bluuebunny/crossref_metadata_2025 huggingface dataset:
A functional variant of the dopamine D
3
receptor is associated with risk and age-at-onset of essential tremor
Authors: Jeanneteau Freddy , Funalot Benoît , Jankovic Joseph , Deng Hao , Lagarde Jean-Pierre , Lucotte Gérard , Sokoloff Pierre
Published: June 2006

Familial essential tremor (ET), the most common inherited movement disorder, is generally transmitted as an autosomal dominant trait. A genome-wide scan for ET revealed one major locus on chromosome 3q13. Here, we report that the Ser9Gly variant in the dopamine D
3
receptor gene (
DRD3
), localized on 3q13.3, is associated and cosegregates with familial ET in 23 out of 30 French families. Sequencing revealed no other nonsynonymous variants in the DRD3-coding sequence and in the first 871 bp of the 5’ flanking region. Moreover, Gly-9 homozygous patients presented with more severe and/or earlier onset forms of the disease than heterozygotes. A replication study comparing 276 patients with ET and 184 normal controls confirmed the association of the Gly-9 variant with risk and age-at-onset of ET. In human embryonic kidney (HEK) 293-transfected cells, the Gly-9 variant did not differ from the Ser-9 variant with respect to glycosylation and to anterograde and retrograde trafficking, but dopamine had an affinity that was four to five times higher. With the Gly-9 variant, the dopamine-mediated cAMP response was increased, and the mitogen-associated protein kinase (MAPK) signal was prolonged, as compared with the Ser-9 variant. The gain-of-function produced by the Gly-9 variant may explain why drugs active against tremor in Parkinson's disease (PD) are usually not effective in the treatment of ET and suggests that DRD3 partial agonists or antagonists should be considered as novel therapeutic options for patients with ET.
Functional uncoupling between Ca
2+
release and afterhyperpolarization in mutant hippocampal neurons lacking junctophilins
Authors: Moriguchi Shigeki , Nishi Miyuki , Komazaki Shinji , Sakagami Hiroyuki , Miyazaki Taisuke , Masumiya Haruko , Saito Shin-ya , Watanabe Masahiko , Kondo Hisatake , Yawo Hiromu , Fukunaga Kohji , Takeshima Hiroshi
Published: June 2006

Junctional membrane complexes (JMCs) composed of the plasma membrane and endoplasmic/sarcoplasmic reticulum seem to be a structural platform for channel crosstalk. Junctophilins (JPs) contribute to JMC formation by spanning the sarcoplasmic reticulum membrane and binding with the plasma membrane in muscle cells. In this article, we report that mutant JP double-knockout (JP-DKO) mice lacking neural JP subtypes exhibited an irregular hindlimb reflex and impaired memory. Electrophysiological experiments indicated that the activation of small-conductance Ca
2+
-activated K
+
channels responsible for afterhyperpolarization in hippocampal neurons requires endoplasmic reticulum Ca
2+
release through ryanodine receptors, triggered by NMDA receptor-mediated Ca
2+
influx. We propose that in JP-DKO neurons lacking afterhyperpolarization, the functional communications between NMDA receptors, ryanodine receptors, and small-conductance Ca
2+
-activated K
+
channels are disconnected because of JMC disassembly. Moreover, JP-DKO neurons showed an impaired long-term potentiation and hyperactivation of Ca
2+
/calmodulin-dependent protein kinase II. Therefore, JPs seem to have an essential role in neural excitability fundamental to plasticity and integrated functions.
Dissociation of pathological and molecular phenotype of variant Creutzfeldt–Jakob disease in transgenic human prion protein 129 heterozygous mice
Authors: Asante Emmanuel A. , Linehan Jacqueline M. , Gowland Ian , Joiner Susan , Fox Katie , Cooper Sharon , Osiguwa Olufumilayo , Gorry Michelle , Welch Julie , Houghton Richard , Desbruslais Melanie , Brandner Sebastian , Wadsworth Jonathan D. F. , Collinge John
Published: June 2006

All neuropathologically confirmed cases of variant Creutzfeldt–Jakob disease (vCJD), characterized by abundant florid plaques and type 4 disease-related prion protein (PrP
Sc
) in the brain, have been homozygous for methionine at polymorphic residue 129 of
PRNP
. The distinctive neuropathological and molecular phenotype of vCJD can be faithfully recapitulated in
Prnp
-null transgenic mice homozygous for human PrP M129 but not V129, where a distinct prion strain is propagated. Here we model susceptibility of 129MV heterozygotes, the most common
PRNP
genotype, in transgenic mice and show that, remarkably, propagation of type 4 PrP
Sc
was not associated with characteristic vCJD neuropathology. Depending on the source of the inoculum these mice can develop four distinct disease phenotypes after challenge with bovine spongiform encephalopathy (BSE) prions or vCJD (human-passaged BSE) prions. vCJD-challenged mice had higher attack rates of prion infection than BSE-challenged recipients. These data argue that human
PRNP
129 heterozygotes will be more susceptible to infection with vCJD prions than to cattle BSE prions and may present with a neuropathological phenotype distinct from vCJD.
Color Doppler twinkling artifact related to chronic pancreatitis with parenchymal calcification
Authors: Tsao T.-F. , Kang R.-J. , Tyan Y.-S. , Gueng M.-K. , Lee T. , Lee S.-K.
Published: June 2006

