allelic tracks ready to be viewed on genome browsers. The pipeline has been validated using human and hybrid mouse ChIP-seq and RNA-seq data.

Availability: The package, test data and usage instructions are available online at http://www.bcgsc.ca/platform/bioinfo/software/alea.

Contact: mkarimi1@interchange.ubc.ca or sjones@bcgsc.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
TSSer: an automated method to identify transcription start sites in prokaryotic genomes from differential RNA sequencing data
Authors: Jorjani Hadi , Zavolan Mihaela
Published: December 2013

Motivation: Accurate identification of transcription start sites (TSSs) is an essential step in the analysis of transcription regulatory networks. In higher eukaryotes, the capped analysis of gene expression technology enabled comprehensive annotation of TSSs in genomes such as those of mice and humans. In bacteria, an equivalent approach, termed differential RNA sequencing (dRNA-seq), has recently been proposed, but the application of this approach to a large number of genomes is hindered by the paucity of computational analysis methods. With few exceptions, when the method has been used, annotation of TSSs has been largely done manually.

Results: In this work, we present a computational method called ‘TSSer’ that enables the automatic inference of TSSs from dRNA-seq data. The method rests on a probabilistic framework for identifying both genomic positions that are preferentially enriched in the dRNA-seq data as well as preferentially captured relative to neighboring genomic regions. Evaluating our approach for TSS calling on several publicly available datasets, we find that TSSer achieves high consistency with the curated lists of annotated TSSs, but identifies many additional TSSs. Therefore, TSSer can accelerate genome-wide identification of TSSs in bacterial genomes and can aid in further characterization of bacterial transcription regulatory networks.

Availability: TSSer is freely available under GPL license at http://www.clipz.unibas.ch/TSSer/index.php

Contact:  mihaela.zavolan@unibas.ch

Supplementary information:  Supplementary data are available at Bioinformatics online.
MSIsensor: microsatellite instability detection using paired tumor-normal sequence data
Authors: Niu Beifang , Ye Kai , Zhang Qunyuan , Lu Charles , Xie Mingchao , McLellan Michael D. , Wendl Michael C. , Ding Li
Published: December 2013

Motivation: Microsatellite instability (MSI) is an important indicator of larger genome instability and has been linked to many genetic diseases, including Lynch syndrome. MSI status is also an independent prognostic factor for favorable survival in multiple cancer types, such as colorectal and endometrial. It also informs the choice of chemotherapeutic agents. However, the current PCR–electrophoresis-based detection procedure is laborious and time-consuming, often requiring visual inspection to categorize samples. We developed MSIsensor, a C++ program for automatically detecting somatic microsatellite changes. It computes length distributions of microsatellites per site in paired tumor and normal sequence data, subsequently using these to statistically compare observed distributions in both samples. Comprehensive testing indicates MSIsensor is an efficient and effective tool for deriving MSI status from standard tumor-normal paired sequence data.

Availability and implementation:  https://github.com/ding-lab/msisensor

Contact:  kye@genome.wustl.edu or lding@genome.wustl.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Loss of MHC II ubiquitination inhibits the activation and differentiation of CD4 T cells
Authors: Ishikawa Rikiya , Kajikawa Mizuho , Ishido Satoshi
Published: December 2013

Peptide–MHC class II complexes (pMHC II) are degraded by MARCH-I-mediated ubiquitination, and the stabilization of pMHC II by loss of its ubiquitination is one phenotype defining the activation of conventional dendritic cells (cDCs). However, the role of such stabilization of pMHC II in the context of T-cell activation/differentiation remains unclear. Here, we show that loss of pMHC II ubiquitination inhibits the activation and differentiation of CD4 T cells, probably through down-regulation of CD18/integrin β2 and their diminished IL-12 production in a cell intrinsic manner. The cDCs generated from mice whose pMHC II ubiquitination is inhibited had a decreased ability to activate naive CD4 T cells and induce Th1/Th17 differentiation. In addition, cDCs whose MHC II ubiquitination was inhibited showed down-regulation of CD18/integrin beta 2 and of IL-12 production. This unexpected finding suggests that loss of MHC II ubiquitination contributes to the negative feedback of CD4 T-cell immune responses.
RNase L restricts the mobility of engineered retrotransposons in cultured human cells
Authors: Zhang Ao , Dong Beihua , Doucet Aurélien J. , Moldovan John B. , Moran John V. , Silverman Robert H.
Published: December 2013

