bluuebunny/crossref_metadata_2025 huggingface dataset:
Estimating average annual per cent change in trend analysis
Authors: Clegg Limin X. , Hankey Benjamin F. , Tiwari Ram , Feuer Eric J. , Edwards Brenda K.
Published: October 2009

Trends in incidence or mortality rates over a specified time interval are usually described by the conventional annual per cent change (cAPC), under the assumption of a constant rate of change. When this assumption does not hold over the entire time interval, the trend may be characterized using the annual per cent changes from segmented analysis (sAPCs). This approach assumes that the change in rates is constant over each time partition defined by the transition points, but varies among different time partitions. Different groups (e.g. racial subgroups), however, may have different transition points and thus different time partitions over which they have constant rates of change, making comparison of sAPCs problematic across groups over a common time interval of interest (e.g. the past 10 years). We propose a new measure, the average annual per cent change (AAPC), which uses sAPCs to summarize and compare trends for a specific time period. The advantage of the proposed AAPC is that it takes into account the trend transitions, whereas cAPC does not and can lead to erroneous conclusions. In addition, when the trend is constant over the entire time interval of interest, the AAPC has the advantage of reducing to both cAPC and sAPC. Moreover, because the estimated AAPC is based on the segmented analysis over the entire data series, any selected subinterval within a single time partition will yield the same AAPC estimate—that is it will be equal to the estimated sAPC for that time partition. The cAPC, however, is re‐estimated using data only from that selected subinterval; thus, its estimate may be sensitive to the subinterval selected. The AAPC estimation has been incorporated into the segmented regression (free) software Joinpoint, which is used by many registries throughout the world for characterizing trends in cancer rates. Copyright © 2009 John Wiley & Sons, Ltd.
Assessment of risks by predicting counterfactuals
Authors: Zou G. Y.
Published: October 2009

Risk assessment is fundamental to most epidemiological and biomedical investigations. In this article, risks are assessed in terms of risk difference and risk ratio by predicting counterfactual outcomes. Models considered for binary outcomes are probit, logistic, and extreme‐value regressions. New confidence intervals for the effect measures are proposed using the method of variance estimates recovery, and evaluated by a simulation study. A SAS macro is provided for the calculations. A risk ratio obtained using counterfactuals is also compared in the simulation with that directly estimated from the modified Poisson model to answer a recent concern about the validity of the latter approach. Two examples are used to illustrate the methods. Copyright © 2009 John Wiley & Sons, Ltd.
Classification of array CGH data using smoothed logistic regression model
Authors: Huang Jian , Salim Agus , Lei Kaibin , O'Sullivan Kathleen , Pawitan Yudi
Published: October 2009

Array comparative genomic hybridization (aCGH) provides a genome‐wide information of DNA copy number that is potentially useful for disease classification. One immediate problem is that the data contain many features (probes) but only a few samples. Existing approaches to overcome this problem include features selection, ridge regression and partial least squares. However, these methods typically ignore the spatial characteristic of aCGH data. To explicitly make use of this spatial information we develop a procedure called smoothed logistic regression (SLR) model. The procedure is based on a mixed logistic regression model, where the random component is a mixture distribution that controls smoothness and sparseness. Conceptually such a procedure is straightforward, but its implementation is complicated due to computational problems. We develop a fast and reliable iterative weighted least‐squares algorithm based on the singular value decomposition. Simulated data and two real data sets are used to illustrate the procedure. For real data sets, error rates are calculated using the leave‐one‐out cross validation procedure. For both simulated and real data examples, SLR achieves better misclassification error rates compared with previous methods. Copyright © 2009 John Wiley & Sons, Ltd.
Response and recovery of hybrid sturgeon from subchronic oral administration of cyanobacteria
Authors: Dong Guifang , Zhu Xiaoming , Han Dong , Yang Yunxia , Song Lirong , Xie Shouqi
Published: October 2009

A 90‐day growth trial was conducted on hybrid sturgeon (Acipenser baeri ♀ × A. gueldenstaedtii ♂) to investigate the effect of dietary inclusion of cyanobacteria on growth, feed utilization, and fish tissue microcystins (MCs) accumulation and the recovery of fish when they were free of cyanobacteria. Four diets were formualted isonitrogenous and isocaloric to contain different MCs concentrations: the control diet (free of cyanobacteria), low cyanobacteria diet (LCD, 26.60 μg MCs/g diet), medium cyanobacteria diet (MCD, 78.82 μg MCs/g diet), and high cyanobacteria diet (HCD, 201.03 μg MCs/g diet). During the first 47 days, each diet was fed to fish in five replicates and then all fish were fed the control diet during the next 43 days. The results showed that a dose‐dependent decrease in feeding rate (FR) and specific growth rate (SGR) were observed in the fish fed with MCD and HCD. MCs contents in fish liver, intestine, and dorsal white muscle increased with dietary MCs and were time dependent (P < 0.05). After the 43‐day recovery, there were no significant differences in FR or SGR between the fish previously fed LCD or MCD and the fish fed with the control diet (P > 0.05), while the fish previously fed HCD showed higher FR and SGR than those fed the control diet (P < 0.05). MCs clearance in fish liver and intestine showed time‐dependence during the 43‐day recovery. © 2009 Wiley Periodicals, Inc. Environ Toxicol 2009.
Dimensions of the fetal facial profile in normal pregnancy
Authors: Goldstein I. , Tamir A. , Weiner Z. , Jakobi P.
Published: October 2009

Objective

To determine sonographic dimensions of the fetal facial profile in normal pregnancy.