Color Doppler twinkling artifact is known as a rapidly changing mixture of red and blue behind certain strongly reflecting structures. This artifact has been described behind calcifications in various tissues. We describe a case of twinkling artifact related to chronic pancreatitis with parenchymal calcification.
Diffuse cerebral white matter T2-weighted hyperintensity: a new finding of general paresis
Authors: Alam F. , Yasutomi H. , Fukuda H. , Horiguchi J. , Murakami Y. , Ohshita T. , Inoue K. , Ito K.
Published: June 2006

General paresis (parenchymatous neurosyphilis) is a rare disease, and in recent years the number of papers published on the magnetic resonance imaging findings has been limited. The findings are as follows: cerebral atrophy; mesiotemporal T2 hyperintensity; ventriculomegaly; pathological T2 hypointensity of the globus pallidus, putamen, the head of the caudate nucleus and thalamus. We present a new finding, diffuse cerebral white matter T2 hyperintensity, observed in a patient with general paresis with a 5-year history of progressive dementia.
Long-term computed tomography follow-up after open surgical repair of abdominal aortic aneurysms
Authors: Mantoni M. , Neergaard K. , Christoffersen J. K. , Lambine T. L. , BÆkgaard N.
Published: June 2006

Purpose: To describe the findings on computed tomography (CT) of the aortic sac (AS) in patients operated on for abdominal aortic aneurysm (AAA) with insertion of a coated Dacron prosthesis.

Material and Methods: A prospective study of 36 consecutive patients operated on for AAA over 2 years and followed longitudinally with CT for up to 10 years.

Results: All patients had a fluid-filled AS on CT 7–10 days postoperatively. At 6 months, the AS had decreased in most patients, mainly in the antero-posterior diameter, and in two had disappeared completely. In five patients with complications, the AS increased in size. The AS disappeared completely at 10 years' follow-up in 13 patients. When present, a retroperitoneal hematoma always disappeared after 6 months.

Conclusion: These data indicate that the AS after graft implantation will diminish gradually but will persist for at least 6 months. Usually the transverse diameter is bigger than the antero-posterior diameter. If the AS enlarges and becomes rounded and distended with an inhomogeneous interior, it might be a sign of graft infection. In these cases an ultrasound-guided or CT-guided puncture is recommended.
Malignant peripheral nerve sheath tumor of the oculomotor nerve
Authors: Kozic D. , Nagulic M. , Ostojic J. , Samardzic M. , Milic-Rasic V. , Skender Gazibara M. , Nuri Sener R.
Published: June 2006

We present the short-term follow-up magnetic resonance (MR) studies and 1H-MR spectroscopy in a child with malignant peripheral nerve sheath tumor of the oculomotor nerve associated with other less aggressive cranial nerve schwannomas. The tumor revealed perineural extension and diffuse nerve involvement besides rapid growth. 1H-MR spectroscopy was helpful in excluding an intra-axial neoplasm with exophytic growth, mainly due to the absence of creatine and N-acetyl aspartate peaks, and markedly elevated choline peak.
F18-FDG coincidence-PET in patients with suspected gynecological malignancy
Authors: Zor E. , Stokkel M. P. , Özalp S. , Vardarelİ E. , YalÇİn Tarik Ö. , Ak İ.
Published: June 2006

Purpose: To assess the role of F18-FDG imaging with a dual-head coincidence mode gamma camera (Co-PET) in identifying malignant tumors in patients with a suspicious adnexal mass depicted by conventional imaging methods.

Material and Methods: F18-FDG Co-PET was performed preoperatively in 18 women (mean age 56.38 years) with suspected malignant gynecologic tumors according to clinical and abdomino-pelvic/transvaginal ultrasound or computed tomography findings. Exploratory laparotomy was performed in all patients within the 10 days post-F18-FDG Co-PET study, and the definitive diagnosis of the adnexal masses was established by histopathological examination.

Results: Histopathological examinations of the surgically excised adnexal masses revealed eight malignant, one borderline, and nine benign neoplastic tumors. Four benign tumors had no F18-FDG uptake, while the remaining five tumors, all leiomyomas, showed mild FDG accumulation. Eight malignant tumors showed intense F18-FDG uptake. Sensitivity, specificity, PPV, and NPV of F18-FDG co-PET in differentiating benign from malign adnexal masses were 88%, 44%, 61%, and 80%, respectively. Tumor to background ratios (T/B) in benign lesions (2.04 ± 0.27) were significantly lower than in malignant lesions (7.4 ± 0.99).

Conclusion: F18-FDG Co-PET is of clinical value when assessing suspicious malignant adnexal masses. False-negative F18-FDG results might arise from borderline disease. Moderate F18-FDG uptake in leiomyomas can result false-positive, but T/B ratios may be helpful in such cases.
Radiation dose reduction to breast and thyroid during MDCT: effectiveness of an in-plane bismuth shield
Authors: Hohl C. , Wildberger J. E. , Süß C. , Thomas C. , Mühlenbruch G. , Schmidt T. , Honnef D. , Günther R. W. , Mahnken A. H.
Published: June 2006

Purpose: To evaluate dose reduction and image deterioration using in-plane bismuth breast-shielding and thyroid-shielding for MDCT.

