bluuebunny/crossref_metadata_2025 huggingface dataset:
Using morphometrics, in situ observations and genetic characters to distinguish among commercially valuable Hawaiian black coral species; a redescription of Antipathes grandis Verrill, 1928 (Antipatharia:Antipathidae)
Authors: Wagner Daniel , Brugler Mercer R. , Opresko Dennis M. , France Scott C. , Montgomery Anthony D. , Toonen Robert J.
Published: March 2011

The commercially valuable Hawaiian black coral Antipathes grandis Verrill, 1928 is redescribed based on reexamination of the holotype from the Bernice P. Bishop Museum and field collections of 34 specimens from depths of 27–127 m. The first scanning electron micrographs of A. grandis skeletal spines are provided, along with a series of in situ colour photographs and morphometric measurements of spines and polyps. Three colour morphotypes were collected in the field (red, pale red, and white), none of which could be differentiated based on morphological or genetic characters (two mitochondrial and two nuclear markers). In situ observations are used in conjunction with morphological and genetic characters to distinguish among the commercially valuable Hawaiian black coral species A. grandis and A. griggi Opresko, 2009. A. grandis is differentiated from A. griggi by its finer and more irregular branching, smaller and more closely-spaced polyps, and conical spines that are smaller and not characterised by bifurcations towards their apex. Morphologically, the species most closely resembling A. grandis is A. caribbeana Opresko, 1996 from the Caribbean. Among analysed congenerics, DNA sequences of A. grandis were likewise most similar to those of A. caribbeana for three of the four molecular markers used in this study. A combination of low genetic variability, incomplete taxonomic sampling, and unexpected similarity between A. caribbeana and the unbranched whip coral Stichopathes cf. occidentalis (Gray, 1860), hindered our ability to determine the sister relationship of A. grandis. However, in no phylogenetic reconstruction did A. grandis group sister to its sympatric congener A. griggi.
Cladistic analysis of the calanoid Copepoda
Authors: Bradford-Grieve Janet M. , Boxshall Geoff A. , Ahyong Shane T. , Ohtsuka Susumu
Published: March 2011

Calanoid copepods are extremely successful inhabitants of marine, brackish and freshwater plankton. Morphological data are used to arrive at a first, parsimony-based phylogeny for the calanoid copepods. Each family is represented by at least one exemplar, typically a recognised plesiomorphic species. The Epacteriscidae are sister to all other calanoid copepods – an observation that brings into question the concept of an Epacteriscoidea that includes the Ridgewayiidae. The monophyly of the Augaptiloidea, Centropagoidea, Clausocalanoidea and Pseudocyclopoidea is corroborated. The current analysis suggests there may be two major clades, one containing the Augaptiloidea, Centropagoidea and possibly the Pseudocyclopoidea and Ridgewayiidae and the other including the Megacalanidae, Calanidae/Paracalanidae, Bathypontioidea, Eucalanoidea, Ryocalanoidea, Spinocalanoidea and Clausocalanoidea. The relationships of the Pseudocyclopidae, Boholinidae, and Ridgewayiidae to the Centropagoidea/Augaptiloidea clade received low nodal support. Monophyly of an enlarged Bathypontioidea (including the Fosshageniidae) is proposed. A monophyletic Megacalanoidea is not retrieved. The nature of the inferred ancestral Calanoida is discussed. New evolutionary series are proposed for the female genitalia (including several losses and regaining of seminal receptacles, and independent losses of the genital operculum – once lost it is never regained) and leg 1 endopod. Paedomorphosis appears to be a dominant process in the evolution of the Calanoida.
Need morphology always be required for new species descriptions?
Authors: Cook L. G. , Edwards R. D. , Crisp M. D. , Hardy N. B.
Published: March 2011

Despite the widespread and common use of DNA-sequence data to estimate phylogenies, support or contest classifications, and identify species using barcodes, they are not commonly used as the primary or sole source of data for describing species. This is possibly due to actual or perceived pressure from peers to include morphology as the primary source of data for species descriptions. We find no compelling evidence to exclude DNA-only descriptions, or to insist that morphology always be included in a species description. It is not the data type per se that is important, but the science behind the taxonomic conclusions. Using alternative kinds of data for descriptions should not cause problems for taxonomy if links are kept with type specimens.
The effects of slope and fuel bed width on laboratory fire behaviour
Authors: Dupuy J.-L. , Maréchal J. , Portier D. , Valette J.-C.
Published: March 2011

A set of 109 laboratory fires in Pinus halepensis fuel beds (1 kg m–2) was used to test the effects of slope (0°, 10°, 20°, 30°) and fuel bed width (1, 2, 3 m) on fire behaviour variables such as rate of spread, fuel consumption, flame residence time, temperatures and flame geometry. The qualitative behaviour of the fires is also reported. The 20° and 30° upslope fires are pointed in shape and fire whirls moving along the fire flanks in the direction of the fire head are systematically observed in 30° upslope fires. Flame residence time increases with increasing slope angle, and both slope angle and fuel bed width affect rate of spread. The slope effects observed in 10° and 20° slope angles and in the narrowest fuel beds (1 and 2 m) are similar to those predicted by operational models. However, the observed slope effect at the 30° slope angle is underestimated by these models, in particular in 3 m-wide fuel beds. Flame temperatures correlate closely with dimensionless height and flame lengths correlate closely with fire line intensity. Mechanisms that could explain the different effects observed are suggested and discussed.
Gerschgorin’s theorem for generalized eigenvalue problems in the Euclidean metric
Authors: Nakatsukasa Yuji
Published: March 2011

