bluuebunny/crossref_metadata_2025 huggingface dataset:
Privately Owned Small Impoundments in Central Alabama: A Survey and Evaluation of Management Techniques for Largemouth Bass and Bluegill
Authors: Haley Norman V. , Wright Russell A. , DeVries Dennis R. , Allen Micheal S.
Published: November 2012

Small impoundments or ponds represent important fisheries resources, both recreationally and economically. These systems are small relative to most large public reservoirs and natural lakes and thus they are more easily manipulated to improve fishing quality. The utility of some pond management techniques in improving fisheries is not well understood. We combined a telephone survey and field sampling to quantify the characteristics and use(s) of private ponds in central Alabama and determine the efficacy of the most often used pond fishery enhancement techniques. The three most common techniques were fertilization (used by 48% of surveyed pond owners), supplemental feeding with pellets (45%), and the stocking of supplemental prey for largemouth bass Micropterus salmoides (12%; the species most often stocked was threadfin shad Dorosoma petenense). We sampled 66 ponds using boat electrofishing to assess largemouth bass and Lepomis spp. population responses to these management techniques. Fish populations varied greatly within management categories. However, ponds with threadfin shad exhibited overall greater largemouth bass length, length frequency indices (PSD and PSD- P, -M), growth, body condition, and density than ponds without threadfin shad. Bluegill Lepomis macrochirus population characteristics were similar among all ponds using fertilizer and threadfin shad. Of these techniques, we found that fertilization improved bluegill populations and that threadfin shad can improve largemouth bass populations without compromising bluegill size structure and abundance.

Received January 26, 2012; accepted August 7, 2012
Frequency of Strong Year-Classes: Implications on Fishery Dynamics for Three Life History Strategies of Fishes
Authors: Daugherty Daniel J. , Smith Nathan G.
Published: November 2012

Many studies have examined variation in year-class strength and associated density-dependent growth of fishes. Few studies, however, have considered the effects of these factors on fishery quality. We examined how the frequency of strong year-classes affects fish harvest and size structure for three species with varying life histories. We modeled both random and systematic occurrences of strong year-classes for white bass Morone chrysops (short-lived species), largemouth bass Micropterus salmoides (species with intermediate longevity), and blue catfish Ictalurus furcatus (long-lived species). For white bass and largemouth bass, intermediate frequencies of strong year-classes (i.e., every 3–10 years) incrementally reduced harvest but improved the proportional size distribution (PSD) under current fishing regulations. The greatest improvements in PSD with minimal effects on harvest (relative to annual strong year-classes) occurred when strong year-classes were produced every 3 years for white bass and every 5 years for largemouth bass. In contrast, production of strong blue catfish year-classes every 6 years maximized harvest and resulted in a fivefold increase in PSD relative to a strong year-class frequency of every 1–2 years. Greater annual consistency in harvest and PSD for fishes with intermediate and high longevity was achieved when strong year-classes occurred systematically rather than at random. Our results suggest that intermediate frequencies of strong year-class production, relative to species longevity, serve to balance harvest and size structure characteristics. The use of fish stocking or water level manipulations to systematically produce strong year-classes can also improve the consistency of annual harvest and size structure for longer-lived fishes (>10 years).

Received March 28, 2012; accepted August 27, 2012
The Adapted Version of the Sociomoral Reflection Measure (SRM-AV) in Dutch Forensic Psychiatric Patients
Authors: Hornsveld RuudH.J. , Kraaimaat FlorisW. , Zwets AlmarJ.
Published: November 2012

We developed a new instrument for measuring moral maturity in Dutch forensic psychiatric patients with the Sociomoral Reflection Measure-Short Form as a starting point. This instrument contains 11 propositions to which respondents indicate their own perceived level of importance and justifications of their choices. Twenty new statements were added to these 11 propositions. Justifications of the responses were scored with the aid of a seven-point scale, each point representing a (transitional) level of moral maturity. In order to have a practical instrument, we deleted 11 items with the lowest interrater reliability of the 31 items. The internal consistency, interrater reliability and test-retest reliability of the new instrument with the remaining 20 items (SRM-AV) were good. Validity was supported by significant correlations with age, psychopathy, agreeableness, and verbal aggression. Patients scored significantly lower on the SRM-AV than two non-clinical control groups. For the time being, the SRM-AV appears to measure moral maturity in forensic psychiatric patients in a reliable and valid way.
SUMOylation of the small GTPase ARL-13 promotes ciliary targeting of sensory receptors
Authors: Li Yujie , Zhang Qing , Wei Qing , Zhang Yuxia , Ling Kun , Hu Jinghua
Published: November 2012

Primary cilia serve as cellular antenna for various sensory signaling pathways. However, how the sensory receptors are properly targeted to the ciliary surface remains poorly understood. Here, we show that UBC-9, the sole E2 small ubiquitin-like modifier (SUMO)-conjugating enzyme, physically interacts with and SUMOylates the C terminus of small GTPase ARL-13, the worm orthologue of ARL13B that mutated in ciliopathy Joubert syndrome. Mutations that totally abolish the SUMOylation of ARL-13 do not affect its established role in ciliogenesis, but fail to regulate the proper ciliary targeting of various sensory receptors and consequently compromise the corresponding sensory functions. Conversely, constitutively SUMOylated ARL-13 fully rescues all ciliary defects of arl-13–null animals. Furthermore, SUMOylation modification of human ARL13B is required for the ciliary entry of polycystin-2, the protein mutated in autosomal dominant polycystic kidney disease. Our data reveal a novel but conserved role for the SUMOylation modification of ciliary small GTPase ARL13B in specifically regulating the proper ciliary targeting of various sensory receptors.
Optical absorption of Ni2+ and Ni3+ ions in gadolinium gallium garnet epitaxial films
Authors: Vasileva N V , Gerus P A , Sokolov V O , Plotnichenko V G
Published: November 2012