Retrotransposons are mobile genetic elements, and their mobility can lead to genomic instability. Retrotransposon insertions are associated with a diverse range of sporadic diseases, including cancer. Thus, it is not a surprise that multiple host defense mechanisms suppress retrotransposition. The 2′,5′-oligoadenylate (2-5A) synthetase (OAS)-RNase L system is a mechanism for restricting viral infections during the interferon antiviral response. Here, we investigated a potential role for the OAS-RNase L system in the restriction of retrotransposons. Expression of wild type (WT) and a constitutively active form of RNase L (NΔ385), but not a catalytically inactive RNase L mutant (R667A), impaired the mobility of engineered human LINE-1 (L1) and mouse intracisternal A-type particle retrotransposons in cultured human cells. Furthermore, WT RNase L, but not an inactive RNase L mutant (R667A), reduced L1 RNA levels and subsequent expression of the L1-encoded proteins (ORF1p and ORF2p). Consistently, confocal immunofluorescent microscopy demonstrated that WT RNase L, but not RNase L R667A, prevented formation of L1 cytoplasmic foci. Finally, siRNA-mediated depletion of endogenous RNase L in a human ovarian cancer cell line (Hey1b) increased the levels of L1 retrotransposition by ∼2-fold. Together, these data suggest that RNase L might function as a suppressor of structurally distinct retrotransposons.
Single molecule analysis ofThermus thermophilusSSB protein dynamics on single-stranded DNA
Authors: Zhang Jichuan , Zhou Ruobo , Inoue Jin , Mikawa Tsutomu , Ha Taekjip
Published: December 2013

Single-stranded (ss) DNA binding (SSB) proteins play central roles in DNA replication, recombination and repair in all organisms. We previously showed that Escherichia coli (Eco) SSB, a homotetrameric bacterial SSB, undergoes not only rapid ssDNA-binding mode transitions but also one-dimensional diffusion (or migration) while remaining bound to ssDNA. Whereas the majority of bacterial SSB family members function as homotetramers, dimeric SSB proteins were recently discovered in a distinct bacterial lineage of extremophiles, the Thermus–Deinococcus group. Here we show, using single-molecule fluorescence resonance energy transfer (FRET), that homodimeric bacterial SSB from Thermus thermophilus (Tth) is able to diffuse spontaneously along ssDNA over a wide range of salt concentrations (20–500 mM NaCl), and that TthSSB diffusion can help transiently melt the DNA hairpin structures. Furthermore, we show that two TthSSB molecules undergo transitions among different DNA-binding modes while remaining bound to ssDNA. Our results extend our previous observations on homotetrameric SSBs to homodimeric SSBs, indicating that the dynamic features may be shared among different types of SSB proteins. These dynamic features of SSBs may facilitate SSB redistribution and removal on/from ssDNA, and help recruit other SSB-interacting proteins onto ssDNA for subsequent DNA processing in DNA replication, recombination and repair.
Structure modulation of helix 69 from Escherichia coli 23S ribosomal RNA by pseudouridylations
Authors: Jiang Jun , Aduri Raviprasad , Chow Christine S. , SantaLucia John
Published: December 2013

Helix 69 (H69) is a 19-nt stem-loop region from the large subunit ribosomal RNA. Three pseudouridine (Ψ) modifications clustered in H69 are conserved across phylogeny and known to affect ribosome function. To explore the effects of Ψ on the conformations of Escherichia coli H69 in solution, nuclear magnetic resonance spectroscopy was used to reveal the structural differences between H69 with (ΨΨΨ) and without (UUU) Ψ modifications. Comparison of the two structures shows that H69 ΨΨΨ has the following unique features: (i) the loop region is closed by a Watson–Crick base pair between Ψ1911 and A1919, which is potentially reinforced by interactions involving Ψ1911N1H and (ii) Ψ modifications at loop residues 1915 and 1917 promote base stacking from Ψ1915 to A1918. In contrast, the H69 UUU loop region, which lacks Ψ modifications, is less organized. Structure modulation by Ψ leads to alteration in conformational behavior of the 5' half of the H69 loop region, observed as broadening of C1914 non-exchangeable base proton resonances in the H69 ΨΨΨ nuclear magnetic resonance spectra, and plays an important biological role in establishing the ribosomal intersubunit bridge B2a and mediating translational fidelity.
Active site plasticity enables metal-dependent tuning of Cas5d nuclease activity in CRISPR-Cas type I-C system
Authors: Punetha Ankita , Sivathanu Raveendran , Anand Baskaran
Published: December 2013

Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) in association with CRISPR-associated (Cas) proteins constitutes a formidable defense system against mobile genetic elements in prokaryotes. In type I-C, the ribonucleoprotein surveillance complex comprises only three Cas proteins, namely, Cas5d, Csd1 and Csd2. Unlike type I-E that uses Cse3/CasE for metal-independent CRISPR RNA maturation, type I-C that lacks this deputes Cas5d to process the pre-crRNA. Here, we report the promiscuous DNase activity of Cas5d in presence of divalent metals. Remarkably, the active site that renders RNA hydrolysis may be tuned by metal to act on DNA substrates too. Further, the realization that Csd1 is a fusion of its functional homolog Cse1/CasA and Cse2/CasB forecasts that the stoichiometry of the constituents of the surveillance complex in type I-C may differ from type I-E. Although Csd2 seems to be inert, Csd1 too exhibits RNase and metal-dependent DNase activity. Thus, in addition to their proposed functions, the DNase activity of Cas5d and Csd1 may also enable them to be co-opted in adaptation and interference stages of CRISPR immunity wherein interaction with DNA substrates is involved.
Molecular mechanisms of adaptation emerging from the physics and evolution of nucleic acids and proteins
Authors: Goncearenco Alexander , Ma Bin-Guang , Berezovsky Igor N.
Published: December 2013

