bluuebunny/crossref_metadata_2025 huggingface dataset:
The Kakimizu complex of a connected sum of links
Authors: Banks Jessica
Published: March 2013

We show that
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="StartAbsoluteValue normal upper M normal upper S left-parenthesis upper L 1 number-sign upper L 2 right-parenthesis EndAbsoluteValue equals StartAbsoluteValue normal upper M normal upper S left-parenthesis upper L 1 right-parenthesis EndAbsoluteValue times StartAbsoluteValue normal upper M normal upper S left-parenthesis upper L 2 right-parenthesis EndAbsoluteValue times double-struck upper R">

|

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S

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1

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×

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R

|\mathrm {MS}(L_1\# L_2)|=|\mathrm {MS}(L_1)|\times |\mathrm {MS}(L_2)|\times \mathbb {R}

when

L
1

L_1

and

L
2

L_2

are any non-split and non-fibred links. Here

M
S

(
L
)

\mathrm {MS}(L)

denotes the Kakimizu complex of a link

L
L

, which records the taut Seifert surfaces for

L
L

. We also show that the analogous result holds if we study incompressible Seifert surfaces instead of taut ones.
HExpoChem: a systems biology resource to explore human exposure to chemicals
Authors: Taboureau Olivier , Jacobsen Ulrik Plesner , Kalhauge Christian , Edsgärd Daniel , Rigina Olga , Gupta Ramneek , Audouze Karine
Published: March 2013

Summary: Humans are exposed to diverse hazardous chemicals daily. Although an exposure to these chemicals is suspected to have adverse effects on human health, mechanistic insights into how they interact with the human body are still limited. Therefore, acquisition of curated data and development of computational biology approaches are needed to assess the health risks of chemical exposure. Here we present HExpoChem, a tool based on environmental chemicals and their bioactivities on human proteins with the objective of aiding the qualitative exploration of human exposure to chemicals. The chemical–protein interactions have been enriched with a quality-scored human protein–protein interaction network, a protein–protein association network and a chemical–chemical interaction network, thus allowing the study of environmental chemicals through formation of protein complexes and phenotypic outcomes enrichment.

Availability: HExpoChem is available at http://www.cbs.dtu.dk/services/HExpoChem-1.0/.

Contact:  karine@cbs.dtu.dk

Supplementary information:  Supplementary data are available at Bioinformatics online.
NTFD—a stand-alone application for the non-targeted detection of stable isotope-labeled compounds in GC/MS data
Authors: Hiller Karsten , Wegner André , Weindl Daniel , Cordes Thekla , Metallo Christian M. , Kelleher Joanne K. , Stephanopoulos Gregory
Published: March 2013

Summary: Most current stable isotope-based methodologies are targeted and focus only on the well-described aspects of metabolic networks. Here, we present NTFD (non-targeted tracer fate detection), a software for the non-targeted analysis of all detectable compounds derived from a stable isotope-labeled tracer present in a GC/MS dataset. In contrast to traditional metabolic flux analysis approaches, NTFD does not depend on any a priori knowledge or library information. To obtain dynamic information on metabolic pathway activity, NTFD determines mass isotopomer distributions for all detected and labeled compounds. These data provide information on relative fluxes in a metabolic network. The graphical user interface allows users to import GC/MS data in netCDF format and export all information into a tab-separated format.

Availability: NTFD is C++- and Qt4-based, and it is freely available under an open-source license. Pre-compiled packages for the installation on Debian- and Redhat-based Linux distributions, as well as Windows operating systems, along with example data, are provided for download at http://ntfd.mit.edu/.

Contact:  gregstep@mit.edu
JAWAMix5: an out-of-core HDF5-based java implementation of whole-genome association studies using mixed models
Authors: Long Quan , Zhang Qingrun , Vilhjalmsson Bjarni J. , Forai Petar , Seren Ümit , Nordborg Magnus
Published: March 2013

Summary: We present JAWAMix5, an out-of-core open-source toolkit for association mapping using high-throughput sequence data. Taking advantage of its HDF5-based implementation, JAWAMix5 stores genotype data on disk and accesses them as though stored in main memory. Therefore, it offers a scalable and fast analysis without concerns about memory usage, whatever the size of the dataset. We have implemented eight functions for association studies, including standard methods (linear models, linear mixed models, rare variants test, analysis in nested association mapping design and local variance component analysis), as well as a novel Bayesian local variance component analysis. Application to real data demonstrates that JAWAMix5 is reasonably fast compared with traditional solutions that load the complete dataset into memory, and that the memory usage is efficient regardless of the dataset size.

Availability: The source code, a ‘batteries-included’ executable and user manual can be freely downloaded from http://code.google.com/p/jawamix5/.

