In situ fiber-optical monitoring of cytosolic calcium in tissue explant cultures

We present a fluorescence-lifetime based method for monitoring cell and tissue activity in situ, during cell culturing and in the presence of a strong autofluorescence background. The miniature fiber-optic probes are easily incorporated in the tight space of a cell culture chamber or in an endoscope. As a first application we monitored the cytosolic calcium levels in porcine tracheal explant cultures using the Calcium Green-5N (CG5N) indicator. Despite the simplicity of the optical setup we are able to detect changes of calcium concentration as small as 2.5 nM, with a monitoring time resolution of less than 1 s.

Crystal structure of the alpha(6)beta(6) holoenzyme of propionyl-coenzyme A carboxylase.

Propionyl-coenzyme A carboxylase (PCC), a mitochondrial biotin-dependent enzyme, is essential for the catabolism of the amino acids Thr, Val, Ile and Met, cholesterol and fatty acids with an odd number of carbon atoms. Deficiencies in PCC activity in humans are linked to the disease propionic acidaemia, an autosomal recessive disorder that can be fatal in infants. The holoenzyme of PCC is an alpha(6)beta(6) dodecamer, with a molecular mass of 750 kDa. The alpha-subunit contains the biotin carboxylase (BC) and biotin carboxyl carrier protein (BCCP) domains, whereas the beta-subunit supplies the carboxyltransferase (CT) activity. Here we report the crystal structure at 3.2-A resolution of a bacterial PCC alpha(6)beta(6) holoenzyme as well as cryo-electron microscopy (cryo-EM) reconstruction at 15-A resolution demonstrating a similar structure for human PCC. The structure defines the overall architecture of PCC and reveals unexpectedly that the alpha-subunits are arranged as monomers in the holoenzyme, decorating a central beta(6) hexamer. A hitherto unrecognized domain in the alpha-subunit, formed by residues between the BC and BCCP domains, is crucial for interactions with the beta-subunit. We have named it the BT domain. The structure reveals for the first time the relative positions of the BC and CT active sites in the holoenzyme. They are separated by approximately 55 A, indicating that the entire BCCP domain must translocate during catalysis. The BCCP domain is located in the active site of the beta-subunit in the current structure, providing insight for its involvement in the CT reaction. The structural information establishes a molecular basis for understanding the large collection of disease-causing mutations in PCC and is relevant for the holoenzymes of other biotin-dependent carboxylases, including 3-methylcrotonyl-CoA carboxylase (MCC) and eukaryotic acetyl-CoA carboxylase (ACC).

The Dissociation of Location and Object Working Memory using fMRI and MEG

Visual working memory (VWM) involves maintaining and processing visual information, often for the purpose of making immediate decisions. Neuroimaging experiments of VWM provide evidence in support of a neural system mainly involving a fronto-parietal neuronal network, but the role of specific brain areas is less clear. A proposal that has recently generated considerable debate suggests that a dissociation of object and location VWM occurs within the prefrontal cortex, in dorsal and ventral regions, respectively. However, re-examination of the relevant literature presents a more robust distribution suggestive of a general caudal-rostral dissociation from occipital and parietal structures, caudally, to prefrontal regions, rostrally, corresponding to location and object memory, respectively. The purpose of the present study was to identify a dissociation of location and object VWM across two imaging methods (magnetoencephalography, MEG, and functional magnetic imaging, fMRI). These two techniques provide complimentary results due the high temporal resolution of MEG and the high spatial resolution of fMRI. The use of identical location and object change detection tasks was employed across techniques and reported for the first time. Moreover, this study is the first to use matched stimulus displays across location and object VWM conditions. The results from these two imaging methods provided convergent evidence of a location and object VWM dissociation favoring a general caudal-rostral rather than the more common prefrontal dorsal-ventral view. Moreover, neural activity across techniques was correlated with behavioral performance for the first time and provided convergent results. This novel approach of combining imaging tools to study memory resulted in robust evidence suggesting a novel interpretation of location and object memory. Accordingly, this study presents a novel context within which to explore the neural substrates of WM across imaging techniques and populations.