We present Gerschgorin-type eigenvalue inclusion sets applicable to generalized eigenvalue problems. Our sets are defined by circles in the complex plane in the standard Euclidean metric, and are easier to compute than known similar results. As one application we use our results to provide a forward error analysis for a computed eigenvalue of a diagonalizable pencil.
The sufficient minimal set of miRNA seed types
Authors: Ellwanger Daniel C. , Büttner Florian A. , Mewes Hans-Werner , Stümpflen Volker
Published: March 2011

Motivation: Pairing between the target sequence and the 6–8 nt long seed sequence of the miRNA presents the most important feature for miRNA target site prediction. Novel high-throughput technologies such as Argonaute HITS-CLIP afford meanwhile a detailed study of miRNA:mRNA duplices. These interaction maps enable a first discrimination between functional and non-functional target sites in a bulky fashion. Prediction algorithms apply different seed paradigms to identify miRNA target sites. Therefore, a quantitative assessment of miRNA target site prediction is of major interest.

Results: We identified a set of canonical seed types based on a transcriptome wide analysis of experimentally verified functional target sites. We confirmed the specificity of long seeds but we found that the majority of functional target sites are formed by less specific seeds of only 6 nt indicating a crucial role of this type. A substantial fraction of genuine target sites arenon-conserved. Moreover, the majority of functional sites remain uncovered by common prediction methods.

Contact:  florian.buettner@helmholtz-muenchen.de  v.stuempflen@helmholtz-muenchen.de

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Comparison of global tests for functional gene sets in two-group designs and selection of potentially effect-causing genes
Authors: Jung Klaus , Becker Benjamin , Brunner Edgar , Beißbarth Tim
Published: March 2011

Motivation: An important object in the analysis of high-throughput genomic data is to find an association between the expression profile of functional gene sets and the different levels of a group response. Instead of multiple testing procedures which focus on single genes, global tests are usually used to detect a group effect in an entire gene set. In a simulation study, we compare the power and computation times of four different approaches for global testing. The applicability of one of these methods to gene expression data is demonstrated for the first time. In addition, we propose an algorithm for the detection of those genes which might be responsible for a group effect.

Results: We could detect that the power of three of the approaches is comparable in many settings but considerable differences were detected in the computation times. Our proposed gene selection algorithm was able to detect potentially effect-causing genes in artificial sets with high power when many genes were altered with a small effect, while classical multiple testing was more powerful when few genes were altered with a large effect.

Availability: An R-package called ‘RepeatedHighDim’ which implements our new global test procedures is made available from http://cran.r-project.org/.

Contact:  tim.beissbarth@ams.med.uni-goettingen.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
PlantMiRNAPred: efficient classification of real and pseudo plant pre-miRNAs
Authors: Xuan Ping , Guo Maozu , Liu Xiaoyan , Huang Yangchao , Li Wenbin , Huang Yufei
Published: March 2011

Motivation: MicroRNAs (miRNAs) are a set of short (21–24 nt) non-coding RNAs that play significant roles as post-transcriptional regulators in animals and plants. While some existing methods use comparative genomic approaches to identify plant precursor miRNAs (pre-miRNAs), others are based on the complementarity characteristics between miRNAs and their target mRNAs sequences. However, they can only identify the homologous miRNAs or the limited complementary miRNAs. Furthermore, since the plant pre-miRNAs are quite different from the animal pre-miRNAs, all the ab initio methods for animals cannot be applied to plants. Therefore, it is essential to develop a method based on machine learning to classify real plant pre-miRNAs and pseudo genome hairpins.

Results: A novel classification method based on support vector machine (SVM) is proposed specifically for predicting plant pre-miRNAs. To make efficient prediction, we extract the pseudo hairpin sequences from the protein coding sequences of Arabidopsis thaliana and Glycine max, respectively. These pseudo pre-miRNAs are extracted in this study for the first time. A set of informative features are selected to improve the classification accuracy. The training samples are selected according to their distributions in the high-dimensional sample space. Our classifier PlantMiRNAPred achieves >90% accuracy on the plant datasets from eight plant species, including A.thaliana, Oryza sativa, Populus trichocarpa, Physcomitrella patens, Medicago truncatula, Sorghum bicolor, Zea mays and G.max. The superior performance of the proposed classifier can be attributed to the extracted plant pseudo pre-miRNAs, the selected training dataset and the carefully selected features. The ability of PlantMiRNAPred to discern real and pseudo pre-miRNAs provides a viable method for discovering new non-homologous plant pre-miRNAs.

Availability: The web service of PlantMiRNAPred, the training datasets, the testing datasets and the selected features are freely available at http://nclab.hit.edu.cn/PlantMiRNAPred/.

