Processing of optically-captured digital holograms for three-dimensional display

In digital holography, holograms are usually optically captured and then two-dimensional slices of the reconstruction volume are reconstructed by computer and displayed on a two-dimensional display. When the recording is of a three-dimensional scene then such two-dimensional display becomes restrictive. We outline our progress on capturing larger ranges of perspectives of three-dimensional scenes, and our progress on four approaches to better visualise this three-dimensional information encoded in the digital holograms. The research has been performed within a European Commission funded research project dedicated the capture, processing, transmission, and display of real-world 3D and 4D scenes using digital holography

Stakeholder involvement in systematic reviews: a protocol for a systematic review of methods, outcomes and effects

Background There is an expectation for stakeholders (including patients, the public, health professionals, and others) to be involved in research. Researchers are increasingly recognising that it is good practice to involve stakeholders in systematic reviews. There is currently a lack of evidence about (A) how to do this and (B) the effects, or impact, of such involvement. We aim to create a map of the evidence relating to stakeholder involvement in systematic reviews, and use this evidence to address the two points above. Methods We will complete a mixed-method synthesis of the evidence, first completing a scoping review to create a broad map of evidence relating to stakeholder involvement in systematic reviews, and secondly completing two contingent syntheses. We will use a stepwise approach to searching; the initial step will include comprehensive searches of electronic databases, including CENTRAL, AMED, Embase, Medline, Cinahl and other databases, supplemented with pre-defined hand-searching and contacting authors. Two reviewers will undertake each review task (i.e., screening, data extraction) using standard systematic review processes. For the scoping review, we will include any paper, regardless of publication status or study design, which investigates, reports or discusses involvement in a systematic review. Included papers will be summarised within structured tables. Criteria for judging the focus and comprehensiveness of the description of methods of involvement will be applied, informing which papers are included within the two contingent syntheses. Synthesis A will detail the methods that have been used to involve stakeholders in systematic reviews. Papers from the scoping review that are judged to provide an adequate description of methods or approaches will be included. Details of the methods of involvement will be extracted from included papers using pre-defined headings, presented in tables and described narratively. Synthesis B will include studies that explore the effect of stakeholder involvement on the quality, relevance or impact of a systematic review, as identified from the scoping review. Study quality will be appraised, data extracted and synthesised within tables. Discussion This review should help researchers select, improve and evaluate methods of involving stakeholders in systematic reviews. Review findings will contribute to Cochrane training resources

The actin binding protein drebrin helps to protect against the development of seizure-like events in the entorhinal cortex

The actin binding protein drebrin plays a key role in dendritic spine formation and synaptic plasticity. Decreased drebrin protein levels have been observed in temporal lobe epilepsy, suggesting the involvement of drebrin in the disease. Here we investigated the effect of drebrin knockout on physiological and pathophysiological neuronal network activities in mice by inducing gamma oscillations, involved in higher cognitive functions, and by analyzing pathophysiological epileptiform activity. We found that loss of drebrin increased the emergence of spontaneous gamma oscillations suggesting an increase in neuronal excitability when drebrin is absent. Further analysis showed that although the kainate-induced hippocampal gamma oscillations were unchanged in drebrin deficient mice, seizure like events measured in the entorhinal cortex appeared earlier and more frequently. The results suggest that while drebrin is not essential for normal physiological network activity, it helps to protect against the formation of seizure like activities during pathological conditions. The data indicate that targeting drebrin function could potentially be a preventive or therapeutic strategy for epilepsy treatment

Actively Contracting Bundles of Polar Filaments

We introduce a phenomenological model to study the properties of bundles of polar filaments which interact via active elements. The stability of the homogeneous state, the attractors of the dynamics in the unstable regime and the tensile stress generated in the bundle are discussed. We find that the interaction of parallel filaments can induce unstable behavior and is responsible for active contraction and tension in the bundle. Interaction between antiparallel filaments leads to filament sorting. Our model could apply to simple contractile structures in cells such as stress fibers.Comment: 4 pages, 4 figures, RevTex, to appear in Phys. Rev. Let

Muscle glycogen recovery after exercise measured by13C-magnetic resonance spectroscopy in humans: effect of nutritional solutions

