Palynological variation in Balsaminoid Ericales. II. Balsaminaceae, Tetrameristaceae, Pellicieraceae and general conclusions

BACKGROUND AND AIMS: The objective of this study is to examine the palynological diversity of Balsaminaceae (two genera/+/-1000 species), Tetrameristaceae (two genera/two species) and Pellicieraceae (one genus/one species). The diversity found will be used to infer the systematic value of pollen features within the balsaminoid clade. METHODS: Pollen morphology and ultrastructure of 29 species, representing all families of the balsaminoid clade except Marcgraviaceae, are investigated by means of light microscopy, scanning electron microscopy and transmission electron microscopy. KEY RESULTS: Balsaminaceae pollen is small to medium sized with three to four apertures, which can be either colpate or porate, and a sexine sculpturing varying from coarsely reticulate to almost microreticulate. Tetrameristaceae pollen is small sized, 3-colporate, with a heterobrochate reticulate sculpturing and granules present in the lumina. Pellicieraceae pollen is large sized, 3-colporate with long ectocolpi and a perforate sexine sculpturing with large verrucae. Furthermore, Pelliciera is characterized by the occurrence of aggregated orbicules, while orbicules are completely absent in both Balsaminaceae and Tetrameristaceae. Balsaminaceae pollen differs from the other balsaminoid families due to the occurrence of colpate or porate grains with an oblate to peroblate shape, a very thin foot layer and a lamellated endexine. CONCLUSIONS: From a pollen morphological point of view, Balsaminaceae are completely different from the other balsaminoid families. Therefore, no pollen morphological synapomorphies could be defined for the balsaminoid clade. However, various pollen features were observed that could indicate a possible relationship between Tetrameristaceae, Pellicieraceae and Marcgraviaceae. Despite the palynological similarities in the latter three families, it remains unclear to what extent they are related to each other.     

Noninvasive visualisation of coronary atherosclerosis with multislice computed tomography

Computed Tomography (Electron Beam Tomography: EBCT and multislice computed tomography: MSCT) have recently emerged as non-invasive diagnostic modalities that can quantify coronary calcium which is not only as indicator of coronary risk, but also permits assessment of the coronary lumen. The 16-slice MS-CT, the most recent CT-scanner has a very high resolution, which allows non-invasive assessment of coronary plaques. This has led to a stimulus for further research to assess the role of MSCT coronary plaque imaging in the identification of high-risk coronary plaques.     

Pleiotropic benefit of monomeric and oligomeric flavanols on vascular health--a randomized controlled clinical pilot study

Background

Cardiovascular diseases are expanding to a major social-economic burden in the Western World and undermine man''s deep desire for healthy ageing. Epidemiological studies suggest that flavanol-rich foods (e.g. grapes, wine, chocolate) sustain cardiovascular health. For an evidenced-based application, however, sound clinical data on their efficacy are strongly demanded.

Methods

In a double-blind, randomized, placebo-controlled intervention study we supplemented 28 male smokers with 200 mg per day of monomeric and oligomeric flavanols (MOF) from grape seeds. At baseline, after 4 and 8 weeks we measured macro- and microvascular function and a cluster of systemic biomarkers for major pathological processes occurring in the vasculature: disturbances in lipid metabolism and cellular redox balance, and activation of inflammatory cells and platelets.

Results

In the MOF group serum total cholesterol and LDL decreased significantly (P≤0.05) by 5% (n = 11) and 7% (n = 9), respectively in volunteers with elevated baseline levels. Additionally, after 8 weeks the ratio of glutathione to glutathione disulphide in erythrocytes rose from baseline by 22% (n = 15, P<0.05) in MOF supplemented subjects. We also observed that MOF supplementation exerts anti-inflammatory effects in blood towards ex vivo added bacterial endotoxin and significantly reduces expression of inflammatory genes in leukocytes. Conversely, alterations in macro- and microvascular function, platelet aggregation, plasma levels of nitric oxide surrogates, endothelin-1, C-reactive protein, fibrinogen, prostaglandin F2alpha, plasma antioxidant capacity and gene expression levels of antioxidant defense enzymes did not reach statistical significance after 8 weeks MOF supplementation. However, integrating all measured effects into a global, so-called vascular health index revealed a significant improvement of overall vascular health by MOF compared to placebo (P≤0.05).