Contact:  maozuguo@hit.edu.cn; yufei.huang@utsa.edu
Anaphylaxis
Authors: Simon Chantal
Published: March 2011

Anaphylaxis is a severe life-threatening generalized or systemic allergic reaction. Although only 1 in 1333 people in the UK will ever suffer an anaphylactic reaction and less than 1% of those that suffer an anaphylactic attack die as a result of that attack, anaphylaxis is an important condition. Each year in the UK, there are approximately 20 deaths as a direct result of anaphylaxis (one death per 3 million population). Risk of death is increased in those with pre-existing asthma, particularly if the asthma is poorly controlled. Prompt recognition and appropriate management save lives.
Management of Dyspepsia
Authors: Bakashi Ranjeeta , Sood Ruchit
Published: March 2011

The prevalence of dyspepsia is 25–40% and it is a common presenting symptom in general practice consultations. Only a small percentage of patients have any organic pathology; the remainder have functional (idiopathic) dyspepsia, which can result in significant morbidity as well as significant costs to the health service when not managed appropriately. As most patients with dyspepsia are managed in the community, GPs should have a framework from which they can manage dyspepsia and understand when it is appropriate to refer for further investigations, such as upper gastrointestinal (GI) endoscopy.
Change Comes with Time: Substantive Interpretation of Nonproportional Hazards in Event History Analysis
Authors: Licht Amanda A.
Published: March 2011

Although methodologists have provided us ample notice of both the problem of nonproportional hazards (NPHs) and the means of correcting for them, less attention has been paid to the postestimation interpretation. The suggested inclusion of time interactions in our models is more than a statistical fix: These corrections alter the substantive meaning and interpretation of results. Framing the issue as a specific case of multiplicative-interaction modeling, I provide detailed discussion of the problem of NPHs and present several appropriate means of interpreting both the substantive impact and the significance of variables whose effects may change over time.
Molecular Characterization of Potato leafroll virus, Potato virus A, and Potato virus X Isolates from Potatoes in Alaskan Cities and Villages
Authors: Robertson Nancy L. , Smeenk Jeffrey , Anderson Jodie M.
Published: March 2011

Although all three viruses are commonly found in potatoes throughout the world, this is the first report of potato viruses from Alaska to be sequenced and molecularly analyzed for comparisons with known viruses.

Accepted for publication 17 January 2011. Published 9 February 2011.
Brote Grande, A New Phytoplasma Associated Disease of Chile Peppers in the Desert Southwest
Authors: Randall Jennifer J. , Bosland Paul W. , Hanson Stephen F.
Published: March 2011

Chile is one of the most important crops in New Mexico, contributing both to the agricultural economy and cultural identity of the state. Diseases are a major constraint on chile production in New Mexico and across the Desert Southwest. Chile producers in New Mexico recently reported a disorder of unknown etiology that was observed in increasing frequency for the past four years. Affected plants have a bushy appearance, develop overly large green calyces instead of normal flowers, and fail to set fruit. This characteristic phyllody has led the disorder to be referred to as “brote grande” which is Spanish for “big bud.” The phyllody is reminiscent of the aberrant flower development associated with tomato big bud, a phytoplasma disease of tomatoes. Microscopic analysis, including light microscopy and TEM along with PCR detection using phytoplasma specific primer sets, indicates that brote grande disease is associated with a novel phytoplasma. Field surveys conducted in 2008 and 2009 indicate that this new disease is widely distributed at low levels across chile production areas in New Mexico and Arizona.

Accepted for publication 10 January 2011. Published 1 March 2011.
Ascochyta Blight of Peas
Authors: Skoglund Linnea G. , Harveson Robert M. , Chen Weidong , Dugan Frank , Schwartz Howard F. , Markell Samuel G. , Porter Lyndon , Burrows Mary L. , Goswami Rubella
Published: March 2011

Field pea is an annual, cool-season legume native to northwest to southwest Asia. It was among the first crops cultivated by man. The crop is grown primarily in North Dakota, Washington, Montana, Idaho, Oregon, and southern Canada. Ascochyta blight is a serious disease affecting above ground portions at all growth stages. Stem, crown, pod, and foliar diseases of pea are caused by a complex of Ascochyta pisi, Mycosphaerella pinodes, and Phoma pinodella. This paper reviews the disease and the pathogens involved.

Accepted for publication 28 January 2011. Published 30 March 2011.
A novel interference behaviour: invasive wasps remove ants from resources and drop them from a height
Authors: Grangier Julien , Lester Philip J.
Published: March 2011

This study reports a novel form of interference behaviour between the invasive wasp
Vespula vulgaris
and the New Zealand native ant
Prolasius advenus
. By videotaping interactions at bait stations, we found that wasps commonly remove ant competitors from food resources by picking up the workers in their mandibles, flying backward and dropping them unharmed some distance from the food. Both the frequency and the efficiency of the wasp behaviour significantly increased with the abundance of ant competitors. Ant removals were the most common interference events initiated by wasps when ants were numerous, while intraspecific conflicts among wasps were prominent when few ants were present. The ‘ant-dropping’ behaviour emphasizes how asymmetry in body sizes between competitors can lead to a pronounced form of interference, related to asymmetric locomotion modes.
Disruption of LACCASE4 and 17 Results in Tissue-Specific Alterations to Lignification of Arabidopsis thaliana Stems
Authors: Berthet Serge , Demont-Caulet Nathalie , Pollet Brigitte , Bidzinski Przemyslaw , Cézard Laurent , Le Bris Phillipe , Borrega Nero , Hervé Jonathan , Blondet Eddy , Balzergue Sandrine , Lapierre Catherine , Jouanin Lise
Published: March 2011

