Spitsbergen glacial bays macrobenthos – a comparative study

Macrobenthos was studied in seven glacial bays situated along the Spitsbergen coast between 77 and 79°N. The fauna was dominated by deposit-feeding or carnivorous polychaetes and bivalves. Only 4 of 118 species identified in the collected material occurred in all the west Spitsbergen localities examined (the polychaetes Chaetozone/Tharyx sp., Cossura longocirrata, Lumbrinereis fragilis s.l. (sensu lato), and the bivalve Thyasira flexuosa). Clustering of samples showed a difference between the faunas of east and west Spitsbergen; the latter formed two subgroups, localities open to Atlantic waters and those from inner fjord basins. The fauna in open basins was dominated by cosmopolitan species, whereas arctic elements shares were higher in inner basins and predominated in the fauna in Bettybukta (east Spitsbergen). This indicates arctic, relict character of the inner fjords sites. The biomass ranged from 6 to 310 g/m² and Shannon diversities from 0.49 to 2.54. Received: 16 July 1997 / Accepted: 9 February 1998     

Hatching glands in cephalopods – A comparative study

Hatching of embryos from their eggs involves either mechanical and/or chemical support. In particular enzymes are widely used in the animal kingdom to weaken the egg layers and facilitate the embryo's escape. Although numerous morphological and biochemical studies exist on the hatching glands of invertebrates (such as sea urchins, ascidians, insects) and vertebrates (teleosts, amphibians, and mammals), little is known about the morphology of the hatching glands (Hoyle organs) in cephalopod hatchlings.In this study, the internal gland structure and the external appearance of the Hoyle organ are compared among several cephalopod species (Idiosepius pygmaeus; Euprymna scolopes; Sepia officinalis; Loligo gahi; Sepioteuthis lessoniana; Architeuthis sp.; Octopus vulgaris; Tremoctopus gracilis; Argonauta hians). In almost all cases the glandular system is restricted to the posterior part of the dorsal mantle surface. Only Octopus and Argonauta lack a specific glandular structure in this body region and the animals apparently use other mechanisms to penetrate the egg layers.In all decapod species (Idiosepius; Euprymna; Sepia; Loligo; Sepioteuthis; Architeuthis) as well as in Tremoctopus only one specific cell type is present in the Hoyle organ, which synthesizes granular material. The secretory droplets are more or less uniform in electron density in Idiosepius, Euprymna and Tremoctopus but exhibit translucent inclusions in the other decapods. The time of gland development, first synthesis of secretory products and later degeneration after hatching vary between the species.The present study contributes to our knowledge of glandular systems in cephalopods and allows comparison with hatching structures in other invertebrates and vertebrates.     

Hatching glands in cephalopods – A comparative study

Hatching of embryos from their eggs involves either mechanical and/or chemical support. In particular enzymes are widely used in the animal kingdom to weaken the egg layers and facilitate the embryo's escape. Although numerous morphological and biochemical studies exist on the hatching glands of invertebrates (such as sea urchins, ascidians, insects) and vertebrates (teleosts, amphibians, and mammals), little is known about the morphology of the hatching glands (Hoyle organs) in cephalopod hatchlings.     

Physiology of trans-translation deficiency in Bacillus subtilis – a comparative proteomics study

trans-Translation is the most effective ribosome rescue system known in bacteria. While it is essential in some bacteria, Bacillus subtilis possesses two additional alternative ribosome rescue mechanisms that require the proteins BrfA or RqcH. To investigate the physiology of trans-translation deficiency in the model organism B. subtilis, we compared the proteomes of B. subtilis 168 and a ΔssrA mutant in the mid-log phase using gel-free label-free quantitative proteomics. In chemically defined medium, the growth rate of the ssrA deletion mutant was 20% lower than that of B. subtilis 168. An ³⁵S-methionine incorporation assay demonstrated that protein synthesis rates were also lower in the ΔssrA strain. Alternative rescue factors were not detected. Among the 34 proteins overrepresented in the mutant strain were eight chemotaxis proteins. Indeed, both on LB agar and minimal medium the ΔssrA strain showed an altered motility and chemotaxis phenotype. Despite the lower growth rate, in the mutant proteome ribosomal proteins were more abundant while proteins related to amino acid biosynthesis were less abundant than in the parental strain. This overrepresentation of ribosomal proteins coupled with a lower protein synthesis rate and down-regulation of precursor supply reflects the slow ribosome recycling in the trans-translation-deficient mutant.     