DNA, RNA and proteins are major biological macromolecules that coevolve and adapt to environments as components of one highly interconnected system. We explore here sequence/structure determinants of mechanisms of adaptation of these molecules, links between them, and results of their mutual evolution. We complemented statistical analysis of genomic and proteomic sequences with folding simulations of RNA molecules, unraveling causal relations between compositional and sequence biases reflecting molecular adaptation on DNA, RNA and protein levels. We found many compositional peculiarities related to environmental adaptation and the life style. Specifically, thermal adaptation of protein-coding sequences in Archaea is characterized by a stronger codon bias than in Bacteria. Guanine and cytosine load in the third codon position is important for supporting the aerobic life style, and it is highly pronounced in Bacteria. The third codon position also provides a tradeoff between arginine and lysine, which are favorable for thermal adaptation and aerobicity, respectively. Dinucleotide composition provides stability of nucleic acids via strong base-stacking in ApG dinucleotides. In relation to coevolution of nucleic acids and proteins, thermostability-related demands on the amino acid composition affect the nucleotide content in the second codon position in Archaea.
The structure of metallo-DNA with consecutive thymine–HgII–thymine base pairs explains positive entropy for the metallo base pair formation
Authors: Yamaguchi Hiroshi , Šebera Jakub , Kondo Jiro , Oda Shuji , Komuro Tomoyuki , Kawamura Takuya , Dairaku Takenori , Kondo Yoshinori , Okamoto Itaru , Ono Akira , Burda Jaroslav V. , Kojima Chojiro , Sychrovský Vladimír , Tanaka Yoshiyuki
Published: December 2013

We have determined the three-dimensional (3D) structure of DNA duplex that includes tandem HgII-mediated T–T base pairs (thymine–HgII–thymine, T–HgII–T) with NMR spectroscopy in solution. This is the first 3D structure of metallo-DNA (covalently metallated DNA) composed exclusively of ‘NATURAL’ bases. The T–HgII–T base pairs whose chemical structure was determined with the 15N NMR spectroscopy were well accommodated in a B-form double helix, mimicking normal Watson–Crick base pairs. The Hg atoms aligned along DNA helical axis were shielded from the bulk water. The complete dehydration of Hg atoms inside DNA explained the positive reaction entropy (ΔS) for the T–HgII–T base pair formation. The positive ΔS value arises owing to the HgII dehydration, which was approved with the 3D structure. The 3D structure explained extraordinary affinity of thymine towards HgII and revealed arrangement of T–HgII–T base pairs in metallo-DNA.
Solution structure and tandem DNA recognition of the C-terminal effector domain of PmrA from Klebsiella pneumoniae
Authors: Lou Yuan-Chao , Wang Iren , Rajasekaran M. , Kao Yi-Fen , Ho Meng-Ru , Hsu Shang-Te Danny , Chou Shan-Ho , Wu Shih-Hsiung , Chen Chinpan
Published: December 2013

Klebsiella pneumoniae PmrA is a polymyxin-resistance-associated response regulator. The C-terminal effector/DNA-binding domain of PmrA (PmrAC) recognizes tandem imperfect repeat sequences on the promoters of genes to induce antimicrobial peptide resistance after phosphorylation and dimerization of its N-terminal receiver domain (PmrAN). However, structural information concerning how phosphorylation of the response regulator enhances DNA recognition remains elusive. To gain insights, we determined the nuclear magnetic resonance solution structure of PmrAC and characterized the interactions between PmrAC or BeF3−-activated full-length PmrA (PmrAF) and two DNA sequences from the pbgP promoter of K. pneumoniae. We showed that PmrAC binds to the PmrA box, which was verified to contain two half-sites, 5′-CTTAAT-3′ and 5′-CCTAAG-3′, in a head-to-tail fashion with much stronger affinity to the first than the second site without cooperativity. The structural basis for the PmrAC–DNA complex was investigated using HADDOCK docking and confirmed by paramagnetic relaxation enhancement. Unlike PmrAC, PmrAF recognizes the two sites simultaneously and specifically. In the PmrAF–DNA complex, PmrAN may maintain an activated homodimeric conformation analogous to that in the free form and the interactions between two PmrAC molecules aid in bending and binding of the DNA duplex for transcription activation.
Carbon source-dependent alteration of Puf3p activity mediates rapid changes in the stabilities of mRNAs involved in mitochondrial function
Authors: Miller Melanie A. , Russo Joseph , Fischer Anthony D. , Lopez Leban Florencia A. , Olivas Wendy M.
Published: December 2013