Peroxidases have been shown to be involved in the polymerization of lignin precursors, but it remains unclear whether laccases (EC 1.10.3.2) participate in constitutive lignification. We addressed this issue by studying laccase T-DNA insertion mutants in Arabidopsis thaliana. We identified two genes, LAC4 and LAC17, which are strongly expressed in stems. LAC17 was mainly expressed in the interfascicular fibers, whereas LAC4 was expressed in vascular bundles and interfascicular fibers. We produced two double mutants by crossing the LAC17 (lac17) mutant with two LAC4 mutants (lac4-1 and lac4-2). The single and double mutants grew normally in greenhouse conditions. The single mutants had moderately low lignin levels, whereas the stems of lac4-1 lac17 and lac4-2 lac17 mutants had lignin contents that were 20 and 40% lower than those of the control, respectively. These lower lignin levels resulted in higher saccharification yields. Thioacidolysis revealed that disrupting LAC17 principally affected the deposition of G lignin units in the interfascicular fibers and that complementation of lac17 with LAC17 restored a normal lignin profile. This study provides evidence that both LAC4 and LAC17 contribute to the constitutive lignification of Arabidopsis stems and that LAC17 is involved in the deposition of G lignin units in fibers.
Sulphilimine/Sulfilimine cross-links in Goodpasture's disease
Authors: Vanacore R , Pedchenko V , Bhave G , Hudson B G
Published: March 2011

The sulphilimine/sulfilimine cross-link of the Goodpasture (GP) autoantigen is a novel molecular mechanism (structural constraint) for conferring immune privilege to a site which otherwise is susceptible to structural changes that induce an immunogenic and pathogenic conformation. Perturbation of the assembly or cleavage of the sulphilimine/sulfilimine cross-links could be a key factor in the aetiology of Goodpasture's disease in susceptible individuals.
Pathological classification of anti-neutrophil cytoplasmic antibody (ANCA)-associated glomerulonephritis
Authors: Bajema I M
Published: March 2011

What drives human beings to classify? It seems as if it is within our nature to do so. Clinical classification systems for the systemic vasculitides were composed a long time ago, and they are constantly being revised and altered. The histopathological features of many diseases are so diverse that classification is called for. The histopathological classification for anti-neutrophil cytoplasmic antibody (ANCA)-associated glomerulonephritis was the culmination of results produced from a number of clinicopathological studies conducted within the European Vasculitis Study Group (EUVAS). The classification scheme has four general categories, named focal, crescentic, sclerotic and mixed. The first three categories are based on the predominance of normal glomeruli, glomeruli with cellular crescents and globally sclerotic glomeruli. The mixed category represents a heterogeneous phenotype of biopsies in which none of the aforementioned features is dominant. Results from a validation study incorporating 100 patients with at least 1-year follow-up showed that the phenotypical order of the four classes corresponded to the severity of renal function impairment. The new histopathological classification for ANCA-associated glomerulonephritis provides a logical structure for the categorization of patients into four subgroups defined according to glomerular features. This classification will be of use for future studies, such as clinical trials.
Epigenetics and complementary proteins
Authors: Ciavatta D , Falk R J
Published: March 2011

Although studies on the immunopathogenesis of anti-neutrophil cytoplasm antibody (ANCA) vasculitis have been directed at understanding the autoantibody, there is growing evidence that points to the importance of ANCA autoantigen genes and their regulation. Transcriptional analysis indicates that ANCA autoantigen genes are active in mature neutrophils of ANCA vasculitis patients compared to healthy controls. The unusual transcriptional state of neutrophils from ANCA vasculitis patients appears to be a consequence of failed or disrupted epigenetic silencing. Defective epigenetic silencing could have global effects, by altering the transcriptional and phenotypic state of neutrophils, or local effects by permitting transcription of autoantigen genes from both strands resulting in anti-sense transcripts. Although the role of anti-sense transcripts is currently unknown, there are two intriguing possibilities. Anti-sense transcripts could function (as described for other genes) in transcriptional silencing of autoantigen genes, which takes place in normal neutrophil progenitors. In the setting of failed epigenetic silencing, the fate of anti-sense transcripts may be pathological and serve as a template for production of complementary autoantigens. The observation that ANCA vasculitis patients have anti-sense transcripts and antibodies to complementary proteins is consistent with a role of anti-sense transcripts in complementary protein production. A better understanding of epigenetic silencing and complementary proteins in ANCA vasculitis may unlock the underlying pathology of this condition.
Pathogenesis of anti-neutrophil cytoplasmic autoantibody (ANCA)-associated vasculitis
Authors: Savage C O S
Published: March 2011

Anti-neutrophil cytoplasmic autoantibody (ANCA)-associated vasculitis is an autoimmune disease in which the contributions of genetic, epigenetic and environmental factors to aetiology and pathogenesis are being unravelled. The ANCA immunoglobulin G targeting proteinase 3 and myeloperoxidase affects several neutrophil functions, usually to augment or dysregulate these, promoting a proinflammatory phenotype whereby neutrophils have enhanced capabilities of causing collateral damage to endothelial and other cells. In addition, B cells are intimately involved in pathogenesis as anti-B cell therapies are highly effective, but the manner of this involvement still needs to be delineated. Similarly, the T cell compartment is disturbed in ANCA vasculitis and numerous alterations in T cell subsets have been described, but recognition of a novel CD8+ T cell transcription signature which can predict likelihood of relapse in ANCA vasculitis indicates that more needs to be learnt about the influence of T cells in the disease process. Finally, the role of the alternative complement pathway and the potential therapeutic value of its neutralization is under active investigation after compelling studies in murine models have demonstrated that C5 and factor-B knock-out mice are protected.
Peak and trough growth hormone (GH) concentrations influence growth and serum insulin like growth factor‐1 (IGF‐1) concentrations in short children
Authors: Achermann J. C. , Brook C. G. D. , Robinson I. C. A. F. , Matthews D. R. , Hindmarsh P. C.
Published: March 2011

OBJECTIVE Growth hormone (GH) is secreted in a pulsatile fashion promoting growth and a number of diverse metabolic actions. The precise components of the pulsatile signal involved in growth regulation are unclear.