Contact:  quan.long@gmi.oeaw.ac.at

Supplementary information:  Supplementary data are available at Bioinformatics online.
Organohalide respiration: microbes breathing chlorinated molecules
Authors: Leys David , Adrian Lorenz , Smidt Hauke
Published: March 2013

Bacterial respiration has taken advantage of almost every redox couple present in the environment. The reduction of organohalide compounds to release the reduced halide ion drives energy production in organohalide respiring bacteria. This process is centred around the reductive dehalogenases, an iron–sulfur and corrinoid containing family of enzymes. These enzymes, transcriptional regulators and the bacteria themselves have potential to contribute to future bioremediation solutions that address the pollution of the environment by halogenated organic compounds.
Identification of
Dehalobacter
reductive dehalogenases that catalyse dechlorination of chloroform, 1,1,1-trichloroethane and 1,1-dichloroethane
Authors: Tang Shuiquan , Edwards Elizabeth A.
Published: March 2013

Two novel reductive dehalogenases (RDases) that are highly similar to each other but catalyse distinct dechlorination reactions were identified from
Dehalobacter
-containing mixed cultures. These two RDases were partially purified from crude protein extracts of anaerobic dechlorinating enrichment cultures using blue native polyacrylamide gel electrophoresis. Gel slices were assayed for dechlorinating activity, and associated proteins were identified using liquid chromatography tandem mass spectrometry with the metagenome of the parent culture as the reference database. The two RDases identified, annotated as CfrA and DcrA, share an amino acid identity of 95.2 per cent, but use different substrates: CfrA dechlorinates chloroform (CF) and 1,1,1-trichloroethane (1,1,1-TCA), but not 1,1-dichloroethane; DcrA dechlorinates 1,1-dichloroethane, but not CF or 1,1,1-TCA. These two novel RDases share no more than 40 per cent amino acid identity to any other known or putative RDases, but both have a twin-arginine motif and two iron–sulfur binding motifs conserved in most RDases. Peptides specific to two putative membrane anchor proteins, annotated as CfrB and DcrB, were also detected in gel slices.
The transcriptional regulator CprK detects chlorination by combining direct and indirect readout mechanisms
Authors: Kemp Laura R. , Dunstan Mark S. , Fisher Karl , Warwicker Jim , Leys David
Published: March 2013

The transcriptional regulator CprK controls the expression of the reductive dehalogenase CprA in organohalide-respiring bacteria.
Desulfitobacterium hafniense
CprA catalyses the reductive dechlorination of the terminal electron acceptor
o
-chlorophenol acetic acid, generating the phenol acetic acid product. It has been shown that CprK has ability to distinguish between the chlorinated CprA substrate and the de-halogenated end product, with an estimated an estimated 10
4
-fold difference in affinity. Using a green fluorescent protein GFP
UV
-based transcriptional reporter system, we establish that CprK can sense
o
-chlorophenol acetic acid at the nanomolar level, whereas phenol acetic acid leads to transcriptional activation only when approaching micromolar levels. A structure–activity relationship study, using a range of
o
-chlorophenol acetic-acid-related compounds and key CprK mutants, combined with p
K
a
calculations on the effector binding site, suggests that the sensitive detection of chlorination is achieved through a combination of direct and indirect readout mechanisms. Both the physical presence of the bulky chloride substituent as well as the accompanying electronic effects lowering the inherent phenol p
K
a
are required for high affinity. Indeed, transcriptional activation by CprK appears strictly dependent on establishing a phenolate–K133 salt bridge interaction, rather than on the presence of a halogen atom
per se
. As K133 is strictly conserved within the CprK family, our data suggest that physiological function and future applications in biosensing are probably restricted to phenolic compounds.
Identification of a reductive tetrachloroethene dehalogenase in
Shewanella sediminis
Authors: Lohner Svenja T. , Spormann Alfred M.
Published: March 2013

The genome sequence of psychrophilic
Shewanella sediminis
revealed the presence of five putative reductive dehalogenases (Rdhs). We found that cell extracts of pyruvate/fumarate-grown
S. sediminis
cells catalysed reduced methyl viologen-dependent reductive dechlorination of tetrachloroethene (PCE) to trichloroethene (TCE) at a specific activity of approximately 1 nmol TCE min
−1
(mg protein)
−1
. Dechlorination of PCE followed Michaelis–Menten kinetics with an apparent
K
m
of 120 μM PCE. No PCE dechlorination was observed with heat-denatured extract or when cyanocobalamin was omitted from the growth medium; however, the presence of PCE in the growth medium increased PCE transformation rates. Analysis of mutants carrying in-frame deletions of all five Rdhs encoding genes showed that only deletion of Ssed_3769 resulted in the loss of PCE dechlorination activity suggesting that Ssed_3769 is a functional Rdh. This is the first study to show reductive dechlorination activity of PCE in a sediment-dwelling
Shewanella
species that may be important for linking the flux of organohalogens to organic carbon via reductive dehalogenation in marine sediments.
Low photosynthesis of treeline white spruce is associated with limited soil nitrogen availability in the Western Brooks Range, Alaska
Authors: McNown Robert W. , Sullivan Patrick F.
Published: March 2013

The prevailing hypothesis states that treeline positions are defined by the direct effects of cold temperatures on cell division and tree growth. Meanwhile, photosynthesis is thought to be relatively unrestricted in treeline trees. Support for this hypothesis comes from the global correlation between temperature and treeline position, the observation that many treelines have advanced in response to recent warming and the frequent use of increment cores from treeline trees to reconstruct past climates. However, studies of the physiology of trees at the Arctic treeline are rare, and this hypothesis remains largely untested.

To improve our understanding of the relationships between temperature and performance of white spruce near the Arctic treeline, we made measurements of needle gas exchange, needle nutrition and soil nutrient availability over 2 years in three contrasting habitats: riverside terrace, hillslope forest and treeline. The sites had similar above‐ground microclimates, but very different soil conditions. Soils were warm and dry on the terrace, cool and moist in the forest and cold and seasonally wet the treeline.

Photosynthesis, needle nitrogen (N) concentration and soil N availability declined from the terrace to the forest to the treeline. Low N availability at the treeline was likely a consequence of limited microbial activity in the cold and seasonally wet soils. Soils at the treeline were colder than the terrace during the growing season and colder than the forest in winter, when the treeline maintains a shallow snowpack.