Single-crystal Ni-doped gadolinium gallium garnet films were grown for the first time from supercooled Bi2O3–B2O3-based melt solutions by liquid-phase epitaxy. Optical absorption bands due to Ni2+, Ni3+ and Bi3+ ions were observed in those films. Interpretation and tabulation of all absorption bands of nickel ions occupying octahedral and tetrahedral sites in the garnet lattice are presented.
Towards understanding ELM mitigation: the effect of axisymmetric lobe structures near the X-point on ELM stability
Authors: Chapman I.T. , Kirk A. , Saarelma S. , Harrison J.R. , Scannell R.
Published: November 2012

The application of resonant magnetic perturbations (RMPs) with toroidal mode number n = 4 or n = 6 is observed to result in a significant increase in ELM frequency, despite a reduction in the edge pressure gradient. A picture for how type-I ELMs are mitigated, or destabilized, when magnetic perturbations are applied is proposed. Despite the magnetic perturbation incurring a drop in the pedestal pressure gradient, the critical pressure for an ELM to be triggered is dropped even further. Various mechanisms which could cause this degradation of the stability boundary are outlined. The stability of the edge of MAST H-mode plasmas has been tested when lobe structures are present in the separatrix after application of RMPs. The axisymmetric stability analysis presented here shows that when the plasma boundary is simulated with a model for the observed lobe structures included, the ballooning stability is degraded. This degradation in ballooning stability originates from the perturbed field lines dwelling in the region of unfavourable curvature due to the presence of lobe structures rather than the change in the plasma boundary shape.
Asymptotic cycles for actions of Lie groups
Authors: Schwartzman Sol
Published: November 2012

Let

M
k

M^k

be a compact

C
∞

C^\infty

manifold and suppose we are given a

C
∞

C^\infty

action of

R

n

\mathbb {R}^n

on

M
k

M^k

. If

p
p

is a quasiregular point for this action and

v
v

is an

r
r

-vector over the Lie algebra of

R

n

\mathbb {R}^n

, we show how to associate with

p
p

and

v
v

an element

A
p
v

A_p^v

in

H
r

(

M
k

;

R

)

H_r(M^k;\mathbb {R})

. When

n
=
1

n=1

and

v
v

is the usual generator for the Lie algebra of

R

\mathbb {R}

,

A
p
v

A_p^v

coincides with the asymptotic cycle associated with

p
p

by our flow. Just as in the one dimensional case, with any invariant probability measure we can associate an element

A
μ
v

A_\mu ^v

in

H
r

(

M
k

;

R

)
.

H_r(M^k;\mathbb {R}).

Several results known in the one dimensional case generalize to our present situation. The results we have stated for actions of

R

n

\mathbb {R}^n

are obtained from a discussion of what we can say when we have a smooth action of an arbitrary connected Lie group on

M
k

M^k

.
From triangulated categories to module categories via localisation
Authors: Buan Aslak , Marsh Robert
Published: November 2012

We show that the category of finite dimensional modules over the endomorphism algebra of a rigid object in a Hom-finite triangulated category is equivalent to the Gabriel-Zisman localisation of the category with respect to a certain class of maps. This generalises the

2
2

-Calabi-Yau tilting theorem of Keller-Reiten, in which the module category is obtained as a factor category, to the rigid case.
FOLD-EM: automated fold recognition in medium- and low-resolution (4–15 Å) electron density maps
Authors: Saha Mitul , Morais Marc C.
Published: November 2012

Motivation: Owing to the size and complexity of large multi-component biological assemblies, the most tractable approach to determining their atomic structure is often to fit high-resolution radiographic or nuclear magnetic resonance structures of isolated components into lower resolution electron density maps of the larger assembly obtained using cryo-electron microscopy (cryo-EM). This hybrid approach to structure determination requires that an atomic resolution structure of each component, or a suitable homolog, is available. If neither is available, then the amount of structural information regarding that component is limited by the resolution of the cryo-EM map. However, even if a suitable homolog cannot be identified using sequence analysis, a search for structural homologs should still be performed because structural homology often persists throughout evolution even when sequence homology is undetectable, As macromolecules can often be described as a collection of independently folded domains, one way of searching for structural homologs would be to systematically fit representative domain structures from a protein domain database into the medium/low resolution cryo-EM map and return the best fits. Taken together, the best fitting non-overlapping structures would constitute a ‘mosaic’ backbone model of the assembly that could aid map interpretation and illuminate biological function.

Result: Using the computational principles of the Scale-Invariant Feature Transform (SIFT), we have developed FOLD-EM—a computational tool that can identify folded macromolecular domains in medium to low resolution (4–15 Å) electron density maps and return a model of the constituent polypeptides in a fully automated fashion. As a by-product, FOLD-EM can also do flexible multi-domain fitting that may provide insight into conformational changes that occur in macromolecular assemblies.

Availability and implementation: FOLD-EM is available at: http://cs.stanford.edu/~mitul/foldEM/, as a free open source software to the structural biology scientific community.