A new application of emulsions to measure the gravitational force on antihydrogen

We propose to build and operate a detector based on the emulsion film technology for the measurement of the gravitational acceleration on antimatter, to be performed by the AEgIS experiment (AD6) at CERN. The goal of AEgIS is to test the weak equivalence principle with a precision of 1% on the gravitational acceleration g by measuring the vertical position of the annihilation vertex of antihydrogen atoms after their free fall while moving horizontally in a vacuum pipe. With the emulsion technology developed at the University of Bern we propose to improve the performance of AEgIS by exploiting the superior position resolution of emulsion films over other particle detectors. The idea is to use a new type of emulsion films, especially developed for applications in vacuum, to yield a spatial resolution of the order of one micron in the measurement of the sag of the antihydrogen atoms in the gravitational field. This is an order of magnitude better than what was planned in the original AEgIS proposal.

Continuous Flow Analysis Method for Determination of Dissolved Reactive Phosphorus in Ice Cores

Phosphorus (P) is an essential macronutrient for all living organisms. Phosphorus is often present in nature as the soluble phosphate ion PO43– and has biological, terrestrial, and marine emission sources. Thus PO43– detected in ice cores has the potential to be an important tracer for biological activity in the past. In this study a continuous and highly sensitive absorption method for detection of dissolved reactive phosphorus (DRP) in ice cores has been developed using a molybdate reagent and a 2-m liquid waveguide capillary cell (LWCC). DRP is the soluble form of the nutrient phosphorus, which reacts with molybdate. The method was optimized to meet the low concentrations of DRP in Greenland ice, with a depth resolution of approximately 2 cm and an analytical uncertainty of 1.1 nM (0.1 ppb) PO43–. The method has been applied to segments of a shallow firn core from Northeast Greenland, indicating a mean concentration level of 2.74 nM (0.26 ppb) PO43– for the period 1930–2005 with a standard deviation of 1.37 nM (0.13 ppb) PO43– and values reaching as high as 10.52 nM (1 ppb) PO43–. Similar levels were detected for the period 1771–1823. Based on impurity abundances, dust and biogenic particles were found to be the most likely sources of DRP deposited in Northeast Greenland.

Regulation of angiogenesis by interferon-beta

The purpose of these studies was to investigate the role of interferon-beta (IFN-$\beta$) in angiogenesis. IFN-$\alpha/\beta$ have been implicated in inhibiting a number of steps in the angiogenic pathway. We examined the balance of angiogenesis-regulating molecules in several systems including human infantile hemangiomas, UV-B irradiated mice, and dorsal incisional wound healing in mice. In each system, epidermal hyperplasia and cutaneous angiogenesis were directly related to the expression of positive angiogenic factors (bFGF and VEGF) and inversely related to the expression of endogenous IFN-$\beta.$ The re-expression of IFN-$\beta$ correlated with tumor regression and/or resolution of wound healing. In contrast to control mice, UV-B-induced cutaneous angiogenesis and hyperplasia persisted in IFN-$\alpha/\beta$ receptor knock-out mice. In normal mice, endogenous IFN-$\beta$ was expressed by all differentiated epithelial cells exposed to environmental stimuli. The expression of endogenous IFN-$\beta$ was necessary but insufficient for complete differentiation of epidermal keratinocytes.^ The tumor organ microenvironment can regulate angiogenesis. Human bladder carcinoma cells growing in the bladder wall of nude mice express high levels of bFGF, VEGF, and MMP-9, have higher vascular densities, and produce metastases to lymph nodes and lungs, whereas the same cells growing subcutaneously express less bFGF, VEGF, and MMP-9, have lower vascular densities, and do not metastasize. IFN-$\alpha/\beta$ was found to inhibit bFGF and MMP-9 expression both in vitro and in vivo in human bladder carcinoma cells. Systemic therapy with human IFN-$\alpha$ of human bladder cancer cells growing orthotopically in nude mice, resulted in decreased vascularity, tumorigenicity, and metastasis as compared to saline treated mice. Human bladder cancer cells resistant to the antiproliferative effects of IFN were transfected with the human IFN-$\beta$ gene. Hu-IFN-$\beta$ transfected cells expressed significantly less bFGF protein and gelatinase activity than parental or control-transfected cells and did not grow at ectopic or orthotopic sites. Collectively the data provide direct evidence that IFN-$\alpha/\beta$ can inhibit angiogenesis via down-regulation of angiogenesis-stimulating cytokines. ^