Our results highlight the potential for an indirect effect of temperature on the growth of trees at the Arctic treeline and suggest that treeline responses to changes in climate may be more complex than previously thought.
Improving distance sampling: accounting for covariates and non‐independency between sampled sites
Authors: Oedekoven Cornelia S. , Buckland Stephen T. , Mackenzie Monique L. , Evans Kristine O. , Burger Loren W.
Published: March 2013

There is currently much interest in replacing the design‐based component of conventional distance sampling methods by a modelling approach where animal densities are related to environmental covariates. These models allow identification of relationships between density and covariates. One of the uses of such models is to assess the effects of some intervention on numbers for species of conservation interest in designed distance sampling experiments.

In this context, we use an integrated likelihood approach for modelling sample counts, adopting a Poisson model and allowing imperfect detectability on the sample plots. We use the method of Royle, Dawson & Bates (2004,Ecology,85, 1591), extended to model heterogeneity in detection probabilities using either multiple covariate distance sampling methods or stratification. Moreover, we include a random effect for site in the plot abundance model to accommodate correlation in repeat counts at a single site.

These developments were motivated by a large‐scale experimental study to assess the effects of establishing conservation buffers along field margins on indigo buntings in severalUSstates. We analyse the data using an integrated likelihood and include model selection for both the Poisson rate of counts and detection probabilities. We assess model performance by comparing our results with those using a two‐stage approach (Bucklandet al. 2009,Journal of Agricultural, Biological, and Environmental Statistics,14, 432) which we extended by including a random effect for site in the plot abundance model.

The two methods led to the same selected models and gave similar results for parameters, which revealed significant beneficial effects of buffers on indigo bunting densities. Densities on buffered fields were on average 35% higher than on unbuffered fields. Using a detection function stratified by state captured some of the heterogeneity in detection probabilities between the nine states included in the analyses.

Synthesis and applications. We develop and compare two methods for analysing data from large‐scale distance sampling experiments with imbalanced repeat measures. By including a random site effect in the plot abundance model, we relax the assumption of independent sample counts which is generally made for distance sampling methods, and we allow inference to be drawn for the wider region that the sites represent.
Using Illumina next generation sequencing technologies to sequence multigene families in de novo species
Authors: Hughes Graham M. , Gang Li , Murphy William J. , Higgins Desmond G. , Teeling Emma C.
Published: March 2013

The advent of Next Generation Sequencing Technology (NGST) has revolutionized molecular biology research, allowing for rapid gene/genome sequencing from a multitude of diverse species. As high throughput sequencing becomes more accessible, more efficient workflows must be developed to deal with the amounts of data produced and better assemble the genomes of de novo lineages. We combine traditional laboratory methods with Illumina NGST to amplify and sequence the largest mammalian multigene family, the Olfactory Receptor gene family, for species with and without a reference genome. We develop novel assembly methods to annotate and filter these data, which can be utilized for any gene family or any species. We find no significant difference between the ratio of genes within their respective gene families of our data compared with available genomic data. Using simulated data we explore the limitations of short‐read sequence data and our assembly in recovering this gene family. We highlight the benefits and shortcomings of these methods. Compared with data generated from traditional polymerase chain reaction, cloning and Sanger sequencing methodologies, sequence data generated using our pipeline increases yield and sequencing efficiency without reducing the number of unique genes amplified. A cloning step is not required, therefore shortening data generation time. The novel downstream methodologies and workflows described provide a tool to be utilized by many fields of biology, to access and analyze the vast quantities of data generated. By combining laboratory and in silico methods, we provide a means of extracting genomic information for multigene families without complete genome sequencing.
Suppression of B‐cell activation and IgE, IgA, IgG1 and IgG4 production by mammalian telomeric oligonucleotides
Authors: Sackesen C. , van de Veen W. , Akdis M. , Soyer O. , Zumkehr J. , Ruckert B. , Stanic B. , Kalaycı O. , Alkan S. S. , Gursel I. , Akdis C. A.
Published: March 2013

Background

The fine balance of immunoglobulins (Ig) E, IgG1, IgG4 and IgA in healthy production is maintained by the interaction of B cells with adaptive and innate immune response. The regulation of toll‐like receptors (TLRs)‐driven innate and adaptive immune effector B‐cell response and the role of mammalian telomeric TTAGGG repeat elements represent an important research area.

Methods

Human PBMC and purified naive and memory B cells were stimulated with specific ligands for TLR2, TLR3, TLR4, TLR5, TLR7, TLR8 and TLR9 in the presence or absence of telomeric oligonucleotides. B‐cell proliferation, differentiation and antibody production were determined.

Results

TLR9 ligand directly activates naive and memory B cells, whereas TLR7 can stimulate them in the presence of plasmacytoid dendritic cells. Human B cells proliferate and turn into antibody‐secreting cells in response to TLR3, TLR7 and TLR9, but not to TLR2, TLR4, TLR5 and TLR8 ligands. Stimulation of B cells with intracellular TLR3, TLR7 and TLR9 induced an activation cascade leading to memory B‐cell generation and particularly IgG1, but also IgA, IgG4 and very low levels of IgE production. Mammalian telomeric oligodeoxynucleotide (ODN) significantly inhibited all features of TLR ligand‐induced events in B cells including B‐cell proliferation, IgE, IgG1, IgG4, IgA production, class switch recombination, plasma cell differentiation induced by TLR3, TLR7 and TLR9 ligands.