DESIGN A retrospective analysis of 24 h serum GH concentration profiles to evaluate the relative contribution of peak and trough serum GH concentrations to growth regulation, GH response to insulin induced hypoglycaemia (ITT) and serum insulin like growth factor‐1 (IGF‐1) concentration.

PATIENTS Fifty short prepubertal children (age 5·2–11·9 years).

MEASUREMENT Analysis of the hormone profile by a concentration distribution method that determines the concentration at or below which the serum GH concentrations in the 24 hour profile spend a percentage of the total time. The method generates an estimate of the observed concentrations (OC) below which 95 % and 5 % of the values in the time series lie: OC 95 (peaks) and OC5 (troughs).

RESULTS Twenty six of the children were growing at a normal rate for short children with a height velocity standard deviation score (HVSDS) between +0·4 and −0·8 whereas twenty four were growing more slowly (HVSDS between −0·9 to −3·9). The former group had a mean peak GH response to ITT of 27·3 (11·1) mU/l whereas the latter had a mean value of 8·7 (6·5) mU/l. There was no relationship between (peak and trough GH concentration) and the age of the individual or body mass index. Peak GH levels were positively related to HVSDS and serum IGF‐1 values (r = 0·44; P= 0·002 and r = 0·53; P= 0·002, respectively). GH trough levels were inversely related to these measurements (r = 0·29; P= 0·05; and r = 0·46; P= 0·002, respectively). Further analysis showed that individuals with the slowest growth rates and lowest IGF‐1 concentrations had the lowest peak and highest trough GH concentrations (anova F = 6·0; P= 0·002). Similarly, the peak GH response to ITT was lowest in those individuals with high troughs and low peaks (anova F = 9·99; P < 0·001).

CONCLUSIONS These results suggest that the peak values of a GH concentration profile influence growth rate and the IGF‐1 axis whereas elevated trough values have the greatest influence on growth rate and IGF‐1 values when GH peaks are low.
ICE1 Ser403 is necessary for protein stabilization and regulation of cold signaling and tolerance
Authors: Miura Kenji , Ohta Masaru , Nakazawa Machiko , Ono Michiyuki , Hasegawa Paul M.
Published: March 2011

ICE1, a MYC‐type transcription factor, has an important role in the induction of CBF3/DREB1A for regulation of cold signaling and tolerance. Here we reveal that serine 403 of ICE1 is involved in regulating the transactivation and stability of the ICE1 protein. Substitution of serine 403 by alanine enhanced the transactivational activity of ICE1 in Arabidopsis protoplasts. Over‐expression of ICE1(S403A) conferred more freezing tolerance than ICE1(WT) in Arabidopsis, and the expression of cold‐regulated genes such as CBF3/DREB1A, COR47 and KIN1 was enhanced in plants over‐expressing ICE1(S403A). Furthermore, the ICE1(S403A) protein level was not changed after cold treatment, whereas the ICE1(WT) protein level was reduced. Interestingly, polyubiquitylation of the ICE1(S403A) protein in vivo was apparently blocked. These results demonstrate that serine 403 of ICE1 has roles in both transactivation and cold‐induced degradation of ICE1 via the ubiquitin/26S proteasome pathway, suggesting that serine 403 is a key residue for the attenuation of cold‐stress responses by HOS1‐mediated degradation of ICE1.
Married to M. tuberculosis: risk of infection and disease in spouses of smear‐positive tuberculosis patients
Authors: Crampin A. , Kasimba S. , Mwaungulu N. J. , Dacombe R. , Floyd S. , Glynn J. R. , Fine P. E. M.
Published: March 2011

Objectives  To quantify the risk of infection and disease in spouses of tuberculosis patients and the extent to which intervention could reduce the risk in this highly exposed group.

Methods  We compared HIV prevalence, TB prevalence and incidence and tuberculin skin test (TST) results in spouses of TB patients and community controls. HIV‐positive spouses were offered isoniazid preventive therapy (IPT), and TST was repeated at 6, 12 and 24 months.

Results  We recruited 148 spouses of smear‐positive patients ascertained prospectively and 3% had active TB. We identified 203 spouses of previously diagnosed smear‐positive patients, 11 had already had TB, and the rate of TB was 2.4 per 100 person years(py) over 2 years (95% CI 1.15–5.09). 116 were found alive and recruited. HIV prevalence was 37% and 39% in the prospective and retrospective spouse groups and 17% in controls. TST was ≥10 mm in 80% of HIV negative and in 57% of HIV‐positive spouses ascertained retrospectively; 74% HIV negative and 62% HIV‐positive spouses ascertained prospectively, and 48% HIV negative and 26% HIV‐positive community controls. Of 54 HIV‐positive spouses, 18 completed 6‐month IPT. At 2 year follow‐up, 87% of surviving spouses had TST ≥10 mm and the rate of TB was 1.1 per 100 py (95% CI 0.34–3.29).