Methods

This was a prospective, cross‐sectional study of 397 normal healthy fetuses at 14–33 weeks of gestation. After exclusion of the small numbers of patients at the upper GAs, 379 patients between 14.0 and 26.9 weeks of gestation were included in the analyses. The sagittal plane of the fetal facial profile was evaluated using transvaginal and transabdominal ultrasound. Distances from the tip of the nose to the mouth (the line between the lips), from the mouth to the gnathion (lower chin), from the upper philtrum to the mouth, and from the mouth to the upper concavity of the chin were measured and are presented according to gestational age (GA).

Results

There was a significant linear correlation between GA and the distance from the tip of the nose to the mouth (r = 0.943; P < 0.00001; y = −37.98 + 7.54 × GA), from the mouth to the gnathion (r = 0.946; P < 0.00001; y = −46.34 + 7.95 × GA), from the upper level of the philtrum to the mouth (r = 0.71; P < 0.00001; y = 0.22 + 3.33 × GA) and from the mouth to the upper concavity of the chin (r = 0.665; P < 0.00001; y = 1.65 + 2.95 × GA). The ratio between the distance from the tip of the nose to the mouth and that from the mouth to the gnathion was also almost constant throughout gestation, as was the ratio between the distance from the upper philtrum to the mouth and that from the mouth to the upper concavity of the chin.

Conclusions

We provide normative data of the fetal facial profile across GA. Our data offer a potential tool for the prenatal diagnosis of abnormal fetal facial profile. Copyright © 2009 ISUOG. Published by John Wiley & Sons, Ltd.
Clinical outcomes of magnetic resonance‐guided focused ultrasound surgery for uterine myomas: 24‐month follow‐up
Authors: Funaki K. , Fukunishi H. , Sawada K.
Published: October 2009

Objectives

To assess the volume reduction ratio, symptom improvement and reintervention rate following magnetic resonance‐guided focused ultrasound surgery (MRgFUS) for uterine myomas.

Methods

A total of 91 Japanese women with symptomatic myomas underwent MRgFUS between June 2004 and June 2008 using the ExAblate 2000 system. The volume change ratio was calculated at 6, 12 and 24 months following MRgFUS based on T2‐weighted magnetic resonance images. The symptom severity score (SSS) was examined before and after the treatment (at 3, 6, 12 and 24 months). Additional post‐MRgFUS treatments, such as hysterectomy, myomectomy, uterine artery embolization or repeat MRgFUS, were recorded and the reinterventional treatment rates were compared according to the signal intensity of pretreatment T2‐weighted magnetic resonance images of the myomas.

Results

The mean volume change ratios of low‐ and intermediate‐intensity (Type 1/2) myomas were −36.5% 6 months post‐procedure and −39.5% 24 months post‐procedure. The mean ± SD SSS value for patients with Type 1/2 myomas before MRgFUS was 35.1 ± 21.0, and the values diminished significantly during the 24‐month follow‐up period to a mean value of around 15.0. High‐intensity (Type 3) myomas were not observed to have decreased in size 6 months after MRgFUS. Of the 45 Type 1/2 myoma patients with complete follow‐up, seven required reinterventional treatment within 24 months. The reintervention rates were 14.0% for Type 1/2 patients and 21.6% for Type 3 patients at 24 months post‐treatment.

Conclusions

Moderate volume reductions of Type 1/2 myomas were noted following MRgFUS, and the reduction in SSS values and the relatively low reintervention rates observed are encouraging. We found MRgFUS to be an appropriate treatment method for Type 1/2 uterine myomas. Copyright © 2009 ISUOG. Published by John Wiley & Sons, Ltd.
Primary Care Providers’ Responses to Patient‐Generated Family History
Authors: Fuller Melissa , Myers Melanie , Webb Thomas , Tabangin Meredith , Prows Cynthia
Published: October 2009

Family health history is one of the best predictors of an individual's risk for common disease, yet it is underutilized in routine care. Although the Surgeon General has recommended consumers record their family health history and share it with their health care provider, providers’ perceptions of patient‐generated family histories are unknown. To learn more about providers’ experience with and perceptions about patient‐generated family histories, we mailed surveys to 301 providers and had a response rate of 24% (n = 68). Seventy‐three percent felt a patient‐generated computer pedigree would improve their ability to assess risk as compared to their current methods. Seventy percent felt a patient‐generated computer pedigree would either have no effect on or would increase the number of patients that could be seen in a day. Results suggest that providers appreciate the potential benefits of patient‐generated family histories. Genetic counselors and nurses are in a prime position to promote and facilitate the use of patient‐generated family health histories in routine care.
High Pressure Micronization of Tristearate
Authors: Mandžuka Zoran , Škerget Mojca , Knez Željko
Published: October 2009

The effect of the pre‐expansion temperature, pre‐expansion pressure and storage time was studied in order to investigate the crystal form, degree of crystallinity, particle size, particle size distribution and morphology of the tristearate. The experiments were performed at pressures between 115 and 215 bar and at temperatures of 54, 60 and 70 °C with the substance being already melted. Samples were characterized immediately after the experiments and later after 3 months of storage at 5 and 20 °C. Results showed an increase in the amorphous phase. During the storage, the micronized samples re‐crystallized. With time, the agglomeration was more emphasized for particles produced at higher temperatures and pressures and stored at a higher temperature. The results of X‐ray analysis did not show a change in crystal form of tristearate (β′ form) before and after micronization, however, for samples stored at 20 °C slow transformation from the β′ (less stable) form to the β (more stable) form occurred. In addition, the morphology of micronized samples showed an irregular and porous shape. The re‐crystallization was more evident with time for samples stored at 20 °C where needle‐like crystals appeared on the surface.
The History of ICRP and the Evolution of its Policies
Authors: Clarke R.H. , Valentin J.
Published: October 2009