Conclusion

B cells require specific TLR stimulation, T‐cell and plasmacytoid dendritic cell help for distinct activation and Ig production profiles. Host‐derived telomeric ODN suppress B‐cell activation and antibody production demonstrating a natural mechanism for the control of overexuberant B‐cell activation, antibody production and generation of memory.
Meta‐analysis: serological markers and the risk of acute and chronic pouchitis
Authors: Singh S. , Sharma P. K. , Loftus E. V. , Pardi D. S.
Published: March 2013

Background

Serological markers such as anti‐neutrophil cytoplasmic antibody (ANCA) and anti‐Saccharomyces cerevisiae antibody (ASCA) may be associated with pouchitis after ileal pouch‐anal anastomosis (IPAA).

Aim

To perform a systematic review with meta‐analysis of studies evaluating the association of ANCA and ASCA status with risk of acute and chronic pouchitis after IPAA.

Methods

We searched multiple databases (upto September 2012) for studies reporting ANCA and/or ASCA status along with risk of acute or chronic pouchitis after IPAA in adults with ulcerative colitis (UC). We abstracted odds ratio (OR) or raw data from the individual studies to calculate summary OR estimates with 95% CIs using random‐effects model.

Results

Eight studies reporting 184 cases of acute pouchitis and six studies reporting 151 cases of chronic pouchitis were included. The odds of chronic pouchitis were 76% higher in ANCA‐positive patients than ANCA‐negative (six studies; OR: 1.76; 95% CI: 1.19–2.61; P < 0.01). ASCA‐positivity was not associated with the risk of chronic pouchitis (three studies; OR: 0.89; 95% CI: 0.49–1.59; P = 0.68). Neither ANCA (eight studies; OR: 1.54; 95% CI: 0.79–3.02; P = 0.21) nor ASCA‐positivity (two studies; OR: 1.28; 95% CI: 0.25–6.54; P = 0.77) were associated with the risk of acute pouchitis.

Conclusions

The risk of chronic pouchitis after IPAA is higher in ANCA‐positive patients, but the risk of acute pouchitis is unaffected by ANCA status. ASCA status was not associated with the risk of acute or chronic pouchitis. This information may be used to counsel UC patients regarding their risk of pouchitis after IPAA.
Evidence for interplay between genes and maternal stress in utero: monoamine oxidase A polymorphism moderates effects of life events during pregnancy on infant negative emotionality at 5 weeks
Authors: Hill J. , Breen G. , Quinn J. , Tibu F. , Sharp H. , Pickles A.
Published: March 2013

The low activity variant of the monoamine oxidase A (MAOA) functional promoter polymorphism, MAOA‐LPR, in interaction with adverse environments (G × E) is associated with child and adult antisocial behaviour disorders. MAOA is expressed during foetal development so in utero G × E may influence early neurodevelopment. We tested the hypothesis that MAOA G × E during pregnancy predicts infant negative emotionality soon after birth. In an epidemiological longitudinal study starting in pregnancy, using a two stage stratified design, we ascertained MAOA‐LPR status (low vs. high activity variants) from the saliva of 209 infants (104 boys and 105 girls), and examined predictions to observed infant negative emotionality at 5 weeks post‐partum from life events during pregnancy. In analyses weighted to provide estimates for the general population, and including possible confounders for life events, there was an MAOA status by life events interaction (P = 0.017). There was also an interaction between MAOA status and neighbourhood deprivation (P = 0.028). Both interactions arose from a greater effect of increasing life events on negative emotionality in the MAOA‐LPR low activity, compared with MAOA‐LPR high activity infants. The study provides the first evidence of moderation by MAOA‐LPR of the effect of the social environment in pregnancy on negative emotionality in infancy, an early risk for the development of child and adult antisocial behaviour disorders.
Temperature response of denitrification rate and greenhouse gas production in agricultural river marginal wetland soils
Authors: Bonnett S. A. F. , Blackwell M. S. A. , Leah R. , Cook V. , O'Connor M. , Maltby E.
Published: March 2013

Soils are predicted to exhibit significant feedback to global warming via the temperature response of greenhouse gas (GHG) production. However, the temperature response of hydromorphic wetland soils is complicated by confounding factors such as oxygen (O2), nitrate () and soil carbon (C). We examined the effect of a temperature gradient (2–25 °C) on denitrification rates and net nitrous oxide (N2O), methane (CH4) production and heterotrophic respiration in mineral (Eutric cambisol and Fluvisol) and organic (Histosol) soil types in a river marginal landscape of the Tamar catchment, Devon, UK, under non‐flooded and flooded with enriched conditions. It was hypothesized that the temperature response is dependent on interactions with ‐enriched flooding, and the physicochemical conditions of these soil types. Denitrification rate (mean, 746 ± 97.3 μg m−2 h−1), net N2O production (mean, 180 ± 26.6 μg m−2 h−1) and net CH4 production (mean, 1065 ± 183 μg m−2 h−1) were highest in the organic Histosol, with higher organic matter, ammonium and moisture, and lower concentrations. Heterotrophic respiration (mean, 127 ± 4.6 mg m−2 h−1) was not significantly different between soil types and dominated total GHG (CO2eq) production in all soil types. Generally, the temperature responses of denitrification rate and net N2O production were exponential, whilst net CH4 production was unresponsive, possibly due to substrate limitation, and heterotrophic respiration was exponential but limited in summer at higher temperatures. Flooding with increased denitrification rate, net N2O production and heterotrophic respiration, but a reduction in net CH4 production suggests inhibition of methanogenesis by or N2O produced from denitrification. Implications for management and policy are that warming and flood events may promote microbial interactions in soil between distinct microbial communities and increase denitrification of excess with N2O production contributing to no more than 50% of increases in total GHG production.
Oxidation of Fe(II) leads to increased C‐2 methylation of pentacyclic triterpenoids in the anoxygenic phototrophic bacterium Rhodopseudomonas palustris strain TIE‐1
Authors: Eickhoff M. , Birgel D. , Talbot H. M. , Peckmann J. , Kappler A.
Published: March 2013