Material and Methods: Skin and organ doses of thyroid and breast were measured with thermoluminescent dosimeters in a female Alderson-Rando Phantom with and without a 4-ply in-plane bismuth shield. Routine neck (120 kVp, 150 mAseff; 16×1.5 mm) and chest (120 kVp, 100 mAseff; 16×1.5 mm) scan protocols were simulated on a 16-row MDCT scanner in three different settings: without shielding, with the shield directly on the surface, and with a 1-cm-thick cotton spacer between surface and shield. Image noise was quantified and compared using the t test.

Results: On average, shielding resulted in a 47% organ-dose reduction for the thyroid and 32% for the breast. Placement of the spacer between shield and surface had no significant impact on the measured doses, but significantly decreased the image noise ( P<0.05).

Conclusion: In-plane bismuth breast and thyroid shielding significantly decreases radiation dose in MDCT without deteriorating image quality.
Inadvertent intra-arterial drug injections: the role of angiographic and clinical findings
Authors: Rautio R. , Keski-Nisula L.
Published: June 2006

Purpose: To evaluate the angiographic findings of patients who have inadvertently injected oral formulations of drugs into an upper extremity artery.

Material and Methods: The radiology files for the previous 4 years were analyzed retrospectively. Seven patients were referred from the Emergency Department for angiography and possible thrombolysis during that time period.

Results: The worst clinical results were found among the patients whose angiographic examinations showed absent flow. Two patients who were treated with local thrombolysis had no better results compared to the other five patients.

Conclusion: Findings of delayed flow and absent flow in angiography should lead to intensified conservative treatment, especially among patients who have clinical findings of delayed capillary refilling or/and impaired muscular strength.
Book Reviews
Authors: Abildgaard Andreas
Published: June 2006

Computed Tomography: Fundamentals, System Technology, Image Quality, Applications. 2nd rev. edn. By Willi A. Kalender. Publicis Corporate Publishing 2005. 306 pages, 130 illustrations, 18 tables, with an enclosed CD-ROM.
Usefulness of measurement of the temporal stem on magnetic resonance imaging in the diagnosis of frontotemporal dementia
Authors: Hayashida Y. , Hirai T. , Korogi Y. , Kimura T. , Ishizuka K. , Kawanaka K. , Yamura M. , Kitajima M. , Ikushima I. , Yamashita Y.
Published: June 2006

Purpose: To investigate whether measurements of brain structures on routine magnetic resonance (MR) images can be used to distinguish between normal subjects and patients with frontotemporal dementia (FTD) or Alzheimer's disease (AD).

Material and Methods: MRI studies were performed on 30 patients with dementia (FTD, n = 15; AD, n = 15) and 15 age-matched controls. Width measurements, obtained at the corpus callosum, the cingulate gyri, the hippocampi, and the temporal stem of the anterior temporal lobes, were compared among FTD and AD patients and control subjects on oblique-coronal T2-weighted images.

Results: The width of the temporal stem was significantly narrower in FTD than in AD patients and control subjects (6.3±1.3 mm, 7.8±1.1 mm, and 8.2±0.9 mm, respectively) ( P<0.05), although there was some overlapping between AD and FTD patients. All patients whose temporal stem width was <6 mm had FTD. While the width of the corpus callosum, cingulate gyri, and hippocampi was significantly narrower in patients with AD and FTD than in the controls, there was no significant difference between the AD and FTD patients.

Conclusion: The width of the temporal stem was significantly narrower in patients with FTD than in those with AD and controls. The described measurements can easily be obtained and may be useful for the diagnosis of FTD.
ET viewer: an application for predicting and visualizing functional sites in protein structures
Authors: Morgan Daniel H. , Kristensen David M. , Mittelman David , Lichtarge Olivier
Published: June 2006

Summary: The Evolutionary Trace Viewer (ETV) provides a one-stop environment in which to run, visualize and interpret Evolutionary Trace (ET) predictions of functional sites in protein structures. ETV is implemented using Java to run across different operating systems using Java Web Start technology.

Availability: The ETV is available for download from our website at . This webpage also links to sample trace results and a user manual that describes ET Viewer functions in detail.

Contact:  lichtarge@bcm.edu
A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-α
Authors: Li Lang , Cheng Alfred S. L. , Jin Victor X. , Paik Henry H. , Fan Meiyun , Li Xiaoman , Zhang Wei , Robarge Jason , Balch Curtis , Davuluri Ramana V. , Kim Sun , Huang Tim H.-M. , Nephew Kenneth P.
Published: June 2006

Motivation: To detect and select patterns of transcription factor binding sites (TFBSs) which distinguish genes directly regulated by estrogen receptor-α (ERα), we developed an innovative mixture model-based discriminate analysis for identifying ordered TFBS pairs.

Results: Biologically, our proposed new algorithm clearly suggests that TFBSs are not randomly distributed within ERα target promoters (P-value < 0.001). The up-regulated targets significantly (P-value < 0.01) possess TFBS pairs, (DBP, MYC), (DBP, MYC/MAX heterodimer), (DBP, USF2) and (DBP, MYOGENIN); and down-regulated ERα target genes significantly (P-value < 0.01) possess TFBS pairs, such as (DBP, c-ETS1-68), (DBP, USF2) and (DBP, MYOGENIN). Statistically, our proposed mixture model-based discriminate analysis can simultaneously perform TFBS pattern recognition, TFBS pattern selection, and target class prediction; such integrative power cannot be achieved by current methods.