The Puf family of RNA-binding proteins regulates gene expression primarily by interacting with the 3′ untranslated region (3′ UTR) of targeted mRNAs and inhibiting translation and/or stimulating decay. Physical association and computational analyses of yeast Puf3p identified >150 potential mRNA targets involved in mitochondrial function. However, only COX17 has been established as a target of Puf3p-mediated deadenylation and decapping. We have identified 10 new targets that are rapidly degraded in a Puf3p-dependent manner. We also observed changes in Puf3p activity in response to environmental conditions. Puf3p promotes rapid degradation of mRNA targets in the fermentable carbon source dextrose. However, Puf3p-mediated decay activity is inhibited in carbon sources that require mitochondrial function for efficient cell growth. In addition, the activity of Puf3p is rapidly altered by changing the carbon source. PUF3 expression is not decreased at the RNA or protein level by different carbon sources and localization is not significantly altered, suggesting that Puf3p activity is regulated posttranslationally. Finally, under conditions when Puf3p is unable to stimulate decay, Puf3p can still bind its target mRNAs. Together, these experiments provide insight into the carbon source-specific control of Puf3p activity and how such alterations allow Puf3p to dynamically regulate mitochondrial function.
Tracking the processing of damaged DNA double-strand break ends by ligation-mediated PCR: increased persistence of 3′-phosphoglycolate termini in SCAN1 cells
Authors: Akopiants Konstantin , Mohapatra Susovan , Menon Vijay , Zhou Tong , Valerie Kristoffer , Povirk Lawrence F.
Published: December 2013

To track the processing of damaged DNA double-strand break (DSB) ends in vivo, a method was devised for quantitative measurement of 3′-phosphoglycolate (PG) termini on DSBs induced by the non-protein chromophore of neocarzinostatin (NCS-C) in the human Alu repeat. Following exposure of cells to NCS-C, DNA was isolated, and labile lesions were chemically stabilized. All 3′-phosphate and 3′-hydroxyl ends were enzymatically capped with dideoxy termini, whereas 3′-PG ends were rendered ligatable, linked to an anchor, and quantified by real-time Taqman polymerase chain reaction. Using this assay and variations thereof, 3′-PG and 3′-phosphate termini on 1-base 3′ overhangs of NCS-C-induced DSBs were readily detected in DNA from the treated lymphoblastoid cells, and both were largely eliminated from cellular DNA within 1 h. However, the 3′-PG termini were processed more slowly than 3′-phosphate termini, and were more persistent in tyrosyl-DNA phosphodiesterase 1-mutant SCAN1 than in normal cells, suggesting a significant role for tyrosyl-DNA phosphodiesterase 1 in removing 3′-PG blocking groups for DSB repair. DSBs with 3′-hydroxyl termini, which are not directly induced by NCS-C, were formed rapidly in cells, and largely eliminated by further processing within 1 h, both in Alu repeats and in heterochromatic α-satellite DNA. Moreover, absence of DNA-PK in M059J cells appeared to accelerate resolution of 3′-PG ends.
Converging pathways involving microRNA-206 and the RNA-binding protein KSRP control post-transcriptionally utrophin A expression in skeletal muscle
Authors: Amirouche Adel , Tadesse Helina , Miura Pedro , Bélanger Guy , Lunde John A. , Côté Jocelyn , Jasmin Bernard J.
Published: December 2013

Several reports have previously highlighted the potential role of miR-206 in the post-transcriptional downregulation of utrophin A in cultured cells. Along those lines, we recently identified K-homology splicing regulator protein (KSRP) as an important negative regulator in the post-transcriptional control of utrophin A in skeletal muscle. We sought to determine whether these two pathways act together to downregulate utrophin A expression in skeletal muscle. Surprisingly, we discovered that miR-206 overexpression in cultured cells and dystrophic muscle fibers causes upregulation of endogenous utrophin A levels. We further show that this upregulation of utrophin A results from the binding of miR-206 to conserved sites located in the 3′-UTR (untranslated region) of KSRP, thus causing the subsequent inhibition of KSRP expression. This miR-206-mediated decrease in KSRP levels leads, in turn, to an increase in the expression of utrophin A due to a reduction in the activity of this destabilizing RNA-binding protein. Our work shows that miR-206 can oscillate between direct repression of utrophin A expression via its 3′-UTR and activation of its expression through decreased availability of KSRP and interactions with AU-rich elements located within the 3′-UTR of utrophin A. Our study thus reveals that two apparent negative post-transcriptional pathways can act distinctively as molecular switches causing repression or activation of utrophin A expression.
Immortality, but not oncogenic transformation, of primary human cells leads to epigenetic reprogramming of DNA methylation and gene expression
Authors: Gordon Katrina , Clouaire Thomas , Bao Xun X. , Kemp Sadie E. , Xenophontos Maria , de Las Heras Jose Ignacio , Stancheva Irina
Published: December 2013