Hopanoids are among the most widespread biomarkers of bacteria that are used as indicators for past and present bacterial activity. Our understanding of the production, function, and distribution of hopanoids in bacteria has improved greatly, partly due to genetic, culture‐independent studies. Culture‐based studies are important to determine hopanoid function and the environmental conditions under which these compounds are produced. This study compares the lipid inventory of Rhodopseudomonas palustris strain TIE‐1 under anoxic photoautotrophic conditions using either H2 or Fe(II) as electron donor. The high amount to which adenosylhopane is produced irrespective of the used electron donor suggests a specific function of this compound rather than its exclusive role as an intermediate in bacteriohopanepolyol biosynthesis. C‐2 methylated hopanoids and tetrahymanol account for as much as 59% of the respective C‐2 methylated/non‐methylated homologs during growth with Fe(II) as electron donor, as compared with 24% C‐2 methylation for growth with H2. This observation reveals that C‐2 methylated hopanoids have a specific function and are preferentially synthesized in response to elevated Fe(II) concentrations. The presence of C‐2 methylated pentacyclic triterpenoids has commonly been used as a biosignature for the interpretation of paleoenvironments. These new findings suggest that increased C‐2 methylation may indicate anoxic ferrous conditions, in addition to other environmental stressors that have been previously reported.
Effectiveness of a motivational–behavioural skills protocol for oral hygiene among patients with hyposalivation
Authors: López‐Jornet Pia , Fabio Camacho‐Alonso , Consuelo Rodríguez Agudo , Paz Andujar Mateos
Published: March 2013

Background

The main objective of this study was to assess the effectiveness of a motivational‐behavioural skills protocol for plaque control in patients with hyposalivation.

Patients and methods

In a randomised, evaluator‐blinded, controlled trial, 60 subjects with hyposalivation (12 men and 48 women) were randomly assigned to two groups: the control group received basic oral hygiene instruction, while for the study (intervention) group, oral hygiene instruction was based on cognitive behavioural principles and motivational interviewing (MI). Both groups were given oral hygiene instruction once every 15 days, with a total of four sessions over a 2‐month period: plaque extension and community periodontal index of treatment needs (CPITN), frequency and duration of brushing, frequency of interdental cleaning and scores based on scale of ‘self‐efficacy for brushing of the teeth’. Clinical characteristics were compared between the two groups.

Results

Both control and intervention group patients showed significantly lower plaque indices, bleeding indices and an improvement in probe depth after the 2‐month study period. Interproximal brushing was significantly more frequent among the intervention group (p = 0.016).

Conclusion

In patients with hyposalivation, the application of oral hygiene instruction based on cognitive principles and MI offers benefits for periodontal health. Longer‐term studies are needed to confirm these results.
Red blood cell morphology
Authors: Ford J.
Published: March 2013

The foundation of laboratory hematologic diagnosis is the complete blood count and review of the peripheral smear. In patients with anemia, the peripheral smear permits interpretation of diagnostically significant red blood cell (RBC) findings. These include assessment of RBC shape, size, color, inclusions, and arrangement. Abnormalities of RBC shape and other RBC features can provide key information in establishing a differential diagnosis. In patients with microcytic anemia, RBC morphology can increase or decrease the diagnostic likelihood of thalassemia. In normocytic anemias, morphology can assist in differentiating among blood loss, marrow failure, and hemolysis—and in hemolysis, RBC findings can suggest specific etiologies. In macrocytic anemias, RBC morphology can help guide the diagnostic considerations to either megaloblastic or nonmegaloblastic causes. Like all laboratory tests, RBC morphologies must be interpreted with caution, particularly in infants and children. When used properly, RBC morphology can be a key tool for laboratory hematology professionals to recommend appropriate clinical and laboratory follow‐up and to select the best tests for definitive diagnosis.
Sirolimus ameliorates inflammatory responses by switching the regulatory T/T helper type 17 profile in murine colitis
Authors: Yin Hui , Li Xiangyong , Zhang Bobin , Liu Tao , Yuan Baohong , Ni Qian , Hu Shilian , Gu Hongbiao
Published: March 2013