Contact:  mitul@cs.stanford.edu or mcmorais@utmb.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data
Authors: Pacini Clare , Iorio Francesco , Gonçalves Emanuel , Iskar Murat , Klabunde Thomas , Bork Peer , Saez-Rodriguez Julio
Published: November 2012

Summary: Drug versus Disease (DvD) provides a pipeline, available through R or Cytoscape, for the comparison of drug and disease gene expression profiles from public microarray repositories. Negatively correlated profiles can be used to generate hypotheses of drug-repurposing, whereas positively correlated profiles may be used to infer side effects of drugs. DvD allows users to compare drug and disease signatures with dynamic access to databases Array Express, Gene Expression Omnibus and data from the Connectivity Map.

Availability and implementation: R package (submitted to Bioconductor) under GPL 3 and Cytoscape plug-in freely available for download at www.ebi.ac.uk/saezrodriguez/DVD/.

Contact:  saezrodriguez@ebi.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Systematic variation of the stellar initial mass function with velocity dispersion in early-type galaxies
Authors: Ferreras Ignacio , Barbera Francesco La , Rosa Ignacio G. de la , Vazdekis Alexandre , Carvalho Reinaldo R. de , Falcón-Barroso Jesús , Ricciardelli Elena
Published: November 2012

An essential component of galaxy formation theory is the stellar initial mass function (IMF) that describes the parent distribution of stellar mass in star-forming regions. We present observational evidence in a sample of early-type galaxies (ETGs) of a tight correlation between central velocity dispersion and the strength of several absorption features sensitive to the presence of low-mass stars. Our sample comprises ∼40 000 ETGs from the Spheroids Panchromatic Investigation in Different Environmental Regions survey (z ≲ 0.1). The data – extracted from the Sloan Digital Sky Survey – are combined, rejecting both noisy data, and spectra with contamination from telluric lines, resulting in a set of 18 stacked spectra at high signal-to-noise ratio (S/N ≳ 400 Å−1). A combined analysis of IMF-sensitive line strengths and spectral fitting is performed with the latest state-of-the-art population synthesis models (an extended version of the MILES models). A significant trend is found between IMF slope and velocity dispersion, towards an excess of low-mass stars in the most massive galaxies. Although we emphasize that accurate values of the IMF slope will require a detailed analysis of chemical composition (such as [α/Fe] or even individual element abundance ratios), the observed trends suggest that low-mass ETGs are better fitted by a Kroupa-like IMF, whereas massive galaxies require bottom-heavy IMFs, exceeding the Salpeter slope at σ ≳ 200 km s−1.
Internal shocks at the origin of the flat spectral energy distribution of compact jets
Authors: Malzac Julien
Published: November 2012

An internal shock model is proposed to interpret the radio to infrared (IR) emission of the compact jets observed in the hard spectral state of X-ray binaries. Assuming that the specific bulk Lorentz factor of the jet at its base varies with a flicker noise power spectrum [i.e. P(f) ∝ 1/f], we estimate the energy dissipation profile along the jet and the resulting partially self-absorbed synchrotron emission. For this type of velocity fluctuations, and a conical jet geometry, the shock dissipation at large distance from the black hole balances exactly the adiabatic losses. This leads to a flat radio to IR spectral energy distribution similar to that observed in compact jets.
Tobacco etch virus Infectivity in Capsicum Spp. Is Determined by a Maximum of Three Amino Acids in the Viral Virulence Determinant VPg
Authors: Perez Kari , Yeam Inhwa , Kang Byoung-Cheorl , Ripoll Daniel R. , Kim Jinhee , Murphy John F. , Jahn Molly M.
Published: November 2012

Potyvirus resistance in Capsicum spp. has been attributed to amino acid substitutions at the pvr1 locus that cause conformational shifts in eukaryotic translation initiation factor eIF4E. The viral genome-linked protein (VPg) sequence was isolated and compared from three Tobacco etch virus (TEV) strains, highly aphid-transmissible (HAT), Mex21, and N, which differentially infect Capsicum genotypes encoding Pvr1+, pvr1, and pvr12. Viral chimeras were synthesized using the TEV-HAT genome, replacing HAT VPg with Mex21 or N VPg. TEV HAT did not infect pepper plants homozygous for either the pvr1 or pvr12 allele. However, the novel chimeric TEV strains, TEV-HATMex21-VPg and TEV-HATN-VPg, infected pvr1 and pvr12 pepper plants, respectively, demonstrating that VPg is the virulence determinant in this pathosystem. Three-dimensional structural models predicted interaction between VPg and the susceptible eIF4E genotype in every case, while resistant genotypes were never predicted to interact. To determine whether there is a correlation between physical interaction of VPg with eIF4E and infectivity, the effects of amino acid variation within VPg were assessed. Interaction between pvr12 eIF4E and N VPg was detected in planta, implying that the six amino acid differences in N VPg relative to HAT VPg are responsible for restoring the physical interaction and infectivity.
First Report of Bacterial Leaf Spot of Rieger Begonia Caused by Xanthomonas campestris pv. begoniae in China
Authors: Zhou L. H. , Ji G. H.
Published: November 2012