Within 12 months of the discovery of X rays in 1895, papers appeared in the literature reporting adverse effects from high exposure. In 1925, the first International Congress of Radiology, held in London, considered the need for a protection committee, which it established at its second congress in Stockholm in 1928. This paper celebrates the 80th anniversary of ICRP by tracing the history of the development of its policies, and identifying a few of the personalities involved from its inception up to the modern era. The paper follows the progress from the early controls on worker doses to avoid deterministic effects, through the identification of stochastic effects, to the concerns about public exposure and increasing stochastic risk estimates. The key features of the recommendations made by ICRP from 1928 up to the most recent in 2007 are identified.
The Bost conjecture, open subgroups and groups acting on trees
Authors: Paravicini Walther
Published: October 2009

We prove that the Bost conjecture with C*-algebra coefficients for locally compact Hausdorff groups passes to open subgroups. We also prove that if a locally compact Hausdorff group acts on a tree, then the Bost conjecture with C*-coefficients is true for the group if and only if it is true for the stabilisers of the vertices.
Handling uncertainty in economic evaluations of patient level data: A review of the use of Bayesian methods to inform health technology assessments
Authors: McCarron C. Elizabeth , Pullenayegum Eleanor M. , Marshall Deborah A. , Goeree Ron , Tarride Jean-Eric
Published: October 2009

Objectives:Due to potential advantages (e.g., using all available evidence), Bayesian methods have been proposed to assist healthcare decision making. This review provides a detailed description of how Bayesian methods have been applied to economic evaluations of patient level data. The results serve both as a reference and as a means by which to examine the appropriate application of Bayesian methods to inform decision making.

Methods:MEDLINE, EMBASE, and Cochrane Economic Evaluation databases were searched to identify studies, published up to November 2007, meeting three inclusion criteria: (i) the study conducted an economic evaluation, (ii) sampling uncertainty was incorporated using Bayesian methods, (iii) the likelihood function was informed by patient level data from a single source. Data were collected on key study characteristics (e.g., prior distribution, likelihood function, presentation of uncertainty).

Results:The search identified 366 potentially relevant studies, from which 103 studies underwent full-text review. Sixteen studies met the inclusion criteria. Half of the studies used uninformative priors; most studies incorporated the potential dependence between costs and effects, and presented cost-effectiveness acceptability curves. Results were sensitive to changes in the priors and likelihoods.

Conclusions:Limited use of informative priors, among the included studies, gives policy makers little guidance on one of the main benefits of Bayesian methods, the ability to integrate all available evidence to capture the uncertainty inherent in decision making.
The feasibility of harmonizing health technology assessments across jurisdictions: A case study of drug eluting stents
Authors: Trueman Paul , Hurry Manjusha , Bending Matthew , Hutton John
Published: October 2009

Objectives: There is considerable interest in the potential for harmonizing health technology assessments (HTA) across jurisdictions. This study aims to consider four HTAs of drug eluting stents to determine the degree to which the methods adopted, evidence considered, and resulting recommendations diverge.

Methods: Four HTAs of drug eluting stents were selected for inclusion and evaluated using a framework developed to systematically capture information on the process adopted, the evidence considered and the recommendations of each HTA.

Results and Conclusions: The findings suggest that, although there is a common core data set considered by most of the agencies, differences in the approach to HTA, heterogeneity of studies, and the limited relevance of research findings to local practice meant that the core data set had only limited influence on the resulting recommendations. Of the HTA agencies considered in the analysis, many sought to generate additional primary research from local settings to help inform the development of recommendations that were relevant to local practice. This raises questions about the extent to which HTA methods can be harmonized across jurisdictions.
Organizational and patient-related assessments in HTAs: State of the art
Authors: Lee Anne , Skött Line Sinding , Hansen Helle Ploug
Published: October 2009

Objectives:The use and implementation of health technologies do influence and are influenced by organizational structures and processes as well as patient's experiences and actions. The objective of this study is to discuss the content and managing of organizational and patient-related assessments in HTAs.

Methods:Quantitative and qualitative analysis were performed based on a review of organizational and patient-related assessments included in a random sample of fifty HTA reports. The reports were identified from INAHTA members’ Web sites where homepages of HTA agencies where searched for full HTA reports, published in English or Scandinavian languages.

Results:HTA reports including organizational assessments mainly comprised issues related to process and structure, while issues such as control and evaluation of the technology were included less often. Cultural and environmental issues were included in a little over half of the reports. Reports including patient-related assessments mainly comprised psychological issues. Patients’ perceptions of the technology's effect on their health, patient-information, and social and ethical issues were included less often. Few reports included implications for the patient's significant others. There was considerable variation in how comprehensive the issues were managed as there was in the methodological transparency of the HTA reports.