Inflammatory bowel disease is characterized by dysregulated immune responses in inflamed intestine, with dominance of interleukin‐17 (IL‐17) ‐producing cells and deficiency of regulatory T (Treg) cells. The aim of this study was to investigate the effect and mechanisms of sirolimus, an inhibitor of the mammalian target of rapamycin, on immune responses in a murine model of Crohn's disease. Murine colitis was induced by intrarectal administration of 2,4,6‐trinitrobenzene sulphonic acid at day 0. Mice were then treated intraperitoneally with sirolimus daily for 3 days. The gross and histological appearances of the colon and the numbers, phenotype and cytokine production of lymphocytes were compared with these characteristics in a control group. Sirolimus treatment significantly decreased all macroscopic, microscopic and histopathological parameters of colitis that were analysed. The therapeutic effects of sirolimus were associated with a down‐regulation of pro‐inflammatory cytokines tumour necrosis factor‐α, IL‐6 and IL‐17A. Intriguingly, sirolimus administration resulted in a prominent up‐regulation of the regulatory cytokine transforming growth factor‐β. Supporting the hypothesis that sirolimus directly affects the functional activity of CD4+ CD25+ Treg cells, we observed a remarkable enhancement of FoxP3 expression in colon tissues and isolated CD4+ T cells of sirolimus‐treated mice. Simultaneously, sirolimus treatment led to a significant reduction in the number of CD4+ IL‐17A+ T cells in the mesenteric lymph node cells as well as IL‐17A production in mesenteric lymph node cells. Therefore, sirolimus may offer a promising new therapeutic strategy for the treatment of inflammatory bowel disease.
USE OF ULTRASOUND TO LOCATE RETAINED TESTES IN DOGS AND CATS
Authors: Felumlee Amy E. , Reichle Jean K. , Hecht Silke , Penninck Dominique , Zekas Lisa , Dietze Yeager Amy , Goggin Justin M. , Lowry Jennifer
Published: March 2013

Ultrasound was used to locate undescended testes in 30 dogs and 4 cats where the final testicular location was determined surgically. Time between ultrasound and surgery ranged between 0 and 17 days. Forty‐three testes (63.2%) were retained and 42/43 (97.7%) were detected ultrasonographically. Retained testes were located in the abdomen (n= 28) and inguinal region (n= 14). One retained testis could not be identified with use of ultrasound. Locations of retained testes ranged from the caudal pole of the kidney to the inguinal region. Descriptions of testicular echogenicity and size were not available for all testes. A 100% positive predictive value was found for all testes with use of ultrasound in both abdominal and inguinal regions. The sensitivity of ultrasound was 96.6% for abdominal and 100% for inguinal testes. Ultrasound is a sensitive test for location of retained testes, and supports the opinion that preoperative ultrasound can help facilitate location of retained testes prior to surgical exploration or laparoscopy. © 2012 Veterinary Radiology & Ultrasound.
EVALUATION OF ERGONOMIC RISK FACTORS AMONG VETERINARY ULTRASONOGRAPHERS
Authors: Randall Elissa , Hansen Chad , Gilkey David , Patil Anuja , Bachand Annette , Rosecrance John , Douphrate David
Published: March 2013

Between 65% and 91% of human‐patient sonographers report musculoskeletal symptoms related to their work activities. Ergonomic risk factors associated with musculoskeletal symptoms and musculoskeletal disorders (MSDs) include force, repetition, and awkward postures of the upper extremities. We hypothesized that veterinary sonographers experience similar risk factor exposures as their colleagues in human‐patient sonography, and that work‐related exposures may lead to similar prevalence of musculoskeletal symptoms and disorders. The Occupational Safety and Health Administration and Society of Diagnostic Medical Sonography published MSD prevention guidelines in 2003. Similar guidance for sonographers examining animal patients does not exist. This cross‐sectional study was designed to evaluate the prevalence of musculoskeletal symptoms among veterinary sonographers and identify reported risk factors. A 59‐item survey questionnaire was administered via email to veterinary specialists likely to perform ultrasound. Musculoskeletal pain related to performing ultrasound exams was reported by 62% of the respondents. Musculoskeletal symptoms were significantly associated with female gender (odds ratio [OR], 4.55; 95% confidence interval [CI], 2.04–10.19), age (OR, 1.06; 95% CI, 1.01, 1.10), previous work‐related trauma (OR, 6.86; 95% CI, 1.71, 27.40), not consistently using a normal height chair (OR, 2.63; 95% CI, 1.19, 5.80), and 15°–45° abduction of shoulder (OR, 2.34; 95% CI, 1.11, 4.92) . It was concluded that the prevalence of musculoskeletal symptoms among veterinary sonographers was similar to that occurring in human‐patient sonographers. © 2012 Veterinary Radiology & Ultrasound.
COLOR AND POWER DOPPLER ULTRASONOGRAPHY FOR CHARACTERIZATION OF SPLENIC MASSES IN DOGS
Authors: Sharpley Jenelle L. , Marolf Angela J. , Reichle Jean K. , Bachand Annette M. , Randall Elissa K.
Published: March 2013

Benign and malignant splenic masses can appear similar on B‐mode imaging, making ultrasound sensitive but not specific in their diagnosis. Our goal was to characterize color and/or power Doppler characteristics of vasculature within and adjacent to a splenic mass, which would distinguish benign vs. malignant lesions. The hypothesis was that malignant splenic masses will have altered vascular patterns compared with benign masses. Color and power Doppler cineloops evaluating the vasculature within the mass and normal splenic parenchyma were obtained in sagittal and transverse planes using a standardized protocol. Categories of evaluation included presence of peritoneal effusion, a large aberrant or tortuous vessel within the mass, relative blood flow within the mass compared with normal parenchyma, and path of vessels in the adjacent parenchyma entering into the mass. All patients had histopathologic or definitive cytologic diagnosis. Thirty‐one dogs were included. There were 13 malignant masses and 18 were benign. Peritoneal effusion was significantly associated with malignancy (P = 0.0007). Presence of an aberrant or tortuous vessel within the mass was nearly significant (P = 0.059). There was no significant difference in any of the color or power Doppler blood flow evaluations. Ultrasonographic findings of a splenic mass and peritoneal effusion may indicate malignancy. The presence of an aberrant vessel within a splenic mass could suggest malignancy; however more data are needed.
COMPARISON OF THE RELATIVE OCCIPITAL BONE VOLUME BETWEEN CAVALIER KING CHARLES SPANIELS WITH AND WITHOUT SYRINGOHYDROMYELIA AND FRENCH BULLDOGS
Authors: Schmidt M.J. , Kramer M. , Ondreka N.
Published: March 2013