Availability: The software is available on request from the authors.

Contact: lali@iupui.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Domain organization within repeated DNA sequences: application to the study of a family of transposable elements
Authors: Tempel Sébastien , Giraud Mathieu , Lavenier Dominique , Lerman Israël-César , Valin Anne-Sophie , Couée Ivan , Amrani Abdelhak El , Nicolas Jacques
Published: June 2006

Motivation: The analysis of repeated elements in genomes is a fascinating domain of research that is lacking relevant tools for transposable elements (TEs), the most complex ones. The dynamics of TEs, which provides the main mechanism of mutation in some genomes, is an essential component of genome evolution. In this study we introduce a new concept of domain, a segmentation unit useful for describing the architecture of different copies of TEs. Our method extracts occurrences of a terminus-defined family of TEs, aligns the sequences, finds the domains in the alignment and searches the distribution of each domain in sequences. After a classification step relative to the presence or the absence of domains, the method results in a graphical view of sequences segmented into domains.

Results: Analysis of the new non-autonomous TE AtREP21 in the model plant Arabidopsis thaliana reveals copies of very different sizes and various combinations of domains which show the potential of our method.

Availability: DomainOrganizer web page is available at

Contact: DomainOrganizer@irisa.fr
Effects of replacing the unreliable cDNA microarray measurements on the disease classification based on gene expression profiles and functional modules
Authors: Wang Dong , Lv Yingli , Guo Zheng , Li Xia , Li Yanhui , Zhu Jing , Yang Da , Xu Jianzhen , Wang Chenguang , Rao Shaoqi , Yang Baofeng
Published: June 2006

Motivation: Microarrays datasets frequently contain a large number of missing values (MVs), which need to be estimated and replaced for subsequent data mining. The focus of the paper is to study the effects of different MV treatments for cDNA microarray data on disease classification analysis.

Results: By analyzing five datasets, we demonstrate that among three kinds of classifiers evaluated in this study, support vector machine (SVM) classifiers are robust to varied MV imputation methods [e.g. replacing MVs by zero, K nearest-neighbor (KNN) imputation algorithm, local least square imputation and Bayesian principal component analysis], while the classification and regression tree classifiers are sensitive in terms of classification accuracy. The KNNclassifiers built on differentially expressed genes (DEGs) are robust to the varied MV treatments, but the performances of the KNN classifiers based on all measured genes can be significantly deteriorated when imputing MVs for genes with larger missing rate (MR) (e.g. MR > 5%). Generally, while replacing MVs by zero performs relatively poor, the other imputation algorithms have little difference in affecting classification performances of the SVM or KNN classifiers. We further demonstrate the power and feasibility of our recently proposed functional expression profile (FEP) approach as means to handle microarray data with MVs. The FEPs, which are derived from the functional modules that are enriched with sets of DEGs and thus can be consistently identified under varied MV treatments, achieve precise disease classification with better biological interpretation. We conclude that the choice of MV treatments should be determined in context of the later approaches used for disease classification. The suggested exclusion criterion of ignoring the genes with larger MR (e.g. >5%), while justifiable for some classifiers such as KNN classifiers, might not be considered as a general rule for all classifiers.

Contact:  guoz@ems.hrbmu.edu.cn; yangbf@ems.hrbmu.edu.cn

Supplementary information: Supplementary data are available at Bioinformatics online.
PDQ Wizard: automated prioritization and characterization of gene and protein lists using biomedical literature
Authors: Grimes G. R. , Wen T. Q. , Mewissen M. , Baxter R. M. , Moodie S. , Beattie J. S. , Ghazal P.
Published: June 2006

Summary: PDQ Wizard automates the process of interrogating biomedical references using large lists of genes, proteins or free text. Using the principle of linkage through co-citation biologists can mine PubMed with these proteins or genes to identify relationships within a biological field of interest. In addition, PDQ Wizard provides novel features to define more specific relationships, highlight key publications describing those activities and relationships, and enhance protein queries. PDQ Wizard also outputs a metric that can be used for prioritization of genes and proteins for further research.

Availability: PDQ Wizard is freely available from

Contact:  Graeme.Grimes@ed.ac.uk

Supplementary Information: Supplementary Data are available
Pathway analysis using random forests classification and regression
Authors: Pang Herbert , Lin Aiping , Holford Matthew , Enerson Bradley E. , Lu Bin , Lawton Michael P. , Floyd Eugenia , Zhao Hongyu
Published: June 2006

Motivation: Although numerous methods have been developed to better capture biological information from microarray data, commonly used single gene-based methods neglect interactions among genes and leave room for other novel approaches. For example, most classification and regression methods for microarray data are based on the whole set of genes and have not made use of pathway information. Pathway-based analysis in microarray studies may lead to more informative and relevant knowledge for biological researchers.