The rate of glycogen resynthesis in human skeletal muscle after glycogen-depleting exercise is known to depend on carbohydrate intake and is reported to reach a platean after an adequate amount of carbohydrate (CHO) consumption. Efforts to maximize the rate of glycogen storage by changing the type and form of CHO, as well as by adding proteins or lipids have yielded inconsistent results. The objective of this study was to assess whether isocaloric addition of proteins and arginine to a CHO diet in the first 4 h after an endurance exercise would increase the rate of glycogen synthesis. The CHO solution, given twice at a 2 h interval according to earlier optimized protocols, contained 1.7 g CHO kgbody weight. The effects of this solution were compared to those of an isocaloric solution containing 1.2 g CHO/kgbody weight plus 0.5 g protein/kgbody weight (including 5 g arginine). Glycogen was measured in quadriceps muscle in vivo with natural abundance13C-magnetic resonance spectroscopy before exercise and twice after exercise, before and at the end of a 4-h period following the intake of one of the solutions. Eight subjects took part in a randomized cross-over trial separated by at least 1 week. Glycogen synthesis was found to be significantly increased with both regimes compared to a zero-caloric placebo diet, but no significant difference in glycogen resynthesis was found between the CHO-only diet and the one supplemented by proteins and arginine. It is estimated that significance would have been reached for an increase of 34%, while the effectively measured synthesis rates only differed by 5

Segregation of COPI-rich and anterograde-cargo-rich domains in endoplasmic-reticulum-to-Golgi transport complexes

AbstractMembrane traffic between the endoplasmic reticulum (ER) and the Golgi complex is regulated by two vesicular coat complexes, COPII and COPI. COPII has been implicated in the selective packaging of anterograde cargo into coated transport vesicles budding from the ER [1]. In mammalian cells, these vesicles coalesce to form tubulo-vesicular transport complexes (TCs), which shuttle anterograde cargo from the ER to the Golgi complex [2–4]. In contrast, COPI-coated vesicles are proposed to mediate recycling of proteins from the Golgi complex to the ER [1,5–7]. The binding of COPI to COPII-coated TCs [3,8,9], however, has led to the proposal that COPI binds to TCs and specifically packages recycling proteins into retrograde vesicles for return to the ER [3,9]. To test this hypothesis, we tracked fluorescently tagged COPI and anterograde-transport markers simultaneously in living cells. COPI predominated on TCs shuttling anterograde cargo to the Golgi complex and was rarely observed on structures moving in directions consistent with retrograde transport. Furthermore, a progressive segregation of COPI-rich domains and anterograde-cargo-rich domains was observed in the TCs. This segregation and the directed motility of COPI-containing TCs were inhibited by antibodies that blocked COPI function. These observations, which are consistent with previous biochemical data [2,9], suggest a role for COPI within TCs en route to the Golgi complex. By sequestering retrograde cargo in the anterograde-directed TCs, COPI couples the sorting of ER recycling proteins [10] to the transport of anterograde cargo

EDGAR 2.0: an enhanced software platform for comparative gene content analyses.

The rapidly increasing availability of microbial genome sequences has led to a growing demand for bioinformatics software tools that support the functional analysis based on the comparison of closely related genomes. By utilizing comparative approaches on gene level it is possible to gain insights into the core genes which represent the set of shared features for a set of organisms under study. Vice versa singleton genes can be identified to elucidate the specific properties of an individual genome. Since initial publication, the EDGAR platform has become one of the most established software tools in the field of comparative genomics. Over the last years, the software has been continuously improved and a large number of new analysis features have been added. For the new version, EDGAR 2.0, the gene orthology estimation approach was newly designed and completely re-implemented. Among other new features, EDGAR 2.0 provides extended phylogenetic analysis features like AAI (Average Amino Acid Identity) and ANI (Average Nucleotide Identity) matrices, genome set size statistics and modernized visualizations like interactive synteny plots or Venn diagrams. Thereby, the software supports a quick and user-friendly survey of evolutionary relationships between microbial genomes and simplifies the process of obtaining new biological insights into their differential gene content. All features are offered to the scientific community via a web-based and therefore platform-independent user interface, which allows easy browsing of precomputed datasets. The web server is accessible at http://edgar.computational.bio

Walks of molecular motors in two and three dimensions

Molecular motors interacting with cytoskeletal filaments undergo peculiar random walks consisting of alternating sequences of directed movements along the filaments and diffusive motion in the surrounding solution. An ensemble of motors is studied which interacts with a single filament in two and three dimensions. The time evolution of the probability distribution for the bound and unbound motors is determined analytically. The diffusion of the motors is strongly enhanced parallel to the filament. The analytical expressions are in excellent agreement with the results of Monte Carlo simulations.Comment: 7 pages, 2 figures, to be published in Europhys. Let