Rieger begonia are collectively referred to as a begonia hybrid group. Its global annual sales is 90,000,000 cutting seedlings. It is one of the top ten potted plants. In the summer of 2011, serious outbreaks of a suspected bacterial leaf spot disease were observed on five Rieger begonia cultivars (Dark Britt, Rebecca, Blitz, Barkos, and Borias). These plants were grown for potted cutting seedling production in commercial nurseries located in Shilin county of Yunnan Province, China. The initial symptoms of the disease were small circular or polygonal water-soaked needle spots on leaf margin that later these spots expanded and joined together, forming bigger inverted V-shaped necrotic specks (4). Yellow-pigmented bacterial colonies were consistently isolated from diseased leaves and stems on NA agar medium and incubated at 28°C. Twelve bacterial strains were isolated and used for further studies. All the isolates were Gram-negative, rod-shaped, motile, aerobic, and non-sporing. All of the bacterial strains isolated in the present study were identified as Xanthomonas campestris pv. begoniae (Xcb) based on biochemical and physiological identification (Biolog carbon source utilization analysis) and 16S rDNA sequences analysis and further pathogenicity determination (1). The results show that the sequence homology rate of HT1-1 (GenBank Accession No. JN648097) and X. euvesicatoria (syn. X. campestris pv vesicatoria) (GeneBank Accession No. AM039952) is 99%. This strongly suggests that the Rieger begonia isolates belong to X. campestris pv. begoniae (2). For Koch's postulates, 10 surface-disinfected young leaves from five susceptible Rieger begonia plants (cv. Dark Britt) were inoculated by spraying a phosphate-buffered saline suspension of each bacterial isolate (3.0 × 108 CFU/ml) onto the leaves (3). Controls were inoculated similarly with phosphate-buffered saline solution. All inoculated plants were covered with polyethylene bags for 24 h at 25°C and then put in the greenhouse. After inoculation, water-soaked and necrotic symptoms were observed on inoculated Rieger begonia leaves within 7 to 9 days. No symptoms were observed on controls. Bacteria were reisolated and confirmed to be identical to the original isolates by the methods described above. To our knowledge, this is the first report of Xcb causing leaf spot on Rieger begonia plants in China. The infection process of Xcb on Rieger begonia plants and rapid detection of this pathogen are underway.

References: (1) M. R. Gillings et al. PNAS 12:102, 2005. (2) C. L. Oliver et al. Plant Dis. 4:96, 2012. (3) H. Ornek et al. New Dis. Rep. 13:40, 2006. (4) O. Pruvost et al. Plant Dis. 4:96, 2012.
Ecological niche structure and rangewide abundance patterns of species
Authors: Martínez-Meyer Enrique , Díaz-Porras Daniel , Peterson A. Townsend , Yáñez-Arenas Carlos
Published: November 2012

Spatial abundance patterns across species' ranges have attracted intense attention in macroecology and biogeography. One key hypothesis has been that abundance declines with geographical distance from the range centre, but tests of this idea have shown that the effect may occur indeed only in a minority of cases. We explore an alternative hypothesis: that species' abundances decline with distance from the centroid of the species' habitable conditions in environmental space (the ecological niche). We demonstrate consistent negative abundance–ecological distance relationships across all 11 species analysed (turtles to wolves), and that relationships in environmental space are consistently stronger than relationships in geographical space.
House finches (
Carpodacus mexicanus
) balance investment in behavioural and immunological defences against pathogens
Authors: Zylberberg Maxine , Klasing Kirk C. , Hahn Thomas P.
Published: November 2012

Infection with parasites and pathogens is costly for hosts, causing loss of nutritional resources, reproductive potential, tissue integrity and even life. In response, animals have evolved behavioural and immunological strategies to avoid infection by pathogens and infestation by parasites. Scientists generally study these strategies in isolation from each other; however, since these defences entail costs, host individuals should benefit from balancing investment in these strategies, and understanding of infectious disease dynamics would benefit from studying the relationship between them. Here, we show that
Carpodacus mexicanus
(house finches) avoid sick individuals. Moreover, we show that individuals investing less in behavioural defences invest more in immune defences. Such variation has important implications for the dynamics of pathogen spread through populations, and ultimately the course of epidemics. A deeper understanding of individual- and population-level disease defence strategies will improve our ability to understand, model and predict the outcomes of pathogen spread in wildlife.
Inferring the inter-host transmission of influenza A virus using patterns of intra-host genetic variation
Authors: Stack J. Conrad , Murcia Pablo R. , Grenfell Bryan T. , Wood James L. N. , Holmes Edward C.
Published: November 2012

Influenza A viruses (IAVs) cause acute, highly transmissible infections in a wide range of animal species. Understanding how these viruses are transmitted within and between susceptible host populations is critical to the development of effective control strategies. While viral gene sequences have been used to make inferences about IAV transmission dynamics at the epidemiological scale, their utility in accurately determining patterns of inter-host transmission in the short-term—i.e. who infected whom—has not been strongly established. Herein, we use intra-host sequence data from the viral HA1 (hemagglutinin) gene domain from two transmission studies employing different IAV subtypes in their natural hosts—H3N8 in horses and H1N1 in pigs—to determine how well these data recapitulate the known pattern of inter-host transmission. Although no mutations were fixed over the course of either experimental transmission chain, we show that some minor, transient alleles can provide evidence of host-to-host transmission and, importantly, can be distinguished from those that cannot.
The Mitochondrial Folylpolyglutamate Synthetase Gene Is Required for Nitrogen Utilization during Early Seedling Development in Arabidopsis
Authors: Jiang Ling , Liu Yanyan , Sun Hong , Han Yueting , Li Jinglai , Li Changkun , Guo Wenzhu , Meng Hongyan , Li Sha , Fan Yunliu , Zhang Chunyi
Published: November 2012