Conclusions  Spouses are a high‐risk group who should be screened for HIV and active TB. TST prevalence was already high by the time the spouses were approached but further infections were seen to occur. Uptake and adherence to IPT was disappointing, lessening the impact of short‐duration therapy.
Genotyping of polymorphic marker (MSP3α and MSP3β) genes of Plasmodium vivax field isolates from malaria endemic of Thailand
Authors: Rungsihirunrat Kanchana , Chaijaroenkul Wanna , Siripoon Napapoon , Seugorn Aree , Na‐Bangchang Kesara
Published: March 2011

Two polymorphic marker genes, merozoite surface protein 3α (PvMSP3α) and merozoite surface protein 3β (PvMSP3β), from 100 Plasmodium vivax field isolates, were investigated using polymerase chain reaction and restriction fragment length polymorphism (PCR/RFLP). Genotyping of PvMSP3α and PvMSP3β revealed marked polymorphisms in length and sequence. Three major types of PvMSP3α (Type A, B and C) and two major types of PvMSP3β (Type A and B) were detected based on the length of PCR products. Fourteen alleles of both genes with difference frequencies were distinguished by restriction fragment length polymorphism, and these results strongly support that P. vivax isolates in Thailand are markedly diverse. PvMSP3α and PvMSP3β are reliable polymorphic markers for population genetic analysis of P. vivax, and PCR/RFLP provides a powerful method for genotyping and identification of mixed parasite infections without requirement of gene sequencing.
Health care‐seeking behaviour and diagnostic delays for Human African Trypanosomiasis in the Democratic Republic of the Congo
Authors: Hasker E. , Lumbala C. , Mbo F. , Mpanya A. , Kande V. , Lutumba P. , Boelaert M.
Published: March 2011

Objective  About half of the patients with Human African trypanosomiasis (HAT) reported in the Democratic Republic of the Congo (DRC) are currently detected by fixed health facilities and not by mobile teams. Given the recent policy to integrate HAT control into general health services, we studied health seeking behaviour in these spontaneously presenting patients.

Methods  We took a random sample from all patients diagnosed with a first‐time HAT episode through passive case finding between 1 October 2008 and 30 September 2009 in the two most endemic provinces of the DRC. Patients were approached at their homes for a structured interview. We documented patient delay (i.e. time between onset of symptoms and contacting a health centre) and health system delay (i.e. time between first contact and correct diagnosis of HAT).

Results  Median patient delay was 4 months (IQR 1–10 months, n = 66); median health system delay was 3 months (IQR 0.5–11 months). Those first presenting to public health centres had a median systems delay of 7 months (IQR 2–14 months, n = 23). On median, patients were diagnosed upon the forth visit to a health facility (IQR 3rd–7th visit).

Conclusions  Substantial patient as well as health system delays are incurred in HAT cases detected passively. Public health centres are performing poorly in the diagnostic work‐up for HAT, mainly because HAT is a relatively rare disease with few and non‐specific early symptoms. Integration of HAT diagnosis and treatment into general health services requires strong technical support and well‐organized supervision and referral mechanisms.
The novel allele, HLA‐B*07:68:02, identified in a German cord blood donor and her father
Authors: Strobel J. , Ringwald J. , Hauck B. , Eckstein R. , Zingsem J.
Published: March 2011

The novel allele HLA‐B*07:68:02 identified in two related individuals of Caucasian origin is described.
Association of HLA alleles withPlasmodium falciparumseverity in Malian children
Authors: Lyke K. E. , Fernández‐Viňa M. A. , Cao K. , Hollenbach J. , Coulibaly D. , Kone A. K. , Guindo A. , Burdett L. A. , Hartzman R. J. , Wahl A. R. , Hildebrand W. H. , Doumbo O. K. , Plowe C. V. , Sztein M. B.
Published: March 2011

Pre‐erythrocytic immunity toPlasmodium falciparummalaria is likely to be mediated by T‐cell recognition of malaria epitopes presented on infected host cells via class I and II major histocompatibility complex (MHC) antigens. To test for associations of human leukocyte antigen (HLA) alleles with disease severity, we performed high‐resolution typing of HLA class I and II loci and compared the distributions of alleles of HLA‐A, ‐B, ‐C and ‐DRB1 loci in 359 Malian children of Dogon ethnicity with uncomplicated or severe malaria. We observed that alleles A*30:01 and A*33:01 had higher frequency in the group of patients with cerebral disease compared to patients with uncomplicated disease [A*30:01: gf = 0.2031vsgf = 0.1064, odds ratio (OR) = 3.17,P= 0.004, confidence interval (CI) (1.94–5.19)] and [A*33:01: gf = 0.0781vsgf = 0.0266, 4.21,P= 0.005, CI (1.89–9.84)], respectively. The A*30:01 and A*33:01 alleles share some sequence motifs and A*30:01 appears to have a unique peptide binding repertoire compared to other A*30 group alleles. Computer algorithms predicted malaria peptides with strong binding affinity for HLA‐A*30:01 and HLA‐A*33:01 but not to closely related alleles. In conclusion, we identified A*30:01 and A*33:01 as potential susceptibility factors for cerebral malaria, providing further evidence that polymorphism ofMHCgenes results in altered malaria susceptibility.
Asbestos use and asbestos‐related diseases in Asia: Past, present and future
Authors: LE GIANG VINH , TAKAHASHI KEN , PARK EUN‐KEE , DELGERMAA VANYA , OAK CHULHO , QURESHI AHMAD MUNIR , ALJUNID SYED MOHAMED
Published: March 2011

Background and objective:  Although there are growing concerns about the global epidemic of asbestos‐related diseases (ARD), the current status of asbestos use and ARD in Asia is elusive. We conducted a descriptive analysis of available data on asbestos use and ARD to characterize the current situation in Asia.