Experimental induction of psychotherapeutically relevant emotional states

Background: Emotion research in neuroscience targets brain structures and processes involved in discrete emotion categories (e.g. anger, fear, sadness) or dimensions (e.g. valence, arousal, approach-avoidance), and usually relies on carefully controlled experimental paradigms with standardized and often simple emotion-eliciting stimuli like e.g. unpleasant pictures. Emotion research in clinical psychology and psychotherapy is often interested in very subtle differences between emotional states, e.g. differences within emotion categories (e.g. assertive, self-protecting vs. rejecting, protesting anger or specific grief vs. global sadness), and/or the biographical, social, situational, or motivational contexts of the emotional experience, which are desired to be minimized in experimental neuroscientific research. Objective: In order to facilitate the experimental and neurophysiological investigation of psychotherapeutically relevant emotional experiences, the present study aims at developing a priming procedure to induce specific, therapeutically and biographically relevant emotional states under controlled experimental conditions. Methodology: N = 50 participants who reported negative feelings towards another close person were randomly assigned to 2 different conditions. They fulfilled 2 different sentence completion tasks that were supposed to prime either ‘therapeutically productive’ or ‘therapeutically unproductive’ emotional states and completed an expressive writing task and several self-report measures of specific emotion-related constructs. The sentence completion task consisted in max. 22 sentence stems drawn from psychotherapy patients’ statements that have been shown to be typical for productive or unproductive therapy sessions. The subjects of the present study completed these sentence stems with regard to their own negative feelings towards the close person. Results: There were a substantial inter-individual variability concerning the number of completed sentences, and significant correlations between number of completed sentences and problem activation in both conditions. No differences were observed in general mood or problem activation between both groups after priming. Descriptively, there were differences between groups concerning emotion regulation aspects. Significant differences between groups in resolution of negative feelings towards the other person were found. Discussion: The results point in the expected direction, however the small sample sizes (after exclusion of several subjects) and low power hinder the detection of convincing significant effects. More data is needed in order to evaluate the efficacy of this emotional priming procedure.

Efficacy of a dilemma-focused intervention for unipolar depression: study protocol for a multicenter randomized controlled trial

BACKGROUND: Depression is one of the more severe and serious health problems because of its morbidity, disabling effects and for its societal and economic burden. Despite the variety of existing pharmacological and psychological treatments, most of the cases evolve with only partial remission, relapse and recurrence.Cognitive models have contributed significantly to the understanding of unipolar depression and its psychological treatment. However, success is only partial and many authors affirm the need to improve those models and also the treatment programs derived from them. One of the issues that requires further elaboration is the difficulty these patients experience in responding to treatment and in maintaining therapeutic gains across time without relapse or recurrence. Our research group has been working on the notion of cognitive conflict viewed as personal dilemmas according to personal construct theory. We use a novel method for identifying those conflicts using the repertory grid technique (RGT). Preliminary results with depressive patients show that about 90% of them have one or more of those conflicts. This fact might explain the blockage and the difficult progress of these patients, especially the more severe and/or chronic. These results justify the need for specific interventions focused on the resolution of these internal conflicts. This study aims to empirically test the hypothesis that an intervention focused on the dilemma(s) specifically detected for each patient will enhance the efficacy of cognitive behavioral therapy (CBT) for depression. DESIGN: A therapy manual for a dilemma-focused intervention will be tested using a randomized clinical trial by comparing the outcome of two treatment conditions: combined group CBT (eight, 2-hour weekly sessions) plus individual dilemma-focused therapy (eight, 1-hour weekly sessions) and CBT alone (eight, 2-hour group weekly sessions plus eight, 1-hour individual weekly sessions). METHOD: Participants are patients aged over 18 years meeting diagnostic criteria for major depressive disorder or dysthymic disorder, with a score of 19 or above on the Beck depression inventory, second edition (BDI-II) and presenting at least one cognitive conflict (implicative dilemma or dilemmatic construct) as assessed using the RGT. The BDI-II is the primary outcome measure, collected at baseline, at the end of therapy, and at 3- and 12-month follow-up; other secondary measures are also used. DISCUSSION: We expect that adding a dilemma-focused intervention to CBT will increase the efficacy of one of the more prestigious therapies for depression, thus resulting in a significant contribution to the psychological treatment of depression. TRIAL REGISTRATION: ISRCTN92443999; ClinicalTrials.gov Identifier: NCT01542957.