Results: In this paper, we describe a pathway-based classification and regression method using Random Forests to analyze gene expression data. The proposed methods allow researchers to rank important pathways from externally available databases, discover important genes, find pathway-based outlying cases and make full use of a continuous outcome variable in the regression setting. We also compared Random Forests with other machine learning methods using several datasets and found that Random Forests classification error rates were either the lowest or the second-lowest. By combining pathway information and novel statistical methods, this procedure represents a promising computational strategy in dissecting pathways and can provide biological insight into the study of microarray data.

Availability: Source code written in R is available from

Contact:  hongyu.zhao@yale.edu

Supplementary Information: Supplementary Data are available at
SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs
Authors: Reumers Joke , Maurer-Stroh Sebastian , Schymkowitz Joost , Rousseau Frederic
Published: June 2006

Summary: Single nucleotide polymorphisms (SNPs) constitute the most fundamental type of genetic variation in human populations. About 75 000 of these reported variations cause an amino acid change in the translated protein. An important goal in genomic research is to understand how this variability affects protein function, and whether or not particular SNPs are associated to disease susceptibility. Accordingly, the SNPeffect database uses sequence- and structure-based bioinformatics tools to predict the effect of non-synonymous SNPs on the molecular phenotype of proteins. SNPeffect analyses the effect of SNPs on three categories of functional properties: (1) structural and thermodynamic properties affecting protein dynamics and stability (2) the integrity of functional and binding sites and (3) changes in posttranslational processing and cellular localization of proteins. The search interface of the database can be used to search specifically for polymorphisms that are predicted to cause a change in one of these properties. Now based on the Ensembl human databases, the SNPeffect database has been remodeled to better fit an automatically updatable structure. The current edition holds the molecular phenotype of 74 567 nsSNPs in 23 426 proteins.

Availability: SNPeffect can be accessed through

Supplementary Material: Statistics on the contents of the database, figures on the workflow used to create the database and information on the used sources and tools is available at .

Contact:  joost.schymkowitz@vub.ac.be or frederic.rousseau@vub.ac.be
An iterative refinement algorithm for consistency based multiple structural alignment methods
Authors: Chen Yu , Crippen Gordon M.
Published: June 2006

Motivation: Multiple STructural Alignment (MSTA) provides valuable information for solving problems such as fold recognition. The consistency-based approach tries to find conflict-free subsets of alignments from a pre-computed all-to-all Pairwise Alignment Library (PAL). If large proportions of conflicts exist in the library, consistency can be hard to get. On the other hand, multiple structural superposition has been used in many MSTA methods to refine alignments. However, multiple structural superposition is dependent on alignments, and a superposition generated based on erroneous alignments is not guaranteed to be the optimal superposition. Correcting errors after making errors is not as good as avoiding errors from the beginning. Hence it is important to refine the pairwise library to reduce the number of conflicts before any consistency-based assembly.

Results: We present an algorithm, Iterative Refinement of Induced Structural alignment (IRIS), to refine the PAL. A new measurement for the consistency of a library is also proposed. Experiments show that our algorithm can greatly improve T-COFFEE performance for less consistent pairwise alignment libraries. The final multiple alignment outperforms most state-of-the-art MSTA algorithms at assembling 15 transglycosidases. Results on three other benchmarks showed that the algorithm consistently improves multiple alignment performance.

Availability: The C++ code of the algorithm is available upon request.

Contact:  gcrippen@umich.edu
Larger ejaculate volumes are associated with a lower degree of polyandry across bushcricket taxa
Authors: Vahed Karim
Published: June 2006

In numerous insects, including bushcrickets (Tettigoniidae), males are known to transfer substances in the ejaculate that inhibit the receptivity of females to further matings, but it has not yet been established whether these substances reduce the lifetime degree of polyandry of the female. The aim of this study was to test the hypothesis that larger ejaculate volumes should be associated with a lower degree of polyandry across tettigoniid taxa, controlling for male body mass and phylogeny. Data on ejaculate mass, sperm number, nuptial gift mass and male mass were taken primarily from the literature. The degree of polyandry for 14 species of European bushcrickets was estimated by counting the number of spermatodoses within the spermathecae of field-caught females towards the end of their adult lifespans. Data for four further species were obtained from the literature. Data were analysed by using both species regression and independent contrasts to control for phylogeny. Multiple regression analysis revealed that, as predicted, there was a significant negative association between the degree of polyandry and ejaculate mass, relative to male body mass, across bushcricket taxa. Nuptial gift size and sperm number, however, did not contribute further to interspecific variation in the degree of polyandry. A positive relationship was found, across bushcricket taxa, between relative nuptial gift size and relative ejaculate mass, indicating that larger nuptial gifts allow the male to overcome female resistance to accepting large ejaculates. This appears to be the first comparative evidence that males can manipulate the lifetime degree of polyandry of their mates through the transfer of large ejaculates.
Sex in advertising: dioecy alters the net benefits of attractiveness in
Sagittaria latifolia
(Alismataceae)
Authors: Vamosi Jana C , Vamosi Steven M , Barrett Spencer C.H
Published: June 2006