Conclusions:There is room for improvement in the assessments of organizational and patient-related issues. Absence of a description of the considerations made when determining the content and methods of the assessments limits the usefulness of an HTA. The reader is left uncertain of the relevance and validity of the organizational and patient-related assessments.
Dialect change?
Authors: Nilsson Jenny
Published: October 2009

The project Dialect Levelling in West Sweden focuses on the dialect situation in the first decade of the 21st century compared with the dialects spoken in the same region in the 1940s–1960s. Seventy teenagers participating in group interviews have been recorded and their use of phonological and morphological variables has been analysed. Comparisons with data recorded in the same region by The Institute of Language and Folklore in 1940–1960 show that dialect levelling is under way. It seems that the population of this area no longer speak a traditional dialect. An important issue, however, is how much the traditional dialects have actually changed, and to what extent the method for collecting data affects the answer. In the mid-20th century, the praxis within Swedish dialectology for selecting informants was to find as old and rural dialect speakers as possible to represent a specific region, and the purpose was that of documenting the dialect as a linguistic system. Today, however, many studies select informants based on speaker variables, because the aim is to document thedialect situation(i.e. who uses what linguistic variants when), rather than the traditional dialect as a linguistic system. Thus, there is a distinct difference between a linguistic interest and a sociolinguistic one. In this paper I suggest that it is critical when discussing dialect change to observe this very methodological change. In order to illustrate this, the use of dialect variants by two informants recorded in 1948 is compared with the use of dialect variants by three informants recorded in 2007 and 2008. The informants are all from around a small rural village located approximately 70 km from Gothenburg in West Sweden. This is an area where a specific variety of West Swedish has been spoken. By comparing these individuals, the concept of dialect change is problematized.
Self-recordings as a social activity
Authors: Schøning Signe , Møller Janus Spindler
Published: October 2009

In this paper, self-recorded interactions from two studies of verbal interaction in Denmark are analysed using key concepts from Erving Goffman's frame analysis and Don Zimmerman's theory of identities in talk. It is documented how the recorder is integrated into everyday interaction as soon as the informant in his or her capacity as temporary fieldworker has explained the reason for its being there and has obtained the permission from his or her partners to record them. In several excerpts ascribed identities and using the recorder as an addressee are used to create amusement and to exploit the possibilities for supplying the innocent overhearing researcher with new and shocking information. The question of language norms during recorded sessions was raised in conversations in both studies and the limits of privacy were brought up.
Evaluation of interventions and vaccination strategies for low pathogenicity avian influenza: spatial and space–time analyses and quantification of the spread of infection
Authors: MULATTI P. , BOS M. E. H. , BUSANI L. , NIELEN M. , MARANGON S.
Published: October 2009

In recent years the control of low pathogenicity avian influenza (LPAI) viruses of the H5 and H7 subtypes has increasingly become a concern. We evaluated the measures (stamping out, controlled marketing, emergency and preventive vaccination, farm density reduction and restocking in homogenous areas) implemented to control the LPAI epidemics that occurred in Italy between 2000 and 2005, using a combination of spatial and space–time analyses and estimates of the basic reproduction ratio (R0). Clustering of infected farms decreased over the years, indicating the effectiveness of the control strategies implemented. Controlled marketing [relative risk (RR) 0·46, 95% confidence interval (CI) 0·27–0·80], emergency (RR 0·47, 95% CI 0·39–0·57) and preventive vaccination (RR 0·19, 95% CI 0·09–0·41) were the most effective measures, yetR0<1 was only for preventive vaccination. Our results are useful for identifying the most effective measures for reducing the risk of the spread of LPAI and optimizing the allocation of resources.
A NEW SPECIES AND A NEW COMBINATION IN FRIESODIELSIA (ANNONACEAE) OF BORNEO
Authors: Turner I. M.
Published: October 2009

A new species of Friesodielsia (Annonaceae), Friesodielsia formosa, is described from Borneo. A large woody climber of lowland forests, the species has been collected from Sabah, Sarawak and Kalimantan. A new combination in Friesodielsia is made for Oxymitra grandifolia Merr. which is resurrected from the synonymy of Friesodielsia latifolia (Hook.f. & Thomson) Steenis. The name Oxymitra grandifolia is lectotypified.
Phycology (4th edition). Robert Edward Lee.
Authors: Sluiman H.
Published: October 2009

..
British Alpine Hawkweeds: A Monograph of British Hieracium section Alpina . D. J. Tennant & T. C. G. Rich.
Authors: Chrtek J.
Published: October 2009

..
Stenosis of the main stem of the left coronary artery in a teenager with Takayasu’s Arteritis
Authors: Reddy Srikrishna Modugula , Reddy Srinivas Pallikala
Published: October 2009

Coronary arterial involvement is rare in Takayasu’s arteritis. We describe successful coronary arterial bypass grafting in a 15 year teenager with Takayasu’s arteritis and unstable angina because of stenosis of the main stem of the left coronary artery.
Poor outcome for patients with totally anomalous pulmonary venous connection and functionally single ventricle
Authors: Sinzobahamvya Nicodème , Arenz Claudia , Reckers Julia , Photiadis Joachim , Murin Peter , Schindler Ehrenfried , Hraska Viktor , Asfour Boulos
Published: October 2009

Totally anomalous pulmonary venous connection, when also associated with a functionally univentricular connection, is known to have a poor outcome. We retrospectively analysed results for 19 patients undergoing surgery for this combination of lesions between 1995 and February 2009.