Dispersal Modeling of Fish Early Life Stages: Sensitivity with Application to Atlantic Cod in the Western Gulf of Maine

As an initial step in establishing mechanistic relationships between environmental variability and recruitment in Atlantic cod Gadhus morhua along the coast of the western Gulf of Maine, we assessed transport success of larvae from major spawning grounds to nursery areas with particle tracking using the unstructured grid model FVCOM (finite volume coastal ocean model). In coastal areas, dispersal of early planktonic life stages of fish and invertebrate species is highly dependent on the regional dynamics and its variability, which has to be captured by our models. With state-of-the-art forcing for the year 1995, we evaluate the sensitivity of particle dispersal to the timing and location of spawning, the spatial and temporal resolution of the model, and the vertical mixing scheme. A 3 d frequency for the release of particles is necessary to capture the effect of the circulation variability into an averaged dispersal pattern of the spawning season. The analysis of sensitivity to model setup showed that a higher resolution mesh, tidal forcing, and current variability do not change the general pattern of connectivity, but do tend to increase within-site retention. Our results indicate strong downstream connectivity among spawning grounds and higher chances for successful transport from spawning areas closer to the coast. The model run for January egg release indicates 1 to 19 % within-spawning ground retention of initial particles, which may be sufficient to sustain local populations. A systematic sensitivity analysis still needs to be conducted to determine the minimum mesh and forcing resolution that adequately resolves the complex dynamics of the western Gulf of Maine. Other sources of variability, i.e. large-scale upstream forcing and the biological environment, also need to be considered in future studies of the interannual variability in transport and survival of the early life stages of cod.

A climatology of the diurnal variations of stratospheric and mesospheric ozone over Bern, Switzerland

The ground-based radiometer GROMOS, stationed in Bern (47.95° N, 7.44° E), Switzerland, has a unique dataset: it obtains ozone profiles from November 1994 to present with a time resolution of 30 min and equal quality during night- and daytime. Here, we derive a monthly climatology of the daily ozone cycle from 17 yr of GROMOS observation. We present the diurnal ozone variation of the stratosphere and mesosphere. Characterizing the diurnal cycle of stratospheric ozone is important for correct trend estimates of the ozone layer derived from satellite observations. The diurnal ozone cycle from GROMOS is compared to two models: The Whole Atmosphere Community Climate Model (WACCM) and the Hamburg Model of Neutral and Ionized Atmosphere (HAMMONIA). Aura Microwave Limb Sounder (Aura/MLS) ozone data, from night- and daytime overpasses over Bern, have also been included in the comparison. Generally, observation and models show good qualitative agreement: in the lower mesosphere, daytime ozone is for both GROMOS and models around 25% less than nighttime ozone (reference is 22:30–01:30). In the stratosphere, ozone reaches its maximum in the afternoon showing values several percent larger than the midnight value. It is important that diurnal ozone variations of this order are taken into account when merging different data sets for the derivation of long-term ozone trends in the stratosphere. Further, GROMOS and models indicate a seasonal behavior of daily ozone variations in the stratosphere with a larger afternoon maximum during daytime in summer than in winter. At 0.35 hPa, observations from GROMOS and Aura/MLS show a seasonal pattern in diurnal ozone variations with larger relative amplitudes during daytime in winter (−25 ± 5%) than in summer (−18 ± 4%) (compared to mean values around midnight). For the first time, a time series of the diurnal variations in ozone is presented: 17 yr of GROMOS data show strong interannual variations in the diurnal ozone cycle for both the stratosphere and the mesosphere. There are some indications that strong temperature tides can suppress the diurnal variation of stratospheric ozone via the anticorrelation of temperature and ozone. That means the spatio-temporal variability of solar thermal tides seems to affect the diurnal cycle of stratospheric ozone.