Our aim was to determine the relative volume of the occipital bone of Cavalier King Charles spaniels with and without syringohydromyelia and normal French bulldogs to reappraise the role of a possible insufficiency of the paraxial mesoderm in the pathogenesis of the caudal occipital malformation syndrome. Analysis of the occipital bone volume of 43 dogs based on computed tomography datasets was performed. Volume was determined by means of three‐dimensional models. Using manual segmentation of the occipital bone in sagittal, transverse, and dorsal images, the volume of the occipital bone and the rest of the skull was calculated. The absolute occipital bone volume was put in relation to the total skull volume, the occipital bone index. For the Cavalier King Charles spaniels without syringomyelia, the median occipital bone index was 0.0681; for Cavalier King Charles spaniels with syringomyelia, it was 0.0646 and for French bulldogs, it was 0.0676. There was no global difference of the occipital bone index between examined groups (P = 0.4331). A reduced volume of the occipital bone was not found in Cavalier King Charles spaniels in general in comparison to French bulldogs, or in Cavalier King Charles spaniels with syringomyelia compared to Cavalier King Charles spaniels without syringomyelia. These results do not support occipital hypoplasia as a cause for syringomyelia development, challenging the paraxial mesoderm insufficiency theory. This also suggests that the term Chiari‐like malformation, a term derived from human studies, is not appropriate in the Cavalier King Charles spaniel.
ASSESSMENT OF FIVE OBLIQUE RADIOGRAPHIC PROJECTIONS OF THE CANINE TEMPOROMANDIBULAR JOINT
Authors: Hammond Gawain , King Alison , LaPaglia John
Published: March 2013

Investigation of temporomandibular joint (TMJ) disease requires a clear diagnostic image, which can be challenging to obtain using conventional radiography. The aim of this study was to compare five different oblique radiographic views with the head in lateral recumbency, assessing the clarity of visualization of the normal TMJ anatomy. The views under investigation were the laterorostral–laterocaudal oblique at a 10° and 20° rotation of the head (“nose‐up” view), laterorostral–laterocaudal oblique with a rostrocaudal X‐ray beam angulation of 10° and 20°, and a parallax view with the beam centered over C2 and collimated to include the TMJ region, using the divergence of the X‐ray beam to project the TMJs separately on the radiograph. The views were performed on both TMJs of thirty canine cadavers and were graded independently by experienced and inexperienced observers. Grading was performed on the mandibular fossa, condylar process, joint space, retroarticular process, and the overall TMJ, and was based on a four‐point scale. Mean grades for each component and for the overall joint were compared for each observer and each projection. Mean grades were significantly (P < 0.05) higher for the “Nose‐up” projections than the angled beam or parallax projections, as was interobserver agreement, and both observers showed significantly higher (P < 0.05) mean grades for the 20o “Nose‐up” angulation than the 10o “Nose‐up” angulation. These results suggest that a latero 20o rostral–laterocaudal oblique gives the best representation of the anatomy of the TMJ of the dog of the projections assessed, and should be considered when investigating clinical cases of TMJ disease.
CLINICAL SIGNIFICANCE AND PROGNOSIS OF DEEP DIGITAL FLEXOR TENDINOPATHY ASSESSED OVER TIME USING MRI
Authors: Vanel Maïa , Olive Julien , Gold Sarah , Mitchell Richard D. , Walker Lea
Published: March 2013

Deep digital flexor (DDF) tendinopathy is one of the most frequent causes of foot lameness and the prognosis is guarded. The progress of lesion healing may be followed by magnetic resonance (MR) imaging to formulate a prognosis and to adapt the rehabilitation program. We assessed the correlation of outcome with total tendon damage and temporal resolution of MR abnormalities. Images from 34 horses with DDF tendinopathy that had undergone at least two low‐field standing MR examinations of the foot (mean 2.5 ± 1.3 times) were reviewed. No horse having a T1‐GRE hyperintense lesion over 30 mm in length or over 10% tendon cross‐sectional area returned to its previous activity level. Horses with concomitant lesions had worse outcome than horses with DDF tendinopathy only (P = 0.005). In all horses including those with excellent outcome, the lesion persisted, even mildly, in T1‐GRE and PD images. Horses with tendon lesion resolution on STIR‐FSE and T2‐FSE images on recheck examination had a better outcome (P = 0.0004 and P = 0.002, respectively), and all horses that returned to their previous level of performance had complete resolution of signal hyperintensity on the STIR‐FSE sequence. Although rehabilitation remains multifactorial, characteristics of DDF tendinopathy and concomitant lesions on first and recheck MR examinations allow refining the prognosis.
UNIQUE TOPOGRAPHIC DISTRIBUTION OF GREYHOUND NONSUPPURATIVE MENINGOENCEPHALITIS
Authors: Terzo Eloisa , McConnell J. Fraser , Shiel Robert E. , McAllister Hester , Behr Sebastien , Priestnall Simon L. , Smith Ken C. , Nolan Catherine M. , Callanan John J.
Published: March 2013