Methods:  We used descriptive indicators of per capita asbestos use (kilograms per capita per year) and age‐adjusted mortality rates (AAMR, persons per million population per year) by country and for the region, with reference to the world.

Results:  The proportion of global asbestos use attributed to Asia has been steadily increasing over the years from 14% (1920–1970) to 33% (1971–2000) to 64% (2001–2007). This increase has been reflected in the absolute level of per capita use across a wide range of countries. In contrast, 12 882 ARD deaths have been recorded cumulatively in Asia, which is equivalent to only 13% of the cumulative number of ARD deaths in the world during the same period. The highest AAMR were recorded in Cyprus (4.8), Israel (3.7) and Japan (3.3), all of which have banned asbestos use.

Conclusions:  There is a paucity of information concerning the current situation of ARD in Asia. The marked increase in asbestos use in Asia since 1970, however, is likely to trigger a surge of ARD in the immediate decades ahead.
Ketamine for perioperative pain management in children: a meta‐analysis of published studies
Authors: Dahmani Souhayl , Michelet Daphné , Abback Paer‐Selim , Wood Chantal , Brasher Christopher , Nivoche Yves , Mantz Jean
Published: March 2011

Introduction:  Balanced analgesia, using both opioid and nonopioids agents, has become the standard care for postoperative pain management. Ketamine, a compound with analgesic and antihyperalgesic properties, has been shown to decrease postoperative pain and opioid requirements in adults. The goal of the present meta‐analysis was to investigate postoperative analgesic properties of ketamine in pediatric patients.

Material and methods:  A comprehensive literature search was conducted to identify clinical trials that used ketamine as a perioperative analgesic compound in children and infants. Outcomes measured were postoperative analgesic consumption, pain intensity and duration of sensory block (when ketamine was used by caudal route) during the postoperative care unit (PACU) stay and the early postoperative period (6–24 h after leaving the operative room). The data from each trial were combined to calculate the pooled odds ratios or standard mean differences and their 95% confidence intervals.

Results:  Thirty‐five randomized, blinded controlled studies were retrieved from the literature. Systemic ketamine was effective in decreasing PACU pain intensity and analgesic requirement but failed to influence early (6–24 h) pain intensity and analgesic requirement. Ketamine administered locally during tonsillectomy, decreased PACU and early (6–24 h) pain intensity and PACU analgesic requirements. Used as an adjuvant for caudal analgesia, ketamine increased the duration of sensory block and PACU analgesic requirement without impacting PACU pain intensity. Ketamine failed to exhibit a postoperative opioid‐sparing effect.

Conclusions:  This meta‐analysis found that administration of ketamine was associated with decreased PACU postoperative pain intensity and nonopioid analgesic requirement. However, ketamine failed to exhibit a postoperative opioid‐sparing effect.
Quantitative pharmacological analysis of antagonist binding kinetics at CRF1 receptors in vitro and in vivo
Authors: Ramsey Simeon J , Attkins Neil J , Fish Rebecca , van der Graaf Piet H
Published: March 2011

BACKGROUND AND PURPOSE A series of novel non‐peptide corticotropin releasing factor type‐1 receptor (CRF1) antagonists were found to display varying degrees of insurmountable and non‐competitive behaviour in functional in vitro assays. We describe how we attempted to relate this behaviour to ligand receptor‐binding kinetics in a quantitative manner and how this resulted in the development and implementation of an efficient pharmacological screening method based on principles described by Motulsky and Mahan.

EXPERIMENTAL APPROACH A non‐equilibrium binding kinetic assay was developed to determine the receptor binding kinetics of non‐peptide CRF1 antagonists. Nonlinear, mixed‐effects modelling was used to obtain estimates of the compounds association and dissociation rates. We present an integrated pharmacokinetic–pharmacodynamic (PKPD) approach, whereby the time course of in vivo CRF1 receptor binding of novel compounds can be predicted on the basis of in vitro assays.

KEY RESULTS The non‐competitive antagonist behaviour appeared to be correlated to the CRF1 receptor off‐rate kinetics. The integrated PKPD model suggested that, at least in a qualitative manner, the in vitro assay can be used to triage and select compounds for further in vivo investigations.

CONCLUSIONS AND IMPLICATIONS This study provides evidence for a link between ligand offset kinetics and insurmountable/non‐competitive antagonism at the CRF1 receptor. The exact molecular pharmacological nature of this association remains to be determined. In addition, we have developed a quantitative framework to study and integrate in vitro and in vivo receptor binding kinetic behaviour of CRF1 receptor antagonists in an efficient manner in a drug discovery setting.
Ecological Risk Assessment, Prediction, and Assessing Risk Predictions
Authors: Gibbs Mark
Published: March 2011

Ecological risk assessment embodied in an adaptive management framework is becoming the global standard approach for formally assessing and managing the ecological risks of technology and development. Ensuring the continual improvement of ecological risk assessment approaches is partly achieved through the dissemination of not only the types of risk assessment approaches used, but also their efficacy. While there is an increasing body of literature describing the results of general comparisons between alternate risk assessment methods and models, there is a paucity of literature that post hoc assesses the performance of specific predictions based on an assessment of risk and the effectiveness of the particular model used to predict the risk. This is especially the case where risk assessments have been used to grant consent or approval for the construction of major infrastructure projects. While postconstruction environmental monitoring is increasingly commonplace, it is not common for a postconstruction assessment of the accuracy and performance of the ecological risk assessment and underpinning model to be undertaken. Without this “assessment of the assessment,” it is difficult for other practitioners to gain insight into the performance of the approach and models used and therefore, as argued here, this limits the rate of improvement of risk assessment approaches.
Using Simulation to Evaluate Time to Detect Incursions in Honeybee Biosecurity in Australia
Authors: Clifford David , Barry Simon , Cook David , Duthie Rob , Anderson Denis
Published: March 2011