Diagnostic utility of musculoskeletal ultrasound in patients with suspected arthritis – a probabilistic approach

Introduction

This study aimed to assess the utility of musculoskeletal ultrasound (MSUS) in patients with joint symptoms using a probabilistic approach.

Methods

One hundred and three patients without prior rheumatologic diagnosis and referred to our clinic for evaluation of inflammatory arthritis were included. Patients were assessed clinically including joint examination, laboratory testing including acute-phase reactants, rheumatoid factor (RF) and anti citrulinated protein antibody (ACPA), and radiographs of hands and feet if clinically indicated. A diagnostic assessment was then performed by the responsible rheumatologist where the probability of a) any inflammatory arthritis and b) rheumatoid arthritis was given on a 5-point scale ranging from 0 to 20% up to 80 to 100% probability. Subsequently, an ultrasound examination of the wrist, metacarpophalangeal (MCP), proximal interphalangeal (PIP) joints 2 to 5 in both hands, metatarsophalangeal (MTP) joints 2 to 5 in both feet and any symptomatic joints was performed and the results presented to the same rheumatologist. The latter then assessed the diagnostic probabilities again, using the same scale.

Results

The rheumatologists’ certainty for presence/absence of inflammatory arthritis and rheumatoid arthritis was increased significantly following ultrasound performance. The proportion of patient for whom diagnostic certainty for inflammatory arthritis was maximal was 33.0% before and 71.8% after musculoskeletal ultrasound (P <0.001). With regard to a diagnosis of RA, the proportions were 31.1% pre-test and 61.2% post-test (P <0.001). MSUS findings agreed with the final diagnosis in 95% of patients.

Conclusion

Musculoskeletal ultrasound, when added to routine rheumatologic investigation, greatly increases the diagnostic certainty in patients referred for the evaluation of inflammatory arthritis. The changes from pre-test to post-test probability quantify the diagnostic utility of musculoskeletal ultrasound in probabilistic terms.     

Percutaneous closure of interatrial communications in adults – prospective embolism prevention study with two- and three-dimensional echocardiography

This review article is aimed at comparing the results of histopathological and clinical imaging studies to assess coronary atherosclerotic plaques in humans. In particular, the gap between the two techniques and its effect on the understanding of the pathophysiological basis of coronary artery disease is critically discussed.     

Policy measures to address bird interactions with power lines – a comparative case study of four countries

Bird mortality caused by electric power lines has been an issue in several countries for more than three decades now. Despite serious efforts by conservationists, government agencies and utility companies assisted by increasing biological and technological knowledge, only a minority of countries has made significant progress in mitigation. In the present article I argue that the policy aspects, which have not been so widely researched so far, have considerable effects on the efficiency of mitigation measures. The problem management methods of four countries—Hungary, Slovakia, South Africa and the USA—are discussed in detail to reveal success criteria. The role of contextual factors, stances and relations of different actors, plus actions and tools applied in the solution process, are demonstrated together with the resulting outcomes. To help strategic planning, I review favourable solution methods (volunteer agreements, legislative steps, mixed solutions, etc.) used in different country-specific contexts, and point out probable consequences of the strategy chosen.     

Benthic fauna in tropical tidal flats – a comparative perspective

Tidal flats extend seaward from mangrove forests along many tropicalcoastlines. This contribution compiles the current knowledge on tropicaltidal flats with regard to species richness, abundance, spatial distributionpatterns and ecological roles taken by major organisms. Tidal flatsencompass a variety of soft-sediment habitats which are inhabited by aspecies-rich fauna. Species numbers are generally higher than in temperatetidal flats, but vary widely between tropical sites where they have not yetbeen fully assessed due to lack of research and taxonomic problems. Theassessment of biodiversity is further complicated by a low species frequency,the small size of macroinfaunal organisms and variations in the occurrence ofspecies between sites. Mean abundance ranges from 1000–2000individuals m^-2, although figures ten times higher have beenrecorded in a mudflat in Costa Rica, and there are great variations in general.Individual densities of small-sized macrofauna are about ten times higher than for larger macrobenthos. A generalized zonation scheme for intertidaldistribution patterns of tropical tidal flat fauna is presented. The comparisonshows that the occurrence of macrofauna and especially of ecosystemengineers varies between sites, which can in turn explain the great variabilityin species abundance patterns recorded in benthic surveys of tidal flatswithin and between regions. This review revealed similarities as well asdifferences between various tropical tidal flats, which underlines the need for further comparative studies to be done, using the same methodology, before generalizations can be made.     