Investigations into the biochemical processes and regulatory mechanisms of nitrogen (N) utilization can aid in understanding how N is used efficiently in plants. This report describes a deficiency in N utilization in an Arabidopsis (Arabidopsis thaliana) transfer DNA insertion mutant of the mitochondrial folylpolyglutamate synthetase gene DFC, which catalyzes the conjugation of glutamate residues to the tetrahydrofolate during folate synthesis. The mutant seedlings displayed several metabolic changes that are typical of plant responses to low-N stress, including increased levels of starch and anthocyanin synthesis as well as decreased levels of soluble protein and free amino acid, as compared with those in wild-type seedlings when external N was sufficient. More striking changes were observed when dfc seedlings were grown under N-limited conditions, including shorter primary roots, fewer lateral roots, higher levels of glycine and carbon-N ratios, and lower N content than those in wild-type seedlings. Gene expression studies in mutant seedlings revealed altered transcript levels of several genes involved in folate biosynthesis and N metabolism. The biochemical and metabolic changes also suggested that N assimilation is drastically perturbed due to a loss of DFC function. The observation that elevated CO2 partly rescued the dfc phenotypes suggests that the alterations in N metabolism in dfc may be mainly due to a defect in photorespiration. These results indicate that DFC is required for N utilization in Arabidopsis and provide new insight into a potential interaction between folate and N metabolism.
Medical versus surgical termination of pregnancy in primigravid women—is the next delivery differently at risk? A population‐based register study
Authors: Männistö J , Mentula M , Bloigu A , Hemminki E , Gissler M , Heikinheimo O , Niinimäki M
Published: November 2012

Objective

To compare the effect of medical versus surgical termination of pregnancy (TOP), performed in primigravid women, on subsequent delivery.

Design

Population‐based register study.

Setting

Finland 2000–2009.

Population

All primigravid women (n = 8294) who underwent TOP during first trimester of pregnancy by medical (n = 3441) or surgical (n = 4853) method, and whose subsequent pregnancy resulted in singleton delivery.

Methods

The women were identified in the Finnish Register of Induced Abortions, and the data were linked to the Medical Birth and the Hospital Discharge Registries.

Main outcome measures

Risk of preterm birth, low birthweight, small‐for‐gestational‐age (SGA) infant and placental complications (placenta praevia, placental abruption, retained placenta, placenta accreta).

Results

No statistically significant differences in the incidences of preterm birth (4.0% in the medical group versus 4.9% in the surgical group), low birthweight (3.4% versus 4.0%), SGA infants (2.6% versus 2.9%) or placental complications (2.6% versus 2.8%) emerged between the two groups. After adjusting for various background factors, medical TOP was not associated with significantly altered risks of preterm birth (odds ratio [OR] 0.87, 95% confidence interval [95% CI] 0.68–1.13), low birthweight (OR 0.90, 95% CI 0.68–1.19), SGA infant (OR 0.87, 95% CI 0.64–1.20) or placental complications (OR 0.98, 95% CI 0.72–1.34) versus surgical TOP. In a sub‐analysis excluding women who underwent surgical evacuation following the index TOP, medical TOP was associated with a reduced risk of preterm birth (P < 0.01), but the difference became insignificant after adjusting for gestational age at the time of TOP, inter‐pregnancy interval, maternal age, cohabitation status, socio‐economic status, residence and smoking during pregnancy.

Conclusions

A history of one medical versus surgical TOP, performed in primigravid women, is associated with similar obstetric risks in the subsequent delivery.
Analytical Thresholds and Sensitivity: Establishing RFU Thresholds for Forensic DNA Analysis,
Authors: Bregu Joli , Conklin Danielle , Coronado Elisse , Terrill Margaret , Cotton Robin W. , Grgicak Catherine M.
Published: November 2012

Determining appropriate analytical thresholds (ATs) for forensic DNA analysis is critical to maximize allele detection. In this study, six methods to determine ATs for forensic DNA purposes were examined and compared. Four of the methods rely on analysis of the baseline noise of a number of negatives, while two utilize the relationship between relative fluorescence unit signal and DNA input in the polymerase chain reaction (PCR) derived from a dilution series ranging from 1 to 0.06 ng. Results showed that when a substantial mass of DNA (i.e., >1 ng) was amplified, the baseline noise increased, suggesting the application of an AT derived from negatives should only be applied to samples with low levels of DNA. Further, the number and intensity of these noise peaks increased with increasing injection times, indicating that to maximize the ability to detect alleles, ATs should be validated for each post‐PCR procedure employed.
FDG PET/CT for the preoperative nodal staging of non‐small cell lung cancer in a tuberculosis‐endemic country: Are maximum standardized uptake values useful?
Authors: Lu Yu‐Yu , Wang Hsin‐Yi , Hsia Jiun‐Yi , Lin Wan‐Yu
Published: November 2012

Background

The aim of this study was to determine an optimum standardized uptake value threshold for identifying nodal metastasis in non‐small cell lung cancer (NSCLC) patients using Fluorine‐18 2‐fluoro‐2‐deoxy‐D‐glucose (FDG) positron emission tomography/computed tomography (PET/CT) in Taiwan, a tuberculosis‐endemic country. The variation in standardized uptake values of nodal metastasis among different NSCLC histological subtypes was also evaluated.

Methods

We retrospectively reviewed 75 NSCLC patients who had received FDG PET/CT before surgery. The diagnostic accuracy of FDG PET/CT for the preoperative nodal staging was evaluated by histopathologic findings.

Results

A total of 316 nodal stations were evaluated. The sensitivity and specificity of FDG PET/CT for nodal staging were 58.6% and 81.8%, respectively, using an SUV cut‐off of 2.6. With regard to the levels of mean SUVmax in true‐positive and false‐positive groups, there was no significant difference among different histological subtypes.

Conclusion

The present study demonstrated that FDG PET/CT for pre‐operative nodal staging using SUVmax > 2.6 is a useful tool (with a higher specificity and a higher negative predictive value) to rule out the possibility of metastatic lymphadenopathy in operable patients with NSCLC.
Independent risk factors for infants who are small for gestational age by customised birthweight centiles in a multi‐ethnic New Zealand population
Authors: Anderson Ngaire H. , Sadler Lynn C. , Stewart Alistair W. , Fyfe Elaine M. , McCowan Lesley M.E.
Published: November 2012

Background

Infants born small for gestational age (SGA) by customised birthweight centiles are at increased risk of adverse outcomes compared with those SGA by population centiles. Risk factors for customised SGA have not previously been described in a general obstetric population.