Tumourigenic transformation of normal cells into cancer typically involves several steps resulting in acquisition of unlimited growth potential, evasion of apoptosis and non-responsiveness to growth inhibitory signals. Both genetic and epigenetic changes can contribute to cancer development and progression. Given the vast genetic heterogeneity of human cancers and difficulty to monitor cancer-initiating events in vivo, the precise relationship between acquisition of genetic mutations and the temporal progression of epigenetic alterations in transformed cells is largely unclear. Here, we use an in vitro model system to investigate the contribution of cellular immortality and oncogenic transformation of primary human cells to epigenetic reprogramming of DNA methylation and gene expression. Our data demonstrate that extension of replicative life span of the cells is sufficient to induce accumulation of DNA methylation at gene promoters and large-scale changes in gene expression in a time-dependent manner. In contrast, continuous expression of cooperating oncogenes in immortalized cells, although essential for anchorage-independent growth and evasion of apoptosis, does not affect de novo DNA methylation at promoters and induces subtle expression changes. Taken together, these observations imply that cellular immortality promotes epigenetic adaptation to highly proliferative state, whereas transforming oncogenes confer additional properties to transformed human cells.
Validation of a Medicare Claims-based Algorithm for Identifying Freestanding Ambulatory Surgery Centers
Authors: Hollingsworth John M. , Dunn Rodney L. , Suskind Anne M. , Banerjee Mousumi , Hollenbeck Brent K.
Published: December 2013

Background and Objective:

With visits to ambulatory surgery centers (ASCs) on the rise, accountability in the care provided by these facilities and the surgeons who staff them is required. This requires the ability to measure and monitor ASC-based care over time. For this reason, we developed and validated a claims-based algorithm to identify ASCs.

Research Design:

Using a 20% sample of Medicare claims (2002–2008), we developed 3 ASC definitions. Definition 1 identified unique facilities with tax identification numbers and appropriate Place of Service and Type of Service codes. Definition 2 had the same conditions but also required specific Specialty codes. Definition 3 involved a multistep cleansing stage, in which facilities with indeterminate information in the fields of interest were eliminated. We assessed agreement between these definitions and findings from alternative data sources.

Results:

Placing additional requirements on how a freestanding ASC was defined within Medicare claims helped in the refinement of our algorithm. Agreement on the number of unique ASCs in Florida over the study interval was greatest between Definition 3 and the State Ambulatory Surgery Databases (concordance correlation coefficient=0.984; 95%, confidence interval, 0.967–0.992). With the Provider of Services Extract serving as the reference standard, our algorithm (based on Definition 3) had a positive predictive value of 99.0% (95% confidence interval, 98.6%–99.4%) for determining health care markets that experienced the opening of an ASC.

Conclusions:

The consequent inference is that our algorithm represents an accurate tool for distinguishing and tracking ASCs in Medicare data.
Assessing the Use of Antiviral Treatment to Control Influenza
Authors: Kramer Sarah , Bansal Shweta
Published: December 2013

Vaccines are the cornerstone of influenza control policy, but can suffer from several drawbacks. Seasonal influenza vaccines are prone to production problems and low efficacies, while pandemic vaccines are unlikely to be available in time to slow a rapidly spreading global outbreak. Antiviral therapy was found to be beneficial during the influenza A(H1N1)pdm09 pandemic even with limited use; however, antiviral use has decreased further since then. We seek to determine the role antiviral therapy can play in pandemic and seasonal influenza control on the population level, and to find optimized strategies for more efficient use of treatment. Using an age-structured contact network model for an urban population, we find that while a conservative antiviral therapy strategy cannot replace a robust influenza vaccine, it can play a role in reducing attack rates and eliminating outbreaks.
Modelling of magnetic data for scaling geology
Authors: Bansal A.R. , Dimri V.P.
Published: December 2013

Interpretation of magnetic data can be carried out either in the space or frequency domain. The interpretation in the frequency domain is computationally convenient because convolution becomes multiplication. The frequency domain approach assumes that the magnetic sources distribution has a random and uncorrelated distribution. This approach is modified to include random and fractal distribution of sources on the basis of borehole data. The physical properties of the rocks exhibit scaling behaviour which can be defined as P(k) = Ak−β, where P(k) is the power spectrum as a function of wave number (k), and A and β are the constant and scaling exponent, respectively. A white noise distribution corresponds to β = 0. The high resolution methods of power spectral estimation e.g. maximum entropy method and multi‐taper method produce smooth spectra. Therefore, estimation of scaling exponents is more reliable. The values of β are found to be related to the lithology and heterogeneities in the crust. The modelling of magnetic data for scaling distribution of sources leads to an improved method of interpreting the magnetic data known as the scaling spectral method. The method has found applicability in estimating the basement depth, Curie depth and filtering of magnetic data.
Analysing Place and Place‐making: Urbanization in Suburban Oslo
Authors: Røe Per Gunnar
Published: December 2013