Identification of differentially regulated proteins in a patient with Leber's Congenital Amaurosis – a proteomic study

Background

Proteomics continues to play a critical role in post-genomic science as continued advances in mass spectrometry and analytical chemistry support the separation and identification of increasing numbers of peptides and proteins from their characteristic mass spectra. In order to facilitate the sharing of this data, various standard formats have been, and continue to be, developed. Still not fully mature however, these are not yet able to cope with the increasing number of quantitative proteomic technologies that are being developed.

Results

We propose an extension to the PRIDE and mzData XML schema to accommodate the concept of multiple samples per experiment, and in addition, capture the intensities of the iTRAQ ^TM reporter ions in the entry. A simple Java-client has been developed to capture and convert the raw data from common spectral file formats, which also uses a third-party open source tool for the generation of iTRAQ ^TM reported intensities from Mascot output, into a valid PRIDE XML entry.

Conclusion

We describe an extension to the PRIDE and mzData schemas to enable the capture of quantitative data. Currently this is limited to iTRAQ ^TM data but is readily extensible for other quantitative proteomic technologies. Furthermore, a software tool has been developed which enables conversion from various mass spectrum file formats and corresponding Mascot peptide identifications to PRIDE formatted XML. The tool represents a simple approach to preparing quantitative and qualitative data for submission to repositories such as PRIDE, which is necessary to facilitate data deposition and sharing in public domain database. The software is freely available from http://www.mcisb.org/software/PrideWizard.     

Identification of differentially regulated proteins in a patient with Leber's Congenital Amaurosis – a proteomic study

Background  

To identify the pattern of protein expression in the retina from a patient with Leber's Congenital Amaurosis (LCA) secondary to a mutation in the AIPL1 gene. The retina from one eye of a patient with LCA and 7 control eyes were studied. The tissue was subjected to high resolution two-dimensional gel electrophoresis, image analysis and mass spectrometry, in an effort to identify differentially regulated proteins.     

CMA – a comprehensive Bioconductor package for supervised classification with high dimensional data

Background  

For the last eight years, microarray-based classification has been a major topic in statistics, bioinformatics and biomedicine research. Traditional methods often yield unsatisfactory results or may even be inapplicable in the so-called p ≫ n setting where the number of predictors p by far exceeds the number of observations n, hence the term ill-posed-problem. Careful model selection and evaluation satisfying accepted good-practice standards is a very complex task for statisticians without experience in this area or for scientists with limited statistical background. The multiplicity of available methods for class prediction based on high-dimensional data is an additional practical challenge for inexperienced researchers.     

Thrombin generation is increased in patients with Clostridium difficile colitis – a pilot study

Background: There are only limited data in the literature on the thrombotic risk of patients with Clostridium difficile (CD) colitis, although this disease is widespread throughout the world.

Objective: The aim of this study was to explore thrombin generation in these patients – the best way to evaluate their coagulation.

Methods: A prospective observational study was conducted during 15 months on hospitalized patients with CD colitis. Thrombin generation was performed in platelet-poor plasma using a Ceveron^® alpha analyzer and was compared with a group of volunteer control subjects.

Results: Thirty-three patients and 51 control subjects were enrolled in the study. Two biomarkers – mean velocity index and peak thrombin – were significantly higher in patient group, compared to the control subjects (p?=?0.010, respectively, p?=?0.0395). This pattern of thrombin generation suggests that patients with CD colitis without septic shock have a potential thrombotic risk. The mean velocity index significantly correlated with the estimated related risk of death according to the Charlson age-comorbidity index.

Conclusions: The higher values of thrombin generation suggest that CD colitis increases the thromboembolic risk. The pattern of thrombin generation could identify patients with particularly higher thromboembolic risk. They are potential candidates for thromboprophylaxis strategies and monitorization.     