Polysomnographic record and successful management of augmentation in restless legs syndrome/Willis-Ekbom disease

BACKGROUND: Dopamine agonists (DAs) represent the first-line treatment in restless legs syndrome (RLS); however, in the long term, a substantial proportion of patients will develop augmentation, which is a severe drug-related exacerbation of symptoms and the main reason for late DA withdrawal. Polysomnographic features and mechanisms underlining augmentation are unknown. No practice guidelines for management of augmentation are available. METHODS: A clinical case series of 24 consecutive outpatients affected by RLS with clinically significant augmentation during treatment with immediate-release DA was performed. All patients underwent a full-night polysomnographic recording during augmentation. A switchover from immediate-release DAs (l-dopa, pramipexole, ropinirole, rotigotine) to the long-acting, extended-release formula of pramipexole was performed. RESULTS: Fifty percent of patients presented more than 15 periodic limb movements per hour of sleep during augmentation, showing longer sleep latency and shorter total sleep time than subjects without periodic limb movements. In all patients, resolution of augmentation was observed within two to four weeks during which immediate-release dopamine agonists could be completely withdrawn. Treatment efficacy of extended-release pramipexole has persisted, thus far, over a mean follow-up interval of 13 months. CONCLUSIONS: Pramipexole extended release could be an easy, safe, and fast pharmacological option to treat augmentation in patients with restless legs syndrome. As such it warrants further prospective and controlled investigations. This observation supports the hypothesis that the duration of action of the drug plays a key role in the mechanism of augmentation.

A climatology of the diurnal variations of stratospheric and mesospheric ozone over Bern, Switzerland

The ground-based radiometer GROMOS, stationed in Bern (47.95° N, 7.44° E), Switzerland, has a unique dataset: it obtains ozone profiles from November 1994 to present with a time resolution of 30 min and equal quality during night- and daytime. Here, we derive a monthly climatology of the daily ozone cycle from 17 yr of GROMOS observation. We present the diurnal ozone variation of the stratosphere and mesosphere. Characterizing the diurnal cycle of stratospheric ozone is important for correct trend estimates of the ozone layer derived from satellite observations. The diurnal ozone cycle from GROMOS is compared to two models: The Whole Atmosphere Community Climate Model (WACCM) and the Hamburg Model of Neutral and Ionized Atmosphere (HAMMONIA). Aura Microwave Limb Sounder (Aura/MLS) ozone data, from night- and daytime overpasses over Bern, have also been included in the comparison. Generally, observation and models show good qualitative agreement: in the lower mesosphere, daytime ozone is for both GROMOS and models around 25% less than nighttime ozone (reference is 22:30–01:30). In the stratosphere, ozone reaches its maximum in the afternoon showing values several percent larger than the midnight value. It is important that diurnal ozone variations of this order are taken into account when merging different data sets for the derivation of long-term ozone trends in the stratosphere. Further, GROMOS and models indicate a seasonal behavior of daily ozone variations in the stratosphere with a larger afternoon maximum during daytime in summer than in winter. At 0.35 hPa, observations from GROMOS and Aura/MLS show a seasonal pattern in diurnal ozone variations with larger relative amplitudes during daytime in winter (−25 ± 5%) than in summer (−18 ± 4%) (compared to mean values around midnight). For the first time, a time series of the diurnal variations in ozone is presented: 17 yr of GROMOS data show strong interannual variations in the diurnal ozone cycle for both the stratosphere and the mesosphere. There are some indications that strong temperature tides can suppress the diurnal variation of stratospheric ozone via the anticorrelation of temperature and ozone. That means the spatio-temporal variability of solar thermal tides seems to affect the diurnal cycle of stratospheric ozone.