Despite developments within planning theory challenging the ideal of the rational master plan it may be argued that there is still use for the production of knowledge through analysis in planning. However, the cultural complexity of today's planning contexts, and a move towards governance and entrepreneurial policies, makes it difficult to make places, to achieve social welfare and sustainability. Traditionally, the analysis of places has been done by architects and planners focusing on physical form, having an essentialist perspective of place resembling the theory of genius loci. In Norway, the planning authorities refined this methodology in the 1990s. This approach is, however, not in tune with a progressive view of places as multiple and dynamic social constructions, and may be accused of ‘symbolic violence’. If one is to take this view seriously and still be able to make plans, planning must also be based on other types of knowledge. In this article I argue for a socio‐cultural approach to reveal social representations and practices that make a place. I use the case of place‐making in Sandvika, a suburban ‘minicity’ outside Oslo, as an example of how a constructivist understanding differs from and may supplement an essentialist approach.
Gifted students' intrinsic and extrinsic motivations and parental influence on their motivation: from the self‐determination theory perspective
Authors: Al‐Dhamit Yahya , Kreishan Lana
Published: December 2013

The aim of this research is to describe and investigate a sample of school gifted students' intrinsic and extrinsic motivations, and the role of their parents in fostering motivational achievements in Jordan. In the study, 122 gifted students were selected to complete a questionnaire (adapted from Pelletier, Fortier and Vallerand et al.) investigating the mentioned constructs. Results showed that students were highly intrinsically and extrinsically motivated. The results also showed significant correlation between intrinsic and extrinsic motivations and perceived competence and parental support scales except for parental control. Other interesting findings were also found regarding the aforementioned constructs. The results further reveal some significant differences in control, achievement goal, amotivation and competence support between genders and education of parents. The possible implications of and recommendations from these findings will be discussed.
Teaching experiences of students with special educational needs in co‐taught and non‐co‐taught classes
Authors: Strogilos Vasilis , Avramidis Elias
Published: December 2013

Co‐teaching has gained considerable interest as a service delivery model for promoting the inclusion of students with special educational needs (SEN) in mainstream classrooms. This study examines whether co‐teaching has an effect on the teaching experiences of 12 students with autism spectrum disorder (ASD) and 10 students with intellectual disability (ID) as compared with the experiences of the same students in non‐co‐taught classes. We implemented 264 structured observations in 22 classes to identify students with SEN grouping arrangements, level of engagement, interactions with teachers and peers, and the nature of the interactions. We also conducted 44 structured interviews with co‐teachers to compound their perceptions with our observations.

Observational results indicate that co‐teaching has a strong effect on students' with SEN level of engagement and on the nature of interactions. The grouping arrangements for these students and their interactions with teachers and peers were slightly different between co‐taught and non‐co‐taught classes. More statistically significant differences were identified between the two conditions for students with ASD than for students with ID. Also, co‐teachers reported that co‐teaching had a positive effect on students with SEN in all researched variables. Our study concludes that co‐teaching has some positive effect on the teaching experiences of students with SEN; nevertheless, there is still scope for improving the employment of co‐teaching in Greek mainstream classrooms. Implications of these findings for current practice are discussed.
Teachers' concerns about inclusive education in Ahmedabad, India
Authors: Shah Rina , Das Ajay , Desai Ishwar , Tiwari Ashwini
Published: December 2013

This study was undertaken to determine the concerns of primary school teachers about the inclusion of students with disabilities in Ahmedabad, India. A total of 560 teachers, working in government‐run schools, returned the completed survey. A two‐part questionnaire was used in this study. Part 1 gathered information relating to personal and professional characteristics of the teachers. Part 2 was a 21‐item Likert scale titled Concerns about Inclusive Education – Gujarati. The major finding of the study was that the teachers in Ahmedabad were moderately concerned about including students with disabilities in their classrooms. The teachers were most concerned about lack of infrastructural resources and least concerned about lack of social acceptance of students with disabilities in inclusive education classrooms. Significant differences existed in teacher concerns based on the following background variables: gender, qualifications in special education, teaching experience and number of students with disabilities in class. A number of implications are discussed to address teacher concerns for inclusive education in India.
Seasonal occurrence of Aphis glycines and physiological responses of soybean plants to its feeding
Authors: Wang Xing‐Ya , Zhou Li‐Hong , Xu Biao , Xing Xing , Xu Guo‐Qing
Published: December 2013