Visualization of lateral phases in cholesterol and phosphatidylcholine monolayers at the air/water interface — a comparative study with two different reporter molecules

This study has compared two chemically distinct NBD-lipids with regard to their partitioning properties into lateral phases of pure and mixed cholesterol/phosphatidylcholine monolayers. Pure NBD-cholesterol (22-(N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino)-23,24-bisnor-5-cholen-3-ol), which has the NBD-function in the sterol side chain (at carbon 22), gave a liquid-expanded force-area isotherm on water at 22°C (having a compressibility of 0.005 to 0.007 m/mN), although epifluorescence microscopy of the compressed NBD-cholesterol monolayer revealed that it had a solid-like surface texture. When the compressed NBD-cholesterol monolayer was allowed to expand, it fragmented into large flakes (tens to hundreds of μm in width) which eventually dissolved into a liquid state. The force-area isotherm of pure NBD-phosphatidylcholine (1-hexadecanoyl-2-(12-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino)dodecyl-sn-glycero-3-phosphocholine) was also liquid-expanded. When a compressed (30 mN/m) monolayer of NBD-phosphatidylcholine was examined by microscopy, it displayed many bright crystalline spots (about 50 μm across) which appeared to form when the monolayer was allowed to stabilize at this lateral surface pressure. These bright spots disappeared when the monolayer was expanded. When the surface texture of a pure cholesterol monolayer was examined, both probes (at 1 mol%) partitioned very similarly in the sterol monolayer. At low lateral surface pressures (1 and 5 mN/m) the probes appeared to be excluded from the cholesterol phase, forming very bright liquid-like areas against a uniformly black cholesterol phase. At 30 mN/m, NBD-phosphatidylcholine appeared to distribute increasingly into the cholesterol phase, whereas NBD-cholesterol still did not to mix with cholesterol. The characteristic surface texture of the liquid-expanded to liquid-condensed lateral phase transition of pure dipalmitoyl phosphatidylcholine (DPPC) monolayers could be visualized identically with both probes, indicating that these were similarly excluded from the liquid-condensed solid phase of DPPC. Finally, in mixed monolayers containing cholesterol and DPPC (molar ratio 33:67), both probes (at 1 mol%) revealed a similar surface texture of the monolayers (examined at a lateral surface pressure of 0.5 mN/m), suggesting that these partitioned similarly between the different lateral phases present in the mixed monolayer. In conclusion, although the two NBD-probes differed from each other in chemical and physical properties, both acted like ‘impurities’ when admixed into pure or mixed monolayers, and appeared to be equally excluded from lateral phases in which the packing density was high.     

Near-bottom performance of the Acoustic Doppler Velocimeter (ADV) – a comparative study

In a laboratory flume, a comparative study on the near-bottom performance of the Acoustic Doppler Velocimeter (ADV) was conducted. Two different ADV systems were tested for different configurations and two flow velocities (9 cm s⁻¹, 18 cm s⁻¹). The results were compared with synchronous measurements with a Laser Doppler Anemometer (LDA). Near-bottom velocity measurements with the ADV have to be interpreted carefully as the ADV technique underestimates flow velocities in a zone close to the sediment. The height of this zone above the sediment varies with different ADV systems and configurations. The values for nominal sampling volume height (SVH) given by the software often underestimate the true, effective sampling volume heights. Smaller nominal SVH improve the ADV near-bottom performance, but the vertical extent of the zone in which the ADV underestimates flow by more than 20% may be larger than true SVH/2 by a factor of 2 (=true SVH). When the measurement volume approaches the bottom, ADV data quality parameters (signal-to-noise-ratio (SNR) and signal amplitude) exceeding the average ‘open water’ level, are clear indicators that the ADV has begun to underestimate the flow velocity. Unfortunately, this is not a safe indicator for the range of reliable measurements as the ADV may begin to underestimate velocities even with unchanged ‘open water’ data quality parameters. Thus, one can only recommend avoiding measurements below a distance from the bottom that was defined empirically comparing the ADV and the LDA velocity profiles. This distance is 2.5 times nominal sampling volume height for the tested ADV systems and experimental settings.     