Aim

To determine independent risk factors for customised SGA in a multi‐ethnic New Zealand population.

Methods

We performed a retrospective cohort analysis of prospectively recorded maternity data from 2006 to 2009 at National Women's Health, Auckland, New Zealand. After exclusion of infants with congenital anomalies and missing data, our final study population was 26,254 singleton pregnancies. Multivariable logistic regression analysis adjusted for ethnicity, body mass index, maternal age, parity, smoking status, social deprivation, hypertensive disease, antepartum haemorrhage (APH), diabetes and relevant pre‐existing medical conditions.

Results

Independent risk factors for SGA included obesity (adjusted odds ratio 1.24 [95% CI 1.11–1.39] relative to normal weight), maternal age ≥ 35 years (1.16 [1.05–1.30] relative to 20–29 years), nulliparity (1.13 [1.04–1.24] relative to parity 1), cigarette smoking (2.01 [1.79–2.27]), gestational hypertension (1.46 [1.21–1.75]), pre‐eclampsia (2.94 [2.49–3.48]), chronic hypertension (1.68 [1.34–2.09]), placental abruption (2.57 [1.74–3.78]) and APH of unknown origin (1.71 [1.45–2.00]). Gestational diabetes (0.80 [0.67–0.96]) and type 1 diabetes (0.26 [0.11–0.64]) were associated with reduced risk.

Conclusions

We report independent pregnancy risk factors for customised SGA in a general obstetric population. In contrast to population SGA, obesity is associated with increased risk. Our findings may help identify pregnancies that require increased fetal growth surveillance.
Grapefruit juice markedly increases the plasma concentrations and antiplatelet effects of ticagrelor in healthy subjects
Authors: Holmberg Mikko T. , Tornio Aleksi , Joutsi‐Korhonen Lotta , Neuvonen Mikko , Neuvonen Pertti J. , Lassila Riitta , Niemi Mikko , Backman Janne T.
Published: November 2012

Aim

This study examined the effects of grapefruit juice on the new P2Y12 inhibitor ticagrelor, which is a substrate of CYP3A4 and P‐glycoprotein.

Methods

In a randomized crossover study, 10 healthy volunteers ingested 200 ml of grapefruit juice or water thrice daily for 4 days. On day 3, they ingested a single 90 mg dose of ticagrelor.

Results

Grapefruit juice increased ticagrelor geometric mean peak plasma concentration (Cmax) to 165% (95% confidence interval 147, 184%) and area under the concentration–time curve (AUC(0,∞)) to 221% of control (95% confidence interval 200, 245%). The Cmax and AUC(0,34 h) (P < 0.05) but not the AUC(0,∞) of the active metabolite C12490XX were decreased significantly. Grapefruit juice had a minor effect on ticagrelor elimination half‐life prolonging it from 6.7 to 7.2 h (P = 0.036). In good correlation with the elevated plasma ticagrelor concentrations, grapefruit juice enhanced the antiplatelet effect of ticagrelor, assessed with VerifyNow® and Multiplate® methods, and postponed the recovery of platelet reactivity.

Conclusions

Grapefruit juice increased ticagrelor exposure by more than two‐fold, leading to an enhanced and prolonged ticagrelor antiplatelet effect. The grapefruit juice–ticagrelor interaction seems clinically important and indicates the significance of intestinal metabolism to ticagrelor pharmacokinetics.
Shortening baroreflex delay in hypertrophic cardiomyopathy patients – an unknown effect of β‐blockers
Authors: Katarzynska‐Szymanska Agnieszka , Ochotny Romuald , Oko‐Sarnowska Zofia , Wachowiak‐Baszynska Hanna , Krauze Tomasz , Piskorski Jaroslaw , Gwizdala Adrian , Mitkowski Przemyslaw , Guzik Przemyslaw
Published: November 2012

Aims

Hypertrophic cardiomyopathy (HCM) is characterized by left ventricular hypertrophy and impaired diastolic and systolic function. Abnormal sympathetic–parasympathetic balance is a potential stimulus for left ventricular hypertrophy in HCM patients. β‐Blockers are routinely used in HCM for their strong negative inotropic effect; however, these drugs also influence the sympathetic–parasympathetic balance. This study aimed to determine the autonomic control of the cardiovascular system and the autonomic effects of β‐blockers in HCM patients treated or untreated with β‐blockers.

Methods

Among 51 HCM outpatients (18–70 years old; 29 men) there were 19 individuals with no medication and 32 subjects treated with a β‐blocker. Fourteen age‐ and gender‐matched (23–70 years old; nine men) healthy volunteers were enrolled in the control group. Continuous, non‐invasive finger blood pressure was recorded during supine rest for 30 min. Autonomic regulation of the cardiovascular system was measured by heart rate variability and spontaneous baroreflex function (cross‐correlation sequence method).

Results

The mean pulse interval, time domain and spectral measures of heart rate variability and baroreflex sensitivity were comparable between HCM patients, treated or not with β‐blockers, and the control group. However, the delay of the baroreflex was significantly longer in HCM patients who were not treated with β‐blockers [2.0 (1.6–2.3) s] in comparison with HCM patients receiving β‐blockers [1.4 (1.1–1.8) s; P = 0.0072] or control subjects [1.2 (0.8–1.8) s; P = 0.0025]. This delay did not differ between HCM patients treated with β‐blockers and the control group.