The soybean aphid Aphis glycines Matsumura (Hemiptera: Aphididae) is an important pest of soybean in China. To monitor and manage this pest effectively it is necessary to understand its population dynamics and demographics, as well as the physiological responses of soybean plants to its feeding. In this study, using field surveying and suction‐trap monitoring, we investigated the population dynamics of the soybean aphid in Xiuyan County, Liaoning Province in northeastern China during 2009–2012. The results indicated that the population dynamics of the soybean aphid followed a unimodal curve distribution, with the insect generally colonizing soybean fields from the middle of June to early July and the population reaching a peak between early July and early August. On the whole, soybean aphids occurred in suction‐traps at least 2 weeks earlier than they were found in field surveys. A total of 72 alates were collected by suction‐trapping over the 4 years, with the earliest alate captures occurring on 28 May in 2009, 2011, 2012 and 4 June in 2010. The life table parameters clearly showed that this aphid had a short doubling time (4.73 ± 0.21 days), and 7.36 ± 0.98 nymphs were produced by a soybean aphid adult during its lifetime (13.57 ± 0.30 days). Finally, biochemical assays indicated that the amount of malondialdehyde and the activities of four defense‐related enzymes in soybean leaves significantly changed between 0 day and 7 days of aphid infestation. Polyphenol oxidase (PPO) and catalase (CAT) activities increased more dramatically after 1 day of aphid feeding. In addition, significantly higher levels of superoxide dismutase and CAT were found after aphid feeding for 7 days, whereas there was no significant change in the activities of peroxidase and PPO. Consequently, this study will be beneficial in determining the seasonal occurrence of the soybean aphid and selecting insect‐resistant soybean varieties, and thus in developing a theoretical framework for appropriate management strategies.
[18F]MK‐9470 PET measurement of cannabinoid CB1 receptor availability in chronic cannabis users
Authors: Ceccarini Jenny , Kuepper Rebecca , Kemels Dieter , van Os Jim , Henquet Cécile , Van Laere Koen
Published: December 2013

Δ9‐Tetrahydrocannabinol, the main psychoactive component of cannabis, exerts its central effects through activation of the cerebral type 1 cannabinoid (CB1) receptor. Pre‐clinical studies have provided evidence that chronic cannabis exposure is linked to decreased CB1 receptor expression and this is thought to be a component underlying drug tolerance and dependence. In this study, we make first use of the selective high‐affinity positron emission tomography (PET) ligand [18F]MK‐9470 to obtain in vivo measurements of cerebral CB1 receptor availability in 10 chronic cannabis users (age = 26.0 ± 4.1 years). Each patient underwent [18F]MK‐9470 PET within the first week following the last cannabis consumption. A population of 10 age‐matched healthy subjects (age = 23.0 ± 2.9 years) was used as control group. Parametric modified standardized uptake value images, reflecting CB1 receptor availability, were calculated. Statistical parametric mapping and volume‐of‐interest (VOI) analyses of CB1 receptor availability were performed. Compared with controls, cannabis users showed a global decrease in CB1 receptor availability (−11.7 percent). VOI‐based analysis demonstrated that the CB1 receptor decrease was significant in the temporal lobe (−12.7 percent), anterior (−12.6 percent) and posterior cingulate cortex (−13.5 percent) and nucleus accumbens (−11.2 percent). Voxel‐based analysis confirmed this decrease and regional pattern in CB1 receptor availability in cannabis users. These findings revealed that chronic cannabis use may alter specific regional CB1 receptor expression through neuroadaptive changes in CB1 receptor availability, opening the way for the examination of specific CB1‐cannabis addiction interactions which may predict future cannabis‐related treatment outcome.
Assessing the test–retest repeatability of theVietnamese version of theNationalEyeInstitute 25‐itemVisualFunctionQuestionnaire among bilateral cataract patients for aVietnamese population
Authors: To Kien Gia , Meuleners Lynn , Chen Huei‐Yang , Lee Andy , Van Do Dung , Van Duong Dat , Phi Tien Duy , Tran Hoang Huy , Nguyen Nguyen Do
Published: December 2013

Aim

To determine the test–retest repeatability of the National Eye Institute 25‐item Visual Function Questionnaire (NEI VFQ‐25) for use with olderVietnamese adults with bilateral cataract.

Methods

The questionnaire was translated intoVietnamese and back‐translated intoEnglish by two independent translators. Patients with bilateral cataract aged 50 and older completed the questionnaire on two separate occasions, one to two weeks after first administration of the questionnaire. Test–retest repeatability was assessed using theCronbach's α and intraclass correlation coefficients.

Results

The average age of participants was 67±8 years and most participants were female (73%). Internal consistency was acceptable with theαcoefficient above 0.7 for all subscales and intraclass correlation coefficients were 0.6 or greater in all subscales.

Conclusion

TheVietnameseNEI VFQ‐25 is reliable for use in studies assessing vision‐related quality of life in older adults with bilateral cataract inVietnam. We propose some modifications to theNEI‐VFQquestions to reflect activities of older people in Vietnam.
Immune Profiling of BALB/C and C57BL/6 Mice Reveals a Correlation Between Ureaplasma parvum‐Induced Fetal Inflammatory Response Syndrome‐Like Pathology and Increased Placental Expression of TLR2 and CD14
Authors: Allam Ayman B. , von Chamier Maria , Brown Mary B. , Reyes Leticia
Published: December 2013

Problem

Both BALB/c and C57BL/6 mice are susceptible to intrauterine infection with Ureaplasma parvum, but only protypical TH2/M2 BALB/c mice develop severe chorioamnionitis, fetal infection, and fetal inflammatory response syndrome‐like (FIRS) pathology.