The flowers and inflorescences of animal-pollinated dioecious plants are generally small and inconspicuous in comparison with outcrossing cosexual species. The net benefits of an attractive floral display may be different for dioecious compared to cosexual populations because dioecious species experience a more severe reduction in pollen delivery when pollinators forage longer on fewer individuals. Here, we develop a model that predicts the decrease in pollen delivery in dioecious relative to cosexual populations from female–female, female–male and male–male visit sequences as the number of individuals visited varies. To evaluate the predictions of our model we conducted a common garden experiment with dioecious and monoecious (cosexual) arrays of the insect-pollinated herb
Sagittaria latifolia
. We find that, although increasing the advertisements of floral rewards (i.e. increasing floral display) attracts more pollinators to individuals, the probability that these pollinators subsequently deliver pollen to neighbouring plants depends on sexual system. Because the number of individual plants visited per foraging trip did not increase significantly with floral display, the relative pollination success of dioecious versus monoecious populations decreases with increased floral display. We propose that this could explain why dioecy is strongly correlated with reduced floral display among angiosperm species.
From nestling calls to fledgling silence: adaptive timing of change in response to aerial alarm calls
Authors: Magrath Robert D , Platzen Dirk , Kondo Junko
Published: June 2006

Young birds and mammals are extremely vulnerable to predators and so should benefit from responding to parental alarm calls warning of danger. However, young often respond differently from adults. This difference may reflect: (i) an imperfect stage in the gradual development of adult behaviour or (ii) an adaptation to different vulnerability. Altricial birds provide an excellent model to test for adaptive changes with age in response to alarm calls, because fledglings are vulnerable to a different range of predators than nestlings. For example, a flying hawk is irrelevant to a nestling in a enclosed nest, but is dangerous to that individual once it has left the nest, so we predict that young develop a response to aerial alarm calls to coincide with fledging. Supporting our prediction, recently fledged white-browed scrubwrens,
Sericornis frontalis
, fell silent immediately after playback of their parents' aerial alarm call, whereas nestlings continued to calling despite hearing the playback. Young scrubwrens are therefore exquisitely adapted to the changing risks faced during development.
Perceptual compression of space through position integration
Authors: Roulston Barrie W , Self Matt W , Zeki Semir
Published: June 2006

The mechanism of positional localization has recently been debated due to interest in the flash-lag effect, which occurs when a briefly flashed stationary stimulus is perceived to lag behind a spatially aligned moving stimulus. Here we report positional localization observed at motion offsets as well as at onsets. In the ‘flash-lead’ effect, a moving object is perceived to be behind a spatially concurrent stationary flash before the two disappear. With ‘reverse-repmo’, subjects mis-localize the final position of a moving bar in the direction opposite to the trajectory of motion. Finally, we demonstrate that simultaneous onset and offset effects lead to a perceived compression of visual space. By characterizing illusory effects observed at motion offsets as well as at onsets, we provide evidence that the perceived position of a moving object is the result of an averaging process over a short time period, weighted towards the most recent positions. Our account explains a variety of motion illusions, including the compression of moving shapes when viewed through apertures.
The effects and consequences of very large explosive volcanic eruptions
Authors: Self S
Published: June 2006

Every now and again Earth experiences tremendous explosive volcanic eruptions, considerably bigger than the largest witnessed in historic times. Those yielding more than 450 km
3
of magma have been called super-eruptions. The record of such eruptions is incomplete; the most recent known example occurred 26 000 years ago. It is more likely that the Earth will next experience a super-eruption than an impact from a large meteorite greater than 1 km in diameter. Depending on where the volcano is located, the effects will be felt globally or at least by a whole hemisphere. Large areas will be devastated by pyroclastic flow deposits, and the more widely dispersed ash falls will be laid down over continent-sized areas. The most widespread effects will be derived from volcanic gases, sulphur gases being particularly important. This gas is converted into sulphuric acid aerosols in the stratosphere and layers of aerosol can cover the global atmosphere within a few weeks to months. These remain for several years and affect atmospheric circulation causing surface temperature to fall in many regions. Effects include temporary reductions in light levels and severe and unseasonable weather (including cool summers and colder-than-normal winters). Some aspects of the understanding and prediction of super-eruptions are problematic because they are well outside modern experience. Our global society is now very different to that affected by past, modest-sized volcanic activity and is highly vulnerable to catastrophic damage of infrastructure by natural disasters. Major disruption of services that society depends upon can be expected for periods of months to, perhaps, years after the next very large explosive eruption and the cost to global financial markets will be high and sustained.
Natural disasters and the challenge of extreme events: risk management from an insurance perspective
Authors: Smolka Anselm
Published: June 2006