Conclusions

Hypertrophic cardiomyopathy not treated with β‐blockers is accompanied by prolonged baroreflex delay. The use of β‐blockers normalizes this delay.
Tropomyosin from tilapia (Oreochromis mossambicus) as an allergen
Authors: Liu R. , Holck A. L. , Yang E. , Liu C. , Xue W.
Published: November 2012

Background

Tilapia is among the most common fresh water fish species raised by fish farms and can cause allergic reactions upon ingestion.

Objective

To investigate important allergens in Tilapia (Oreochromis mossambicus).

Methods

Allergens were detected using immunoblotting. An important allergen was purified to homogeneity by reversed‐phase High Pressure Liquid Chromatography and characterized by enzyme linked immunosorbent assay (ELISA), competitive ELISA, Mass spectrometry (MS), circular dichroism measurements and differential scanning calorimetry.

Results

By immunoblotting using sera from 10 patients with confirmed tilapia allergy, we identified a number of allergens with apparent molecular weights 114 to 17 kD. All patients produced IgE against a 32 kD allergen, Ore m 4, which was identified by MS as tropomyosin (TM). IgE binding of the pure protein was confirmed by immunoblotting, ELISA and ELISA inhibition. cDNA from tilapia tropomyosin (TM) was sequenced and compared with TMs from other species. The tilapia TM showed 53.5% homology to TM from shrimp. Homology was much higher to human TM isoform 5 (87.7%).

Conclusion and Clinical Relevance

TMs are the major allergens in allergy to crustaceans. Auto‐antibodies against human TM isoform 5 have been implicated as a causative agent in inflammatory bowel disease (IBD). Intriguingly, six of the 10 tilapia allergic patients had also been diagnosed with IBD, corroborating a connection between allergy and IBD. To our knowledge, this is the first report of tropomyosin from vertebrates as an allergen.
Glycaemic variability in paediatric patients with type 1 diabetes on continuous subcutaneous insulin infusion (CSII) or multiple daily injections (MDI): a cross‐sectional cohort study
Authors: Schreiver C. , Jacoby U. , Watzer B. , Thomas A. , Haffner D. , Fischer D.‐C.
Published: November 2012

Objective

This cross‐sectional observational cohort study was designed to investigate i) whether glycaemic variability in paediatric patients with type 1 diabetes is lower in those using an insulin pump (CSII) compared with those using multiple daily insulin injections (MDI) and ii) whether urinary F2‐isoprostanes and/or urinary prostaglandin F2 excretion as surrogate marker of oxidative stress and cyclooxygenase activity are associated with glycaemic variability.

Methods

48 paediatric patients with type 1 diabetes (22 using an insulin pump) underwent an ambulatory 3‐day continuous glucose monitoring. All patients continued with normal daily activities and collected urine for two consecutive 24 h periods. The glucose pentagon was used to calculate the glycaemic risk parameter.

Results

Insulin requirements, HDL‐cholesterol, the mean of glycaemic excursions (P < 0·01) and the standard deviation of mean glucose concentration (P < 0·05) were significantly lower in patients with CSII compared with those using MDI. By contrast, averaged HbA1c during the last twelve months as well as at the time of sensor insertion did not differ significantly between both groups. Summarizing characteristic parameter of acute and long‐term metabolic control into the glucose pentagon revealed a significantly lower glycaemic risk parameter in CSI patients compared with both, healthy subjects and patients using MDI (P < 0·05).

Conclusions

Paediatric patients with type 1 diabetes using an insulin pump presented with lower glycaemic variability and a concomitantly lower glycaemic risk parameter compared with those using MDII. Whether these findings translate into a lower risk of diabetes associated cardiovascular complications remains to be elucidated.
Murray and Jackson reply
Authors: Murray Jennie , Jackson Andrew
Published: November 2012

Please also see the letter on this paper by Essex on page 194 of this issue.
Hypoglycaemia risk with insulin degludec compared with insulin glargine in type 2 and type 1 diabetes: a pre‐planned meta‐analysis of phase 3 trials
Authors: Ratner R. E. , Gough S. C. L. , Mathieu C. , Del Prato S. , Bode B. , Mersebach H. , Endahl L. , Zinman B.
Published: November 2012

Aim

Hypoglycaemia and the fear of hypoglycaemia are barriers to achieving normoglycaemia with insulin. Insulin degludec (IDeg) has an ultra‐long and stable glucose‐lowering effect, with low day‐to‐day variability. This pre‐planned meta‐analysis aimed to demonstrate the superiority of IDeg over insulin glargine (IGlar) in terms of fewer hypoglycaemic episodes at equivalent HbA1c in type 2 and type 1 diabetes mellitus (T2DM/T1DM).

Methods

Pooled patient‐level data for self‐reported hypoglycaemia from all seven (five in T2DM and two in T1DM) randomized, controlled, phase 3a, treat‐to‐target trials in the IDeg clinical development programme comparing IDeg once‐daily (OD) vs. IGlar OD were analysed.

Results

Four thousand three hundred and thirty subjects (2899 IDeg OD vs. 1431 IGlar OD) were analysed. Among insulin‐naïve T2DM subjects, significantly lower rates of overall confirmed, nocturnal confirmed and severe hypoglycaemic episodes were reported with IDeg vs. IGlar: estimated rate ratio (RR):0.83[0.70;0.98]95%CI, RR:0.64[0.48;0.86]95%CI and RR:0.14[0.03;0.70]95%CI. In the overall T2DM population, significantly lower rates of overall confirmed and nocturnal confirmed episodes were reported with IDeg vs. IGlar [RR:0.83[0.74;0.94]95%CI and RR:0.68[0.57;0.82]95%CI). In the T1DM population, the rate of nocturnal confirmed episodes was significantly lower with IDeg vs. IGlar during maintenance treatment (RR:0.75[0.60;0.94]95%CI). Reduction in hypoglycaemia with IDeg vs. IGlar was more pronounced during maintenance treatment in all populations.