Method of study

Microscopy, gene expression analysis, and ELISA were used to identify placental innate immune responses relevant to macrophage polarity, severe chorioamnionitis, and fetal infection.

Results

Both mouse strains exhibited a pro‐M2 cytokine profile at the maternal/fetal interface. In BALB/c mice, expression of CD14 and TLRs 1, 2, 6 was increased in infected placentas; TLR2 and CD14 were localized to neutrophils. Increased TLR2/CD14 was also observed in BALB/c syncytiotrophoblasts in tissues with pathological evidence of FIRS. In contrast, expression in C57BL/6 placentas was either unchanged or down‐regulated.

Conclusion

Our findings show a link between increased syncytiotrophoblast expression of CD14/TLR2 and FIRS‐like pathology in BALB/c mice. Functional studies are required to determine if CD14 is contributing to fetal morbidity during chorioamnionitis.
Value of ultrasonography and magnetic resonance imaging for the characterization of uterine mesenchymal tumors
Authors: Bonneau Claire , Thomassin‐Naggara Isabelle , Dechoux Sophie , Cortez Annie , Darai Émile , Rouzier Roman
Published: December 2013

Objective

To evaluate ultrasonography and magnetic resonance imaging (MRI) performance in differentiating benign leiomyomas from malignant mesenchymal or mixed tumors (MMT) and smooth muscle tumors of uncertain malignant potential of the uterus (STUMP).

Design

Retrospective cohort study.

Setting

University hospital, France.

Population

One hundred and eight women who underwent imaging before surgery for uterine mesenchymal tumor (85 with benign leiomyomas and 23 with MMT/STUMP).

Methods

The ultrasonography reports were reviewed. Conventional, perfusion and diffusion MRI were blindly analyzed. Recursive partitioning analysis (RPA) was performed to construct diagnostic flowcharts.

Main outcome measures

Accuracy of a diagnostic flowchart.

Results

At ultrasonography, single tumor, non‐myometrial origin, absence of acoustic shadowing, thickened endometrium and ascites were associated with MMT/STUMP (p = 0.001, p < 0.001, p = 0.03, p < 0.0001 and p = 0.03, respectively). For conventional MRI, single tumor, non‐myometrial origin, large tumor, poorly defined margins, thickened endometrium, peritoneal implants, intermediate or high signal intensity in T1 or T2 sequences, heterogeneous T1 signal, cystic alteration of the tumor and heterogeneity of the tumor's enhancement were significantly associated with MMT/STUMP. Perfusion weighted imaging and perfusion curve types were not discriminant. For diffusion weighted imaging, a high signal intensity at b = 1000 s/mm² was associated with MMT/STUMP (p < 0.001). RPA resulted in a model that ultimately included age, number of tumors and the aspect of the endometrium (both evaluated by MRI) and that had an area under the curve of 0.95.

Conclusions

Simple criteria, such as single tumor, non‐myometrial tumor, abnormal endometrium and age, should question the diagnosis of benign leiomyoma. MRI enhanced the sensitivity of detecting MMT/STUMP.
Desogestrel‐only contraceptive pill versus sequential contraceptive vaginal ring in the treatment of rectovaginal endometriosis infiltrating the rectum: a prospective open‐label comparative study
Authors: Leone Roberti Maggiore Umberto , Remorgida Valentino , Scala Carolina , Tafi Emanuela , Venturini Pier L. , Ferrero Simone
Published: December 2013

Objective

To compare the efficacy of two hormonal therapies in treating symptoms caused by bowel endometriosis.

Design

Patient preference study.

Setting

University hospital.

Population

A total of 143 women with rectovaginal endometriosis infiltrating the rectum.

Methods

This study was performed between January 2008 and June 2011. Patients were treated with a desogestrel‐only contraceptive pill or with the sequential combined contraceptive vaginal ring for 12 months.

Main outcome measures

The primary endpoint of the study was the rate of satisfied patients at 12‐month follow up. The changes in symptoms and in the volume of the nodules were secondary endpoints.

Results

At 12‐month follow up, the rate of satisfied patients was higher in the group treated with the desogestrel‐only contraceptive pill than in the group treated with the sequential combined contraceptive vaginal ring (p = 0.004). When only changes in gastrointestinal symptoms were considered, 50% of patients treated with the desogestrel‐only contraceptive pill and 31.3% of those treated with the sequential combined contraceptive vaginal ring were satisfied (p = 0.037). The reduction in the volume of the nodules, the percentages of patients who discontinued the therapy after the completion of the study and of those who decided to undergo surgery were similar between the two groups.

Conclusions

Both hormonal therapies are efficacious in treating symptoms caused by rectovaginal endometriosis infiltrating the rectum. Patient satisfaction is higher with the desogestrel‐only pill than with a vaginal ring.