Loss statistics for natural disasters demonstrate, also after correction for inflation, a dramatic increase of the loss burden since 1950. This increase is driven by a concentration of population and values in urban areas, the development of highly exposed coastal and valley regions, the complexity of modern societies and technologies and probably, also by the beginning consequences of global warming. This process will continue unless remedial action will be taken. Managing the risk from natural disasters starts with identification of the hazards. The next step is the evaluation of the risk, where risk is a function of hazard, exposed values or human lives and the vulnerability of the exposed objects. Probabilistic computer models have been developed for the proper assessment of risks since the late 1980s. The final steps are controlling and financing future losses. Natural disaster insurance plays a key role in this context, but also private parties and governments have to share a part of the risk. A main responsibility of governments is to formulate regulations for building construction and land use. The insurance sector and the state have to act together in order to create incentives for building and business owners to take loss prevention measures. A further challenge for the insurance sector is to transfer a portion of the risk to the capital markets, and to serve better the needs of the poor. Catastrophe bonds and microinsurance are the answer to such challenges. The mechanisms described above have been developed to cope with well-known disasters like earthquakes, windstorms and floods. They can be applied, in principle, also to less well investigated and less frequent extreme disasters: submarine slides, great volcanic eruptions, meteorite impacts and tsunamis which may arise from all these hazards. But there is an urgent need to improve the state of knowledge on these more exotic hazards in order to reduce the high uncertainty in actual risk evaluation to an acceptable level. Due to the rarity of such extreme events, specific risk prevention measures are hardly justified with exception of attempts to divert earth-orbit crossing meteorites from their dangerous path. For the industry it is particularly important to achieve full transparency as regards covered and non-covered risks and to define in a systematic manner the limits of insurability for super-disasters.
Setting priorities: global patterns of disaster risk
Authors: Dilley Maxx
Published: June 2006

Natural disasters are caused by the exposure and vulnerabilities to natural hazards of people, infrastructure and economic activities. Analysis of these factors has permitted identification of countries and areas within them where disaster-related mortality and economic losses are likely in the future. These high-risk areas are candidates for increased attention to, and investment in, disaster risk identification, reduction and transfer.

Plans are underway to further identify disaster risk levels and factors on national and subnational scales in high-risk countries to create evidence for improved risk management decision-making. In this paper, I review selected recent global and regional risk analyses to highlight findings, areas for improvement and next steps in the overall process of using disaster risk information for more effective risk management and cost-effective reduction of losses.
Genomic clusters, putative pathogen recognition molecules, and antimicrobial genes are induced by infection ofC. eleganswithM. nematophilum
Authors: O’Rourke Delia , Baban Dilair , Demidova Maria , Mott Richard , Hodgkin Jonathan
Published: June 2006

The interaction between the nematodeCaenorhabditis elegansand a Gram-positive bacterial pathogen,Microbacterium nematophilum, provides a model for an innate immune response in nematodes. This pathogen adheres to the rectal and post-anal cuticle of the worm, causing slowed growth, constipation, and a defensive swelling response of rectal hypodermal cells. To explore the genomic responses that the worm activates after pathogenic attack we used microarray analysis of transcriptional changes induced after 6-h infection, comparing virulent with avirulent infection. We defined 89 genes with statistically significant expression changes of at least twofold, of which 68 were up-regulated and 21 were down-regulated. Among the former, those encoding C-type lectin domains were the most abundant class. Many of the 89 genes exhibit genomic clustering, and we identified one large cluster of 62 genes, of which most were induced in response to infection. We tested 41 of the induced genes for involvement in immunity using mutants or RNAi, finding that six of these are required for the swelling response and five are required more generally for defense. Our results indicate that C-type lectins and other putative pathogen-recognition molecules are important for innate immune defense inC. elegans. We also found significant induction of genes encoding lysozymes, proteases, and defense-related proteins, as well as various domains of unknown function. The genes induced during infection byM. nematophilumappear largely distinct from genes induced by other pathogens, suggesting thatC. elegansmounts pathogen-specific responses to infection.
Extensive low-affinity transcriptional interactions in the yeast genome
Authors: Tanay Amos
Published: June 2006

Major experimental and computational efforts are targeted at the characterization of transcriptional networks on a genomic scale. The ultimate goal of many of these studies is to construct networks associating transcription factors with genes via well-defined binding sites. Weaker regulatory interactions other than those occurring at high-affinity binding sites are largely ignored and are not well understood. Here I show that low-affinity interactions are abundant in vivo and quantifiable from current high-throughput ChIP experiments. I develop algorithms that predict DNA-binding energies from sequences and ChIP data across a wide dynamic range of affinities and use them to reveal widespread functionality of low-affinity transcription factor binding. Evolutionary analysis suggests that binding energies of many transcription factors are conserved even in promoters lacking classical binding sites. Gene expression analysis shows that such promoters can generate significant expression. I estimate that while only a small percentage of the genome is strongly regulated by a typical transcription factor, up to an order of magnitude more may be involved in weaker interactions. Low-affinity transcription factor–DNA interaction may therefore be important both evolutionarily and functionally.
Relaxation of selective constraint on dog mitochondrial DNA following domestication
Authors: Björnerfeldt Susanne , Webster Matthew T. , Vilà Carles
Published: June 2006

The domestication of dogs caused a dramatic change in their way of life compared with that of their ancestor, the gray wolf. We hypothesize that this new life style changed the selective forces that acted upon the species, which in turn had an effect on the dog’s genome. We sequenced the complete mitochondrial DNA genome in 14 dogs, six wolves, and three coyotes. Here we show that dogs have accumulated nonsynonymous changes in mitochondrial genes at a faster rate than wolves, leading to elevated levels of variation in their proteins. This suggests that a major consequence of domestication in dogs was a general relaxation of selective constraint on their mitochondrial genome. If this change also affected other parts of the dog genome, it could have facilitated the generation of novel functional genetic diversity. This diversity could thus have contributed raw material upon which artificial selection has shaped modern breeds and may therefore be an important source of the extreme phenotypic variation present in modern-day dogs.
Comparative isoschizomer profiling of cytosine methylation: The HELP assay
Authors: Khulan Batbayar , Thompson Reid F. , Ye Kenny , Fazzari Melissa J. , Suzuki Masako , Stasiek Edyta , Figueroa Maria E. , Glass Jacob L. , Chen Quan , Montagna Cristina , Hatchwell Eli , Selzer Rebecca R. , Richmond Todd A. , Green Roland D. , Melnick Ari , Greally John M.
Published: June 2006