Conclusions

The limitations of this study include the open‐label design and exclusion of subjects with recurrent severe hypoglycaemia. This meta‐analysis confirms that similar improvements in HbA1c can be achieved with fewer hypoglycaemic episodes, particularly nocturnal episodes, with IDeg vs. IGlar across a broad spectrum of patients with diabetes.
Characterization and expression ofdaf‐9anddaf‐12genes in the pinewood nematode,Bursaphelenchus xylophilus
Authors: Wang D.‐D. , Cheng X.‐Y. , Wang Y.‐S. , Pan H.‐Y. , Xie B.‐Y.
Published: November 2012

Dauer formation is a mechanism by which nematodes cope with difficult environmental circumstances. DAF‐encoding genes are known to control the formation of dauer larvae in several nematode species. In this article, two importantdafgenes were isolated from the invasive plant parasitic nematode,Bursaphelenchus xylophilus, which has two dauer larval stages for overwintering and transmitting by vector beetles in its life cycle. A 1915‐bp full‐lengthcDNAofBx‐daf‐9was obtained, containing a 1533‐bp open reading frame (ORF), encoding a polypeptide of 510 amino acids. A 3966‐bp full‐lengthcDNAofBx‐daf‐12was obtained, containing a 2712‐bpORF, which encoded a polypeptide of 903 amino acids. The structures of both genes in nematodes were compared. A 2758‐bp promoter region ofBx‐daf‐9and a 2459‐bp promoter region ofBx‐daf‐12were obtained, with eight putative response elements binding transcription factors in each promoter region. The quantitative real‐time reverse transcription‐polymerase chain reaction (RT‐qPCR) was performed to detect themRNAexpression levels of the two genes in different stages of the nematode. The result showed that expression levels of the two genes were low in egg stage and up‐regulated five to seven times in larval and adult stages. However,Bx‐daf‐9expression in the third dispersal stage was relatively low. Expression ofdaf‐12in the fourth dispersal stage was extraordinarily high. The results imply thatdaf‐9anddaf‐12perhaps have special roles in the dispersal stages ofB. xylophilus.
Core continuing professional development (CPD) topics for the European dentist
Authors: Bailey S. , Bullock A. , Cowpe J. , Barnes E. , Thomas H. , Thomas R. , Kavadella A. , Kossioni A. , Karaharju‐Suvanto T. , Suomalainen K. , Kersten H. , Povel E. , Giles M. , Walmsley A. D. , Soboleva U. , Liepa A. , Akota I.
Published: November 2012

Introduction

In the context of free movement, EU‐citizens need assurance that dental practitioners providing their care have a degree/license to practice that meets EU‐standards and that they maintain their knowledge and skills through ongoing education.

Aim

One aim of the ‘DentCPD’ project (HYPERLINK ‘http://www.dentcpd.org’ www.dentcpd.org) was to identify and agree essential CPD requirements for EU dentists. This paper reports the consensus process and outcomes.

Methods

Agreement on core components of CPD was achieved through a three stage process: an online survey of dental educators' (n = 143) views on compulsory topics; a paper‐based questionnaire to practitioners (n = 411); leading to a proposal discussed at the Association for Dental Education (ADEE) 2011 Lifelong Learning special interest group (SIG).

Results

From the online survey and practitioner questionnaire, high levels of agreement were achieved for medical emergencies (89%), infection control (79%) and the medically compromised patient (71%). The SIG (34 attendees from 16 countries) concluded that these three CPD topics plus radiation protection should be core‐compulsory and three CPD topics should be core‐recommended (health and safety, pain management, and safeguarding children & vulnerable adults). They also agreed that the teaching of all topics should be underpinned by evidence‐based dentistry.

Conclusion

Building four core topics into CPD requirements and making quality‐approved education and training available will ensure that all dentists have up‐to‐date knowledge and skills in topic areas of direct relevance to patient safety. In turn, this will contribute to patients having access to comparably high standards of oral health care across Europe.
Effect of fluoxetine and pergolide on expression of nucleoside transporters and nucleic‐related enzymes in mouse brain
Authors: Nagai Katsuhito , Konishi Hiroki
Published: November 2012

Nucleoside transporter (NT) and nucleic‐related enzyme (NRE) play key roles in the physiology of nucleosides and the pharmacology of its analogs in mammals. In this study, we examined the effect of fluoxetine, a selective serotonin reuptake inhibitor, and pergolide, a dopamine D receptor agonist, on the expression of NTs and NREs in mouse brain. It was confirmed by the detection of corresponding mRNAs that three equilibrative nucleoside transporter (ENT1‐3) isoforms, concentrative nucleoside transporter 2 (CNT2), CNT3, adenosine kinase (AK), and apyrase, but not CNT1, were expressed in brain tissue. Based on an assessment by mRNA determination, the cerebral expression of CNT2 was found to be increased by administration of fluoxetine and pergolide to mice. Furthermore, pergolide increased the expression of ENT2. However, fluoxetine and pergolide had no significant effect on the expression of mRNA for other NTs, AK, and apyrase. Therefore, we concluded that the expression of several NT isoforms, but not NREs, in mouse brain was affected by treatment with fluoxetine and pergolide.