Lung hyperinflation and functional exercise capacity in patients with COPD – a three-year longitudinal study

Background

Lung hyperinflation contributes to dyspnea, morbidity and mortality in chronic obstructive pulmonary disease (COPD). The inspiratory-to-total lung capacity (IC/TLC) ratio is a measure of lung hyperinflation and is associated with exercise intolerance. However, knowledge of its effect on longitudinal change in the 6-min walk distance (6MWD) in patients with COPD is scarce. We aimed to study whether the IC/TLC ratio predicts longitudinal change in 6MWD in patients with COPD.

Methods

This prospective cohort study included 389 patients aged 40–75?years with clinically stable COPD in Global Initiative for Chronic Obstructive Lung Disease stages II-IV. The 6MWD was measured at baseline, and after one and 3 years. We performed generalized estimating equation regression analyses to examine predictors for longitudinal change in 6MWD. Predictors at baseline were: IC/TLC ratio, age, gender, pack years, fat mass index (FMI), fat-free mass index (FFMI), number of exacerbations within 12?months prior to inclusion, Charlson index for comorbidities, forced vital capacity (FVC), forced expiratory volume in 1?s (FEV₁), and light and hard self-reported physical activity.

Results

Reduced IC/TLC ratio (p?<?0.001) was a statistically significant predictor for decline in 6MWD. With a 0.1-unit decrease in baseline IC/TLC ratio, the annual decline in 6MWD was 12.7?m (p?<?0.001). Study participants with an IC/TLC ratio in the upper quartiles maintained their 6MWD from baseline to year 3, while it was significantly reduced for the patients with an IC/TLC ratio in the lower quartiles. Absence of light and hard physical activity, increased age and FMI, decreased FEV₁ and FVC, more frequent exacerbations and higher Charlson comorbidity index were also predictors for lower 6MWD at any given time, but did not predict higher rate of decline over the timespan of the study.

Conclusion

Our findings demonstrated that patients with less lung hyperinflation at baseline maintained their functional exercise capacity during the follow-up period, and that it was significantly reduced for patients with increased lung hyperinflation.

     

Long term feeding of Bt-corn – a ten-generation study with quails

Abstract

A ten-generation experiment with growing and laying quails were carried out to test diets with 40 (starter) or 50% (grower, layer) isogenic or transgenic (Bt 176) corn. Feeding of diets containing genetically-modified corn did not significantly influence health and performance of quails nor did it affect DNA-transfer and quality of meat and eggs of quails compared with the isogenic counterpart.     

Breast MRI in nonpalpable breast lesions: a randomized trial with diagnostic and therapeutic outcome – MONET – study

Background

In orthodontic treatment, anchorage control is a fundamental aspect. Usually conventional mechanism for orthodontic anchorage control can be either extraoral or intraoral that is headgear or intermaxillary elastics. Their use are combined with various side effects such as tipping of occlusal plane or undesirable movements of teeth. Especially in cases, where key-teeth are missing, conventional anchorage defined as tooth-borne anchorage will meet limitations. Therefore, the use of endosseous implants for anchorage purposes are increasingly used to achieve positional stability and maximum anchorage.

Methods/Design

The intended study is designed as a prospective, multicenter randomized controlled trial (RCT), comparing and contrasting the effect of early loading of palatal implant therapy versus implant loading after 12 weeks post implantation using the new ortho-implant type II anchor system device (Orthosystem Straumann, Basel, Switzerland). 124 participants, mainly adult males or females, whose diagnoses require temporary stationary implant-based anchorage treatment will be randomized 1:1 to one of two treatment groups: group 1 will receive a loading of implant standard therapy after a healing period of 12 week (gold standard), whereas group 2 will receive an early loading of orthodontic implants within 1 week after implant insertion. Participants will be at least followed for 12 months after implant placement. The primary endpoint is to investigate the behavior of early loaded palatal implants in order to find out if shorter healing periods might be justified to accelerate active orthodontic treatment. Secondary outcomes will focus e.g. on achievement of orthodontic treatment goals and quantity of direct implant-bone interface of removed bone specimens. As tertiary objective, a histologic and microtomography evaluation of all retrieved implants will be performed to obtain data on the performance of the SLA surface in human bone evaluation of all retrieved implants. Additionally, resonance frequency analysis (RFA, Osstell? mentor) will be used at different times for clinically monitoring the implant stability and for histological comparison in order to measure the reliability of the resonance frequency measuring device.

Trial registration

Current Controlled Trials ISRCTN97142521.