Of the patients, 12 were neonates, with 11 presenting with signs of pulmonary venous obstruction. In 3 patients, a modified Blalock-Taussig shunt had been constructed. The dominant ventricle was of right ventricular morphology in 17 of the 19 patients, and double inlet was present in all bar 1. Pulmonary atresia or stenosis was found in 14 patients, a common atrioventricular junction in 14 patients, and isomerism of the right atrial appendages in 12 patients, respectively. Comprehensive Aristotle scores ranged from 14 to 23.50. The mean was 16.55, with a standard deviation of 2.19. Pulmonary venous rerouting was combined in 6 patients with construction of a modified Blalock-Taussig, in 4 with banding of the pulmonary trunk, in another 4 with a bidirectional Glenn anastomosis, in 3 with creation of a total cavo-pulmonary connection, and in 1 each with enlargement of the right ventricular outflow tract and the Norwood procedure. Of the cohort, 8 patients died early due to pulmonary hypertension, with all patients having Aristotle scores of at least 18 points dying. Among the 11 early survivors, 5 needed mechanical ventilation for over a week, but 5 patients died later, 3 due to pulmonary hypertension and 2 due to infection. Actuarial survival stabilized at 31.6%, with standard error of 10.7%, from one year onwards. Conversion to the Fontan circulation was successful in 5 patients.

Our experience confirms that totally anomalous pulmonary venous connection, when associated with the functionally univentricular arrangement, carries one of the worst outcomes in current surgical practice. Use of the Aristotle comprehensive complexity scores effectively discriminates those patients with this condition at particularly high risk.
Treatment of adult post-traumatic stress disorder using a future-oriented writing therapy approach
Authors: Nixon Reginald D. V. , Kling Leonard W.
Published: October 2009

The aim of this pilot study was to test whether a future-oriented expressive writing intervention is able to reduce post-traumatic stress disorder (PTSD) severity and associated symptoms such as depression and unhelpful trauma-related beliefs. In an uncontrolled pre-/ post-design participants attended 8 weeks of manualized therapy. Assessment was undertaken pre- and post-treatment, and participants also completed a 3-month follow-up assessment. Of the 17 participants who began therapy, 13 were treatment completers. Results indicated a significant decrease in PTSD severity, depression and unhelpful trauma-related cognitions from pre- to post-treatment and at 3-month follow-up. Clinically meaningful change was more modest; however, three participants reported PTSD remission at 3-month follow-up. It is concluded that expressive writing with a focus on achieving future goals and personal change may have some utility in reducing post-traumatic stress but future research will need to investigate this with greater methodological rigour before firm conclusions can be made.
Global‐scale quantification of mineralization pathways in marine sediments: A reaction‐transport modeling approach
Authors: Thullner Martin , Dale Andrew W. , Regnier Pierre
Published: October 2009

The global‐scale quantification of organic carbon (Corg) degradation pathways in marine sediments is difficult to achieve experimentally due to the limited availability of field data. In the present study, a numerical modeling approach is used as an alternative to quantify the major metabolic pathways of Corg oxidation (Cox) and associated fluxes of redox‐sensitive species fluxes along a global ocean hypsometry, using the seafloor depth (SFD) as the master variable. The SFD dependency of the model parameters and forcing functions is extracted from existing empirical relationships or from the NOAA World Ocean Atlas. Results are in general agreement with estimates from the literature showing that the relative contribution of aerobic respiration to Cox increases from <10% at shallow SFD to >80% in deep‐sea sediments. Sulfate reduction essentially follows an inversed SFD dependency, the other metabolic pathways (denitrification, Mn and Fe reduction) only adding minor contributions to the global‐scale mineralization of Corg. The hypsometric analysis allows the establishment of relationships between the individual terminal electron acceptor (TEA) fluxes across the sediment‐water interface and their respective contributions to the Corg decomposition process. On a global average, simulation results indicate that sulfate reduction is the dominant metabolic pathway and accounts for approximately 76% of the total Cox, which is higher than reported so far by other authors. The results also demonstrate the importance of bioirrigation for the assessment of global species fluxes. Especially at shallow SFD most of the TEAs enter the sediments via bioirrigation, which complicates the use of concentration profiles for the determination of total TEA fluxes by molecular diffusion. Furthermore, bioirrigation accounts for major losses of reduced species from the sediment to the water column prohibiting their reoxidation inside the sediment. As a result, the total carbon mineralization rate exceeds the total flux of oxygen into the sediment by a factor of 2 globally.
A 19 to 17 Ma amagmatic extension event at the Mid‐Atlantic Ridge: Ultramafic mylonites from the Vema Lithospheric Section
Authors: Cipriani Anna , Bonatti Enrico , Seyler Monique , Brueckner Hannes K. , Brunelli Daniele , Dallai Luigi , Hemming Sidney R. , Ligi Marco , Ottolini Luisa , Turrin Brent D.
Published: October 2009