Greyhound nonsuppurative meningoencephalitis is an idiopathic breed‐associated fatal meningoencephalitis with lesions usually occurring within the rostral cerebrum. This disorder can only be confirmed by postmortem examination, with a diagnosis based upon the unique topography of inflammatory lesions. Our purpose was to describe the magnetic resonance (MR) imaging features of this disease. Four Greyhounds with confirmed Greyhound nonsuppurative meningoencephalitis were evaluated byMRimaging. Lesions predominantly affected the olfactory lobes and bulbs, frontal, and frontotemporal cortical gray matter, and caudate nuclei bilaterally. Fluid attenuation inversion recovery (FLAIR) andT2 weighted spin‐echo (T2W) sequences were most useful to assess the nature, severity, extension, and topographic pattern of lesions. Lesions were predominantlyT2‐hyperintense andT1‐isointense with minimal or absent contrast enhancement.
MAGNETIC RESONANCE IMAGING OF PULP IN NORMAL AND DISEASED EQUINE CHEEK TEETH
Authors: Gerlach Kerstin , Ludewig Eberhard , Brehm Walter , Gerhards Hartmut , Delling Uta
Published: March 2013

A retrospective analysis of 619 upper and lower cheek teeth from 62 horses was performed. Based on clinical findings, as well as radiographic and magnetic resonance (MR) imaging findings, the teeth were classified into five groups. There were 20 teeth with abnormal MR imaging signals as well as clinical alterations and 599 healthy teeth. Using MR imaging, the appearance of pulp in diseased and disease‐free teeth was compared, and the appearance of abnormal pulp was studied. Subsequently, the ability of MR imaging to diagnose pulpitis and pulp necrosis in teeth with normal external appearance was investigated. In horses with clinically verified dental disease, abnormal MR imaging findings were confirmed in the pulp of all affected teeth. An enlarged blurred pulp image with a lower signal intensity was observed only in clinically diseased teeth and was a reliable criterion for diagnosing dental disease on MR imaging. On the other hand, partial or complete absence of pulp in all MR imaging sequences was observed in both diseased and nondiseased teeth. These data demonstrate that pulp changes in equine cheek teeth can be evaluated using MR imaging.
FEASIBILITY FOR USING DUAL‐PHASE CONTRAST‐ENHANCED MULTI‐DETECTOR HELICAL COMPUTED TOMOGRAPHY TO EVALUATE AWAKE AND SEDATED DOGS WITH ACUTE ABDOMINAL SIGNS
Authors: Shanaman Miriam M. , Hartman Susan K. , O'Brien Robert T.
Published: March 2013

Canine patients with acute abdominal signs are often clinically unstable and need a rapid and accurate diagnosis. Contrast‐enhanced multi‐detector computed tomography (CT) is the current modality of choice for evaluating acute abdominal pain in people. We hypothesized that contrast‐enhanced multi‐detectorCTwould be a feasible and safe technique for use in awake and lightly sedated dogs with acute abdominal signs. Eighteen client‐owned dogs were enrolled, all presenting with acute abdominal signs. Dogs were scanned using a dual‐phase protocol that included precontrast, arterial, and portal venous phases. Eight dogs were scanned awake and ten were given light sedation as chosen by the primary care clinician. Two observers who were unaware of clinical findings and sedation status scored image quality for each scan by consensus opinion. Mean serum creatinine in the sedated group was higher than in the awake group but was within the normal reference range. Other laboratory and physiologic measures did not differ between awake and sedated groups. NoIVcontrast‐related adverse reactions were seen. Median scan time for all patients was less than 10 min. Sixteen of 18 contrast‐enhanced multi‐detectorCTscans were scored fair to excellent in diagnostic quality, with no statistical difference in diagnostic quality for awake vs. sedated patients. Causes for two poor quality diagnostic scans included severe beam hardening from previously administered barium contrast agent and severe motion artifacts. We conclude that dual‐phase contrast‐enhanced multi‐detectorCTis a feasible and safe technique for evaluating awake and minimally sedated dogs presenting with acute abdominal signs.
DIAGNOSTIC SENSITIVITY OF SUBJECTIVE AND QUANTITATIVE LARYNGEAL ULTRASONOGRAPHY FOR RECURRENT LARYNGEAL NEUROPATHY IN HORSES
Authors: Chalmers Heather J. , Yeager Amy E. , Cheetham Jonathan , Ducharme Norm
Published: March 2013

Recurrent laryngeal neuropathy (RLN) is the most common cause of laryngeal hemiplegia in horses and causes neurogenic atrophy of the intrinsic laryngeal muscles, including the cricoarytenoideus lateralis muscle. Recurrent laryngeal neuropathy results in paresis to paralysis of the vocal fold and arytenoid cartilage, which limits performance through respiratory compromise. Ultrasound has previously been reported to be a useful diagnostic technique in horses withRLN. In this report, the diagnostic sensitivity of subjective and quantitative laryngeal ultrasonography was evaluated in 154 horses presented for poor performance due to suspected upper airway disease. Ultrasonographic parameters recorded were: cricoarytenoideus lateralis echogenicity (subjective and quantitative), cricoarytenoideus lateralis thickness, vocal fold movement, and arytenoid cartilage movement. Ultrasonographic parameters were then compared with laryngeal grades based on resting and exercising upper airway endoscopy. Subjectively increased left cricoarytenoideus lateralis echogenicity yielded a sensitivity of 94.59% and specificity of 94.54% for detectingRLN, based on the reference standard of exercising laryngeal endoscopy. Quantitative left cricoarytenoideus lateralis echogenicity values differed among resting laryngeal grades I–IV. Findings from this study support previously published findings and the utility of subjective and quantitative laryngeal ultrasound as diagnostic tools for horses with poor performance.