Multiple independent origins of auto-pollination in tropical orchids (Bulbophyllum) in light of the hypothesis of selfing as an evolutionary dead end

Background: The transition from outcrossing to selfing has long been portrayed as an ‘evolutionary dead end because, first, reversals are unlikely and, second, selfing lineages suffer from higher rates of extinction owing to a reduced potential for adaptation and the accumulation of deleterious mutations. We tested these two predictions in a clade of Madagascan Bulbophyllum orchids (30 spp.), including eight species where auto-pollinating morphs (i.e., selfers, without a ‘rostellum) co-exist with their pollinator-dependent conspecifics (i.e., outcrossers, possessing a rostellum). Specifically, we addressed this issue on the basis of a time-calibrated phylogeny by means of ancestral character reconstructions and within the state-dependent evolution framework of BiSSE (Binary State Speciation and Extinction), which allowed jointly estimating rates of transition, speciation, and extinction between outcrossing and selfing. Results: The eight species capable of selfing occurred in scattered positions across the phylogeny, with two likely originating in the Pliocene (ca. 4.43.1 Ma), one in the Early Pleistocene (ca. 2.4 Ma), and five since the mid-Pleistocene (ca. 1.3 Ma). We infer that this scattered phylogenetic distribution of selfing is best described by models including up to eight independent outcrossing-to-selfing transitions and very low rates of speciation (and either moderate or zero rates of extinction) associated with selfing. Conclusions: The frequent and irreversible outcrossing-to-selfing transitions in Madagascan Bulbophyllum are clearly congruent with the first prediction of the dead end hypothesis. The inability of our study to conclusively reject or support the likewise predicted higher extinction rate in selfing lineages might be explained by a combination of methodological limitations (low statistical power of our BiSSE approach to reliably estimate extinction in small-sized trees) and evolutionary processes (insufficient time elapsed for selfers to go extinct). We suggest that, in these tropical orchids, a simple genetic basis of selfing (via loss of the ‘rostellum) is needed to explain the strikingly recurrent transitions to selfing, perhaps reflecting rapid response to parallel and novel selective environments over Late Quaternary ( 1.3 Ma) time scales.P20726-B03P17124-B0(VLID)243455

Block Crossings in Storyline Visualizations

Storyline visualizations help visualize encounters of the characters in a story over time. Each character is represented by an x-monotone curve that goes from left to right. A meeting is represented by having the characters that participate in the meeting run close together for some time. In order to keep the visual complexity low, rather than just minimizing pairwise crossings of curves, we propose to count block crossings, that is, pairs of intersecting bundles of lines. Our main results are as follows. We show that minimizing the number of block crossings is NP-hard, and we develop, for meetings of bounded size, a constant-factor approximation. We also present two fixed-parameter algorithms and, for meetings of size 2, a greedy heuristic that we evaluate experimentally.Comment: Appears in the Proceedings of the 24th International Symposium on Graph Drawing and Network Visualization (GD 2016

Aldolase-catalyzed C-C bond formation for stereoselective synthesis of nitrogen-containing carbohydrates

Rabbit muscle aldolase was found to catalyze stereoselective aldol addition of dihydroxyacetone phosphate (1) to 3-azido-2-hydroxypropana(2 ). The ketose 1-phosphates were isolated as barium salts, 4a/4b, and hydrolyzed with acid phosphatase. The mixture of 6-azido-6-deoxy-D-fructose(5) and 6-azido-6-deoxy-L-sorbose thus obtained was separated by anion-exchange chromatography. Reductive amination of 5 and 6 yielded, respectively, 1-deoxymannojirimycin (7) and 1-deoxynojirimycin (8), with high diastereoselectivity (>98:2). Analogous aldol addition of 1 to 3-azido-2-hydroxybutanal( 9)( E:Z = 92:8) afforded a mixture of the 6-azido-6,7-dideoxyheptuloses 12 and 13, which contained 88% of 6-azido-6,7-dideoxy-D-altro-heptulose(13 ). After anion-exchange chromatography, 13 was isolated as a 18:82 mixture of the β/α anomers. Reductive amination of pure 13 gave a mixture of 2,6,7-trideoxy-2,6-imino-D-glycero-D-manno and D-gluco-heptitol (14 and 15) (3:2 molar ratio), which likewise was separated by anion-exchange chromatography. If a mixture of 12 and 13 was hydrogenated under identical conditions, 2,6,7-trideoxy-2,6-imino-L-glycero-L-gulo-heptitol(16) could be isolated besides 14 and 15