A >300 km long lithospheric section (Vema Lithospheric Section or VLS) is exposed south of the Vema transform at 11°N in the Atlantic. It is oriented along a seafloor spreading flow line and represents ∼26 Ma of accretion at a single 80 km long segment (EMAR) of the Mid‐Atlantic Ridge. The basal part of the VLS exposes a mantle unit made mostly of relatively undeformed coarse‐grained/porphyroclastic peridotites that were sampled at close intervals. Strongly deformed mylonitic peridotites were found at 14 contiguous sites within a ∼80 km stretch (∼4.7 Ma interval); they are dominant in a time interval of 1.4 Ma, from crustal ages of 16.8 to 18.2 Ma (mylonitic stretch). Some of the mylonites are “dry,” showing anhydrous high‐T deformation, but most contain amphibole. The mylonitic peridotites tend to be less depleted than the porphyroclastic peridotites on the basis of mineral major and trace elements composition, suggesting that the mylonites parent was a subridge mantle that underwent a relatively low degree of melting. The Sr, Nd, and O isotopic composition of the amphiboles is MORB‐like and suggests either that seawater did not contribute to their isotopic signature or that their isotopic ratios re‐equilibrated during fluid circulation in the upper mantle. Four40Ar/39Ar ages, on three amphiboles separated from the peridotites, are close to crustal ages predicted from magnetic anomalies, confirming that the amphiboles formed close to ridge axis. We propose that crustal accretion at the EMAR segment has been mostly symmetrical for the 26 Ma of its recorded history, except for the ∼1.4 Ma interval of prevalent ultramafic mylonites (mylonitic stretch) that may record a period of quasi‐amagmatic asymmetric accretion of oceanic lithosphere close to the ridge–Vema transform intersection, possibly with development of detachment faults. This interval may correspond to a thermal minimum of the subridge upwelling mantle, marking the transition from a period of decreasing to one of increasing mantle melting below the EMAR segment.
Deoxygenation in the oxygen minimum zone of the eastern tropical North Atlantic
Authors: Stramma Lothar , Visbeck Martin , Brandt Peter , Tanhua Toste , Wallace Douglas
Published: October 2009

Observations and model results both indicate increasing oxygen minimum zones (OMZ) in the tropical oceans. Here we report on record low dissolved oxygen minimum concentrations in the eastern tropical North Atlantic in fall of 2008, with less than 40 μmol kg−1 in the core of the OMZ. There we find a deoxygenation rate of ∼0.5 μmol kg−1 a−1 during the last decades on two repeat sections at 7.5 and 11°N. The potential temperature and salinity in the surface and central water layers increased on both sections compared to previous observations. However, in contrast to the oxygen decrease in the core of the OMZ, increasing oxygen concentrations were observed in the central water layer above the OMZ. The observed deoxygenation was thus restricted to the core of the oxygen minimum layer. It remains unclear whether the vertical expansion of the oxygen minimum represents a long time trend or decadal variations.
A thin layer of phytoplankton observed in the Philippine Sea with a synthetic moored array of autonomous gliders
Authors: Hodges Benjamin A. , Fratantoni David M.
Published: October 2009

A synthetic moored array composed of five buoyancy‐propelled autonomous underwater gliders was used to characterize mesoscale variability and phytoplankton distribution in a 100 km × 100 km domain in the Philippine Sea east of Luzon Strait for 10 days in May 2004. The study area, located east of the Kuroshio near the subtropical front, is dominated by strong internal tides, by energetic westward‐propagating mesoscale eddies with azimuthal velocities exceeding 50 cm/s, and by a deep (130 m) maximum in chlorophyll fluorescence. Each glider in the array was instructed to maintain geographic position while repeatedly profiling to 200‐m depth. Good station‐keeping performance enabled the resulting series of vertical profiles to be interpreted in the same manner as a physically moored chain of instruments. Although organized primarily as a demonstration of glider capabilities, this field exercise provides a unique data set for examining biological‐physical interactions in the open ocean. Here we report on the evolution of a thin layer of phytoplankton observed near the deep chlorophyll maximum. Coincident observations of fine structure in temperature and salinity suggest that the thinning process of this layer was driven primarily by physical forcing, most probably vertical shear associated with energetic diurnal internal waves, as opposed to a biological mechanism, such as convergent swimming, grazing, or spatial variation in growth rate.
Using AVHRR lunar observations for NDVI long‐term climate change detection
Authors: Cao Changyong , Vermote Eric , Xiong Xiaoxiong
Published: October 2009

The Moon is believed to be an irrefutably stable calibration reference target for studying climate change from satellites, as demonstrated in several lunar calibration studies of satellite radiometers. However, the potential of using advanced very high resolution radiometer (AVHRR) lunar observations for climate change detection has not been recognized in the past. At the same time, it is known that despite past efforts, there are still significant uncertainties in determining the long‐term trend of climate change using such indices as the Normalized Difference Vegetation Index (NDVI), partly because most AVHRR calibrations to date lack the stability required for climate change detection. This study demonstrates a novel method using the AVHRR lunar band ratio as a stability reference for long‐term NDVI change detection. It shows that despite the incomplete lunar observations and complex space view mechanisms, the AVHRR lunar observations can be used to ensure the stability of the Earth observations at a better than ±1% (1 sigma) level for the lifetime of the AVHRR instrument in the long‐term detection of NDVI trends. This method is compared with the Vermote and Kaufman high‐altitude bright cloud method used by the NASA Long‐Term Data Record (LTDR) project, and preliminary results are very encouraging. The lunar band ratio method has been tested for NOAA 11, 14, and 16 AVHRR and is applicable to all AVHRRs since the early 1980s. It is conceived that the Lunar Band Ratio serves as an important stability reference for ensuring the long‐term confidence for the detection of climate change. The AVHRR lunar band ratio is also useful for deriving the calibration for the problematic band 2 from that of band 1 for establishing a consistent AVHRR fundamental climate data record for a variety of climate applications.
Genetically modified abominations?
Authors: Kwieciński Jakub
Published: October 2009