Optical and scintillation properties of CsBa2I5:Eu2+

The scintillation and luminescence properties of pure CsBa2I5 and CsBa2I5 doped with 0.5% Eu and 5% Eu were studied between 78 K and 600 K. Single crystals were grown by the vertical Bridgman method from the melt. CsBa2I5:5% Eu showed a light yield of 80,000 photons/MeV, an energy resolution of 2.3% for the 662 key full absorption peak, and an excellent proportional response. Two broad emission bands centered at 400 nm and 600 nm were observed in the radioluminescence spectrum of pure CsBa2I5. The Eu2+ 5d-4f emission band was observed at 430 nm. The radiative lifetime of the Eu2+ excited state was determined as 350 ns. With increasing temperature and Eu concentration the Eu2+ emission shifts to longer wavelengths and its decay time lengthens as a result of self-absorption of the Eu2+ emission. Multiple thermoluminescence glow peaks and a sharp decrease of the light yield at temperatures below 200 K were observed and related to the presence of the charge carrier traps in CsBa2I5:Eu.

Effect of standardized training on the reliability of the Cochrane risk of bias assessment tool: a study protocol

BACKGROUND The Cochrane risk of bias (RoB) tool has been widely embraced by the systematic review community, but several studies have reported that its reliability is low. We aim to investigate whether training of raters, including objective and standardized instructions on how to assess risk of bias, can improve the reliability of this tool. We describe the methods that will be used in this investigation and present an intensive standardized training package for risk of bias assessment that could be used by contributors to the Cochrane Collaboration and other reviewers. METHODS/DESIGN This is a pilot study. We will first perform a systematic literature review to identify randomized clinical trials (RCTs) that will be used for risk of bias assessment. Using the identified RCTs, we will then do a randomized experiment, where raters will be allocated to two different training schemes: minimal training and intensive standardized training. We will calculate the chance-corrected weighted Kappa with 95% confidence intervals to quantify within- and between-group Kappa agreement for each of the domains of the risk of bias tool. To calculate between-group Kappa agreement, we will use risk of bias assessments from pairs of raters after resolution of disagreements. Between-group Kappa agreement will quantify the agreement between the risk of bias assessment of raters in the training groups and the risk of bias assessment of experienced raters. To compare agreement of raters under different training conditions, we will calculate differences between Kappa values with 95% confidence intervals. DISCUSSION This study will investigate whether the reliability of the risk of bias tool can be improved by training raters using standardized instructions for risk of bias assessment. One group of inexperienced raters will receive intensive training on risk of bias assessment and the other will receive minimal training. By including a control group with minimal training, we will attempt to mimic what many review authors commonly have to do, that is-conduct risk of bias assessment in RCTs without much formal training or standardized instructions. If our results indicate that an intense standardized training does improve the reliability of the RoB tool, our study is likely to help improve the quality of risk of bias assessments, which is a central component of evidence synthesis.

The geography of large-scale land acquisitions: Analysing socio-ecological patterns of target contexts in the global South

This paper analyses local geographical contexts targeted by transnational large-scale land acquisitions (>200 ha per deal) in order to understand how emerging patterns of socio-ecological characteristics can be related to processes of large-scale foreign investment in land. Using a sample of 139 land deals georeferenced with high spatial accuracy, we first analyse their target contexts in terms of land cover, population density, accessibility, and indicators for agricultural potential. Three distinct patterns emerge from the analysis: densely populated and easily accessible croplands (35% of land deals); remote forestlands with lower population densities (34% of land deals); and moderately populated and moderately accessible shrub- or grasslands (26% of land deals). These patterns are consistent with processes described in the relevant case study literature, and they each involve distinct types of stakeholders and associated competition over land. We then repeat the often-cited analysis that postulates a link between land investments and target countries with abundant so-called “idle” or “marginal” lands as measured by yield gap and available suitable but uncultivated land; our methods differ from the earlier approach, however, in that we examine local context (10-km radius) rather than countries as a whole. The results show that earlier findings are disputable in terms of concepts, methods, and contents. Further, we reflect on methodologies for exploring linkages between socioecological patterns and land investment processes. Improving and enhancing large datasets of georeferenced land deals is an important next step; at the same time, careful choice of the spatial scale of analysis is crucial for ensuring compatibility between the spatial accuracy of land deal locations and the resolution of available geospatial data layers. Finally, we argue that new approaches and methods must be developed to empirically link socio-ecological patterns in target contexts to key determinants of land investment processes. This would help to improve the validity and the reach of our findings as an input for evidence-informed policy debates.