The distribution of cytosine methylation in 6.2 Mb of the mouse genome was tested using cohybridization of genomic representations from a methylation-sensitive restriction enzyme and its methylation-insensitive isoschizomer. This assay, termed HELP (HpaII tiny fragment Enrichment by Ligation-mediated PCR), allows both intragenomic profiling and intergenomic comparisons of cytosine methylation. The intragenomic profile shows most of the genome to be contiguous methylated sequence with occasional clusters of hypomethylated loci, usually but not exclusively at promoters and CpG islands. Intergenomic comparison found marked differences in cytosine methylation between spermatogenic and brain cells, identifying 223 new candidate tissue-specific differentially methylated regions (T-DMRs). Bisulfite pyrosequencing confirmed the four candidates tested to be T-DMRs, while quantitative RT-PCR for two genes with T-DMRs located at their promoters showed the HELP data to be correlated with gene activity at these loci. The HELP assay is robust, quantitative, and accurate and is providing new insights into the distribution and dynamic nature of cytosine methylation in the genome.
Heterozygous carriers of Nijmegen Breakage Syndrome have a distinct gene expression phenotype
Authors: Cheung Vivian G. , Ewens Warren J.
Published: June 2006

Autosomal recessive diseases are those that require mutations in both alleles to exhibit the disorder. Although most recessive conditions are rare, heterozygous carriers of recessive mutations are quite common. In this study, we show that carriers of Nijmegen Breakage Syndrome (NBS) have a distinct gene expression phenotype that differs from that of noncarriers and also from that of carriers of a similar syndrome, Ataxia Telangiectasia (AT). We found 520 genes whose expression levels differ significantly (P ≤ 0.001) between NBS carriers and controls. By linear discriminant analysis, we found a combination of 16 genes that allows 100% correct classification of individuals as either NBS carriers or noncarriers in a training set with 25 individuals, and in a test set with 52 individuals. When applied to AT carriers, the discriminant function misclassified only one out of 18 AT carriers as an NBS carrier. Our result shows that NBS carriers have a specific gene expression phenotype. It suggests that heterozygous mutations can contribute significantly to natural variation in gene expression. This has implications for the role that heterozygosity for recessive diseases plays in the overall genetic architecture of complex human traits and diseases.
Influence of steel composition on strain induced corrosion cracking and other types of corrosion
Authors: Huijbregts W. , Leferink R.
Published: June 2006

Purpose

To make clear that C‐steel can differ very much in corrosion resistance under practical conditions only because of differences in chemical composition of the steels.

Design/methodology/approach

In the electricity generating industry, “mild” (i.e. “plain carbon”) and low‐alloyed steels are used in huge quantities, for instance, in boilers, steam generators, heat recovery boilers and waste incineration boilers. The resistance to strain induced corrosion cracking (SICC) was determined by measuring the “repassivation” behaviour of the steels at freshly ground surfaces with an electrochemical technique. The corrosion current measured with time was used to calculate the cracking rates of a compact tension specimen.

Findings

A correlation was found between chemical composition, corrosion resistance to SICC and experiences under practical conditions. The results of early‐published papers on boiler corrosion (testing in FeCl2 solutions), erosion corrosion (testing in wet steam at 20 bar), nitrate stress corrosion cracking (testing in NH4NO3 solutions) and SICC together with those originating from in‐service failures, were compiled into a reference database. This paper is a compilation of this work too.

Originality/value

The database and formulas presented make clear there is often a direct correlation between chemical composition of ordinary C‐steel and mentioned types of corrosion failures. The paper is of importance to designers, failure analysts and researchers.
Evaluation of mild steel corrosion using a new surfactant inhibition model
Authors: Youp Ryu Dong , Free Michael L.
Published: June 2006

Purpose

To evaluate mild steel corrosion using a new surfactant‐inhibition model which was derived, in part, from the concept of intermolecular energy and molecular separation distance.

Design/methodology/approach

A Gamry potentiostat was used for polarization resistance tests to determine corrosion rate and the level of adsorption of surfactant at the solution‐metal interface was determined using UV‐spectroscopy. The relationship between inhibition and surfactant adsorption as well as metal corrosion was investigated using a traditional surfactant‐inhibition model, which assumes inhibition is directly proportional to surfactant coverage and new model.

Findings

The comparison of adsorption data and corrosion inhibition data shows inhibition was not directly proportional to physical coverage as assumed by the traditional inhibition model. Instead, it was found that coverage was related to inhibition through a power‐law dependency that is similar to that used to determine molecular interaction energies.

Research limitations/implications

The new model was evaluated only for dodecyl pyridinium chloride mild steel system. The evaluation of the new model for various surfactant‐metal systems is suggested for future research.

Originality/value

The new model was found to more accurately predict the relationship between inhibition and coverage rather than traditional models for dodecyl pyridinium chloride‐mild steel system.