Our sometimes‐irrational aversion to certain taboos is often rooted in rational, historical explanations. Modern societies have disposed of many historically relevant taboos, but Jakub Kwieciński wonders whether aversion to genetically modified organisms might be one of those that remains
21 Tesla MRI Microimaging of Rat Heart by Superparamagnetic Antimyoglobin Bound Nanoparticles
Authors: Sharma Rakesh
Published: October 2009

Superparamagnetic iron-oxide bound antimyoglobin (SPIOM) characteristics were analyzed at different pH. After injecting SPIOM in heart, ex vivo magnetic resonance microimaging (MRM) technique was used to visualize microvasculature of rat heart including cardiac arteries, veins, cordate tendons attached with valves. The measurement accuracy of ventricles, aorta, vasculature and dimensions of cordate tendons were close to coregistered histology measurements.
Validation of Computed Tomographic Estimates of Intra‐abdominal and Subcutaneous Adipose Tissue in Rats and Mice
Authors: Hillebrand Jacquelien J.G. , Langhans Wolfgang , Geary Nori
Published: October 2009

We characterized the accuracy, sensitivity, and reliability of computed tomographic (CT) estimates of intra‐abdominal (IA) and subcutaneous (S) adipose tissue (AT) in rats and mice using the Aloka rodent CT. Here, we present the first comparisons of CT estimates of the weights of AT samples ex vivo to balance weights of the same samples, of CT estimates of AT weights in vivo to the weights of resected whole‐body AT, and of CT estimates of the weights of pieces of AT inserted IA or S in vivo to the weights of the same pieces ex vivo. CT underestimated AT weight ex vivo by ∼10%, and correction of the automated categorization of IAAT and SAT by Aloka software was required. After these adjustments, correlations (r) of CT estimates and balance weights of resected AT were ≥0.99 in rats and ≥0.92 in mice. CT was impressively sensitive: the 95% probability range of CT estimates of 10,000 mg AT inserts into rats was ±780 mg and of 500 mg inserts into mice, ±20 mg. Scans limited to the abdominal region correlated well (r > 0.90) with whole‐body scan measures of IAAT and SAT in rats and with IAAT, but not SAT (r < 0.80), in mice. Sums of IAAT and SAT correlated well with body weight in rats (r > 0.90), but not in mice (r < 0.80). Coefficients of variance (CVs) of duplicate scans were <5%. We conclude that CT is a valid tool for studies of AT weight in rats and mice, especially when rapid throughput or longitudinal measures are desired.
Linkage and Genome‐wide Association Analysis of Obesity‐related Phenotypes: Association of Weight With the MGAT1 Gene
Authors: Johansson Åsa , Marroni Fabio , Hayward Caroline , Franklin Christopher S. , Kirichenko Anatoly V. , Jonasson Inger , Hicks Andrew A. , Vitart Veronique , Isaacs Aaron , Axenovich Tatiana , Campbell Susan , Floyd Jamie , Hastie Nick , Knott Sara , Lauc Gordan , Pichler Irene , Rotim Kresimir , Wild Sarah H. , Zorkoltseva Irina V. , Wilson James F. , Rudan Igor , Campbell Harry , Pattaro Cristian , Pramstaller Peter , Oostra Ben A. , Wright Alan F. , van Duijn Cornelia M. , Aulchenko Yurii S. , Gyllensten Ulf ,   EUROSPAN Consortium
Published: October 2009

As major risk‐factors for diabetes and cardiovascular diseases, the genetic contribution to obesity‐related traits has been of interest for decades. Recently, a limited number of common genetic variants, which have replicated in different populations, have been identified. One approach to increase the statistical power in genetic mapping studies is to focus on populations with increased levels of linkage disequilibrium (LD) and reduced genetic diversity. We have performed joint linkage and genome‐wide association analyses for weight and BMI in 3,448 (linkage) and 3,925 (association) partly overlapping healthy individuals from five European populations. A total of four chromosomal regions (two for weight and two for BMI) showed suggestive linkage (lod >2.69) either in one of the populations or in the joint data. At the genome‐wide level (nominal P < 1.6 × 10−7, Bonferroni‐adjusted P < 0.05) one single‐nucleotide polymorphism (SNP) (rs12517906) (nominal P = 7.3 × 10−8) was associated with weight, whereas none with BMI. The SNP associated with weight is located close to MGAT1. The monoacylglycerol acyltransferase (MGAT) enzyme family is known to be involved in dietary fat absorption. There was no overlap between the linkage regions and the associated SNPs. Our results show that genetic effects influencing weight and BMI are shared across diverse European populations, even though some of these populations have experienced recent population bottlenecks and/or been affected by genetic drift. The analysis enabled us to identify a new candidate gene, MGAT1, associated with weight in women.
Microsomal prostaglandin E synthase-1 in both cancer cells and hosts contributes to tumour growth, invasion and metastasis
Authors: Kamei Daisuke , Murakami Makoto , Sasaki Yuka , Nakatani Yoshihito , Majima Masataka , Ishikawa Yukio , Ishii Toshiharu , Uematsu Satoshi , Akira Shizuo , Hara Shuntaro , Kudo Ichiro
Published: October 2009