A key determinant of the efficiency of a surveillance system for exotic mites is whether an incursion might be detected sufficiently quickly to allow successful management actions to occur. To assess this possibility we have developed a spatial modeling system and synthesized knowledge of honeybee and mite behavior to explore the potential spread of exotic mites and the likelihood of their detection in sentinel hives. We find that increasing the number of hives and the efficiency of the detection method are the most effective means of improving the time to detection.
Corporate Governance and Efficiency: Evidence From U.S. Property–Liability Insurance Industry
Authors: Huang Li‐Ying , Lai Gene C. , McNamara Michael , Wang Jennifer
Published: March 2011

Abstract

This study examines the relation between corporate governance and the efficiency of the U.S. property–liability insurance industry during the period from 2000 to 2007. We find a significant relation between efficiency and corporate governance (board size, proportion of independent directors on the audit committee, proportion of financial experts on the audit committee, director tenure, proportion of block shareholding, average number of directorships, proportion of insiders on the board, and auditor dependence). We also find property–liability insurers have complied with the Sarbanes‐Oxley Act (SOX) to a large extent. Although SOX achieved the goal of greater auditor independence and might have prevented Enron‐like scandals, it had some unexpected effects. For example, insurers became less efficient when they had more independent auditors because the insurers were unable to recoup the benefits of auditor independence.
Whose Place Is This Anyway? The Israeli Separation Barrier, International Activists and Graffiti
Authors: Sauders Robert R
Published: March 2011

[in focus, place, Israeli‐Palestinian conflict, graffiti, solidarity, social justice, Israeli Separation Barrier]
Species diversity of grasses promotes genotypic diversity of clover populations in simulated communities
Authors: Adams Rachel I. , Vellend Mark
Published: March 2011

Recent studies in community genetics have demonstrated strong effects of intraspecific genetic variation on the diversity of interacting species but largely ignored the potential for effects of species diversity on genetic diversity, which could also create a positive correlation between these two levels of biodiversity. Here we investigated the role that species diversity of competitors could play in shaping the genotypic diversity of a focal species, using a modified version of an existing model of grass–clover dynamics. We simulated communities in which clover genotypes varied in their relative competitive ability when growing adjacent to different grass species. Under many parameter combinations, communities with greater species richness of grasses retained greater genotypic richness within the clover population. Increasing grass species richness effectively increased biotic environmental heterogeneity with respect to clover growth, thereby promoting the maintenance of genotypic diversity. This result depended on three conditions being met: (1) a sufficiently strong tradeoff among genotypes in their fitness when growing with different grass species, (2) partial de‐coupling of competition and facilitation, with grass and clover capable of sharing microsites rather than strictly excluding one another, and (3) sufficiently high rates of clover growth and clonal spread, which allowed clover genotypes to ‘track’ the shifting mosaic of grass species. Our results demonstrate that species diversity can act as an important promoter of genotypic diversity, and they provide testable predictions concerning the conditions that promote this outcome in nature.
Niches of temperate tree species converge towards nutrient‐richer conditions over ontogeny
Authors: Bertrand Romain , Gégout Jean‐Claude , Bontemps Jean‐Daniel
Published: March 2011

Niche changes during a species’ lifespan are known as ontogenetic niche shifts. These shifts reflect changes in resource availability, requirements, organisms’ foraging ability and/or size‐dependent biotic interactions. In the plant kingdom, however, this issue remains poorly covered.

We investigated nutritional niche shifts over the ontogeny of 23 temperate tree species (among nine phylogenetic families) by a synchronic approach. We used 1963 temporary phytoecological surveys conducted throughout metropolitan French forests. The realised niches of three life‐history stages (seedling: <0.5 m; sapling: >0.5 m and < 8 m; tree: >8 m) in each tree species were modelled on the basis of presence/absence data and the main factors of species distribution (energy, water and nutritional resources). We computed the nutritional optima and amplitudes by bootstrapping partial response curves for the C:N ratio and base saturation rate. We assessed changes in these niche parameters over ontogeny and also evaluated the relative importance of ontogenetic shifts in the differentiation of nutritional niche among the selected tree species.

The tree stage was found to occur mainly at higher nutrient availability than the seedling (+16.3% on the nutritional gradient) or sapling (+11.1%) stages. In addition, nutritional niches of tree species exhibited, successively, a niche enlargement in eutrophic conditions and a niche restriction in oligotrophic conditions during growth. These global nutritional niche shifts observed over the species’ lifespan contributed moderately but significantly to the niche separation in temperate tree communities (up to 4.5%).

We interpreted niche shifts as a response to an increase in nutritional requirements over ontogeny, leading to an intra‐specific selection where individuals established in eutrophic soils have the maximal fitness. Biotic interactions and temporal changes in the environment may secondarily enhance or counteract the process. The importance of ontogenetic niche shifts requires consideration in the study of species autecology and plant community organisation.