Conclusion

Our integrative multi-biomarker approach unveiled the pleiotropic vascular health benefit of an 8 weeks supplementation with 200 mg/d MOF in humans.

Trial Registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT00742287","term_id":"NCT00742287"}}NCT00742287     

GPU accelerated sequence alignment with traceback for GATK HaplotypeCaller

Background

Pairwise sequence alignment is widely used in many biological tools and applications. Existing GPU accelerated implementations mainly focus on calculating optimal alignment score and omit identifying the optimal alignment itself. In GATK HaplotypeCaller (HC), the semi-global pairwise sequence alignment with traceback has so far been difficult to accelerate effectively on GPUs.

Results

We first analyze the characteristics of the semi-global alignment with traceback in GATK HC and then propose a new algorithm that allows for retrieving the optimal alignment efficiently on GPUs. For the first stage, we choose intra-task parallelization model to calculate the position of the optimal alignment score and the backtracking matrix. Moreover, in the first stage, our GPU implementation also records the length of consecutive matches/mismatches in addition to lengths of consecutive insertions and deletions as in the CPU-based implementation. This helps efficiently retrieve the backtracking matrix to obtain the optimal alignment in the second stage.

Conclusions

Experimental results show that our alignment kernel with traceback is up to 80x and 14.14x faster than its CPU counterpart with synthetic datasets and real datasets, respectively. When integrated into GATK HC (alongside a GPU accelerated pair-HMMs forward kernel), the overall acceleration is 2.3x faster than the baseline GATK HC implementation, and 1.34x faster than the GATK HC implementation with the integrated GPU-based pair-HMMs forward algorithm. Although the methods proposed in this paper is to improve the performance of GATK HC, they can also be used in other pairwise alignments and applications.

     

Taxonomic challenges in freshwater fishes: a mismatch between morphology and DNA barcoding in fish of the north‐eastern part of the Congo basin

This study evaluates the utility of DNA barcoding to traditional morphology‐based species identifications for the fish fauna of the north‐eastern Congo basin. We compared DNA sequences (COI) of 821 samples from 206 morphologically identified species. Best match, best close match and all species barcoding analyses resulted in a rather low identification success of 87.5%, 84.5% and 64.1%, respectively. The ratio ‘nearest‐neighbour distance/maximum intraspecific divergence’ was lower than 1 for 26.1% of the samples, indicating possible taxonomic problems. In ten genera, belonging to six families, the number of species inferred from mtDNA data exceeded the number of species identified using morphological features; and in four cases indications of possible synonymy were detected. Finally, the DNA barcodes confirmed previously known identification problems within certain genera of the Clariidae, Cyprinidae and Mormyridae. Our results underscore the large number of taxonomic problems lingering in the taxonomy of the fish fauna of the Congo basin and illustrate why DNA barcodes will contribute to future efforts to compile a reliable taxonomic inventory of the Congo basin fish fauna. Therefore, the obtained barcodes were deposited in the reference barcode library of the Barcode of Life Initiative.     

How Do General Practitioners Conceptualise Advance Care Planning in Their Practice? A Qualitative Study

ObjectivesTo explore how GPs conceptualise advance care planning (ACP), based on their experiences with ACP in their practice.MethodsFive focus groups were held with 36 GPs. Discussions were analysed using a constant comparative method.ResultsFour overarching themes in the conceptualisations of ACP were discerned: (1) the organisation of professional care required to meet patients’ needs, (2) the process of preparing for death and discussing palliative care options, (3) the discussion of care goals and treatment decisions, (4) the completion of advance directives. Within these themes, ACP was both conceptualised in terms of content of ACP and/or in terms of tasks for the GP. A specific task that was mentioned throughout the discussion of the four different themes was (5) the task of actively initiating ACP by the GP versus passively waiting for patients’ initiation.ConclusionsThis study illustrates that GPs have varying conceptualisations of ACP, of which some are more limited to specific aspects of ACP. A shared conceptualisation and agreement on the purpose and goals of ACP is needed to ensure successful implementation, as well as a systematic integration of ACP in routine practice that could lead to a better uptake of all the important elements of ACP.