mPGES-1 (microsomal prostaglandin E synthase-1) is a stimulus-inducible enzyme that functions downstream of COX (cyclo-oxygenase)-2 in the PGE2 (prostaglandin E2)-biosynthesis pathway. Although COX-2-derived PGE2 is known to play a role in the development of various tumours, the involvement of mPGES-1 in carcinogenesis has not yet been fully understood. In the present study, we used LLC (Lewis lung carcinoma) cells with mPGES-1 knockdown or overexpression, as well as mPGES-1-deficient mice to examine the roles of cancer cell- and host-associated mPGES-1 in the processes of tumorigenesis in vitro and in vivo. We found that siRNA (small interfering RNA) silencing of mPGES-1 in LLC cells decreased PGE2 synthesis markedly, accompanied by reduced cell proliferation, attenuated Matrigel™ invasiveness and increased extracellular matrix adhesion. Conversely, mPGES-1-overexpressing LLC cells showed increased proliferating and invasive capacities. When implanted subcutaneously into wild-type mice, mPGES-1-silenced cells formed smaller xenograft tumours than did control cells. Furthermore, LLC tumours grafted subcutaneously into mPGES-1-knockout mice grew more slowly than did those grafted into littermate wild-type mice, with concomitant decreases in the density of microvascular networks, the expression of pro-angiogenic vascular endothelial growth factor, and the activity of matrix metalloproteinase-2. Lung metastasis of intravenously injected LLC cells was also significantly less obvious in mPGES-1-null mice than in wild-type mice. Thus our present approaches provide unequivocal evidence for critical roles of the mPGES-1-dependent PGE2 biosynthetic pathway in both cancer cells and host microenvironments in tumour growth and metastasis.
New biochemical approaches towards understanding the Parkinson's disease-associated kinase, LRRK2
Authors: Liou Geou-Yarh , Gallo Kathleen A.
Published: October 2009

Some 5 years ago, it was first discovered that mutations in the gene encoding LRRK2 (leucine-rich repeat protein kinase 2) are tightly linked with a subset of familial PD (Parkinson's disease). Before this genetic association, LRRK2 had never been investigated biochemically. Now it is of utmost importance to establish whether LRRK2 is a bona fide kinase in vitro and in vivo and to understand how mutations of LRRK2 lead to the specific loss of dopaminergic neurons in the substantia nigra to cause PD. In spite of tremendous efforts in the research community, there is no consensus with regard to the magnitude of the enzymatic activity of LRRK2 mutant forms that segregate with PD owing, in part, to the lack of a highly sensitive kinase assay system, and it is still unclear whether an abnormal increase in kinase activity is responsible for LRRK2-associated PD. As described in this issue of the Biochemical Journal, Nichols et al. have developed an extensive set of molecular tools, including an optimized peptide substrate for determining in vitro kinase activity of LRRK2, a set of kinase inhibitors that can be used to explore LRRK2 substrate specificity and biology, a much-needed murine-specific antibody for immunoprecipation, and efficient gene-silencing approaches. In the present commentary, we discuss some of the components of this new LRRK2 biochemical toolbox and how they can be used to better understand this enigmatic kinase.
Characterization of ferromagnetic contacts to carbon nanotubes
Authors: Preusche D. , Schmidmeier S. , Pallecchi E. , Dietrich Ch. , Hüttel A. K. , Zweck J. , Strunk Ch.
Published: October 2009

We present an investigation of different thin-film evaporated ferromagnetic materials for their suitability as electrodes in individual single-wall and multi-wall carbon nanotube-based spin devices. Various electrode shapes made from permalloy (Ni81Fe19), the diluted ferromagnet PdFe, and PdFe/Fe bilayers are studied for both their micromagnetic properties and their contact formation to carbon nanotubes. Suitable devices are tested in low-temperature electron transport measurements, displaying the typical tunneling magnetoresistance of carbon nanotube pseudo-spin valves.
Structural analysis, elemental profiling, and electrical characterization of HfO2 thin films deposited on In0.53Ga0.47As surfaces by atomic layer deposition
Authors: Long R. D. , O’Connor É. , Newcomb S. B. , Monaghan S. , Cherkaoui K. , Casey P. , Hughes G. , Thomas K. K. , Chalvet F. , Povey I. M. , Pemble M. E. , Hurley P. K.
Published: October 2009

In this work results are presented on the structural analysis, chemical composition, and interface state densities of HfO2 thin films deposited by atomic layer deposition (ALD) from Hf[N(CH3)2]4 and H2O on In0.53Ga0.47As/InP substrates. The structural and chemical properties are investigated using high resolution cross-sectional transmission electron microscopy and electron energy loss spectroscopy. HfO2 films (3–15 nm) deposited on In0.53Ga0.47As are studied following a range of surface treatments including in situ treatment of the In0.53Ga0.47As surface by H2S exposure at 50–350 °C immediately following the metal organic vapor phase epitaxy growth of the In0.53Ga0.47As layer, ex situ treatment with (NH4)2S, and deposition on the native oxides of In0.53Ga0.47As with no surface treatment. The structural analysis indicates that the In0.53Ga0.47As surface preparation prior to HfO2 film deposition influences the thickness of the HfO2 film and the interlayer oxide. The complete interfacial self-cleaning of the In0.53Gas0.47As native oxides is not observed using an ALD process based on the Hf[N(CH3)2]4 precursor and H2O. Elemental profiling of the HfO2/In0.53Ga0.47As interface region by electron energy loss spectroscopy reveals an interface oxide layer of 1–2 nm in thickness, which consists primarily of Ga oxides. Using a conductance method approximation, peak interface state densities in the range from 6×1012 to 2×1013 cm−2 eV−1 are estimated depending on the surface preparation.