Histopathological evaluation of Onchocerca volvulus nodules by microscopy and by digital image analysis for the study of macrofilaricidal drug efficacy

BACKGROUND: Novel drugs or drug combinations that kill or permanently sterilize adult MATERIAL AND METHODS: Two expert microscopists independently assessed 605 nodules by direct microscopy. At least two sections with two different stains hematoxylin & eosin (H&E, APR immunostain) of paraffin-embedded, ethanol-fixed whole-nodule cross-sections were analyzed. After variables were identified prone to observer discrepancies, we performed a second study to compare consolidated results for 100 nodules obtained by the two readers by microscopy and by analysis of scanned, high resolution digital images (20x magnification). The last data set analyzed was a quality panel of 100 nodules that has been previously examined by microscopy, and included additional immunostains for RESULTS: The degree of agreement between assessors varied for different parameters. Agreement for female worm counts in nodules was approximately 80%, while agreement regarding female worm viability was 98%. There were no major differences observed between results obtained by microscopy or digital images. Good agreement for important parameters was also observed for the nodules of the quality panel. CONCLUSION: Nodule analysis by experienced microscopists was reproducible with regard to important parameters such as identification of living female worms or detection of normal embryogenesis. Assessments varied more for other parameters, and we recommend continued use of two independent readers for detailed analyzes. Analysis of scanned images provided similar results to direct microscopy. This facilitates training and comparison of nodule findings by readers in different locations. Analysis of high quality digital images that can be viewed remotely should improve the quality and availability of nodule assessments that are primary endpoints for onchocerciasis clinical trials

Semantic segmentation of surgical hyperspectral images under geometric domain shifts

Robust semantic segmentation of intraoperative image data could pave the way for automatic surgical scene understanding and autonomous robotic surgery. Geometric domain shifts, however, although common in real-world open surgeries due to variations in surgical procedures or situs occlusions, remain a topic largely unaddressed in the field. To address this gap in the literature, we (1) present the first analysis of state-of-the-art (SOA) semantic segmentation networks in the presence of geometric out-of-distribution (OOD) data, and (2) address generalizability with a dedicated augmentation technique termed "Organ Transplantation" that we adapted from the general computer vision community. According to a comprehensive validation on six different OOD data sets comprising 600 RGB and hyperspectral imaging (HSI) cubes from 33 pigs semantically annotated with 19 classes, we demonstrate a large performance drop of SOA organ segmentation networks applied to geometric OOD data. Surprisingly, this holds true not only for conventional RGB data (drop of Dice similarity coefficient (DSC) by 46 %) but also for HSI data (drop by 45 %), despite the latter's rich information content per pixel. Using our augmentation scheme improves on the SOA DSC by up to 67 % (RGB) and 90 % (HSI) and renders performance on par with in-distribution performance on real OOD test data. The simplicity and effectiveness of our augmentation scheme makes it a valuable network-independent tool for addressing geometric domain shifts in semantic scene segmentation of intraoperative data. Our code and pre-trained models are available at https://github.com/IMSY-DKFZ/htc.Comment: The first two authors (Jan Sellner and Silvia Seidlitz) contributed equally to this pape

Powder diffraction computed tomography: A combined synchrotron and neutron study

Diffraction and imaging using x-rays and neutrons are widely utilized in different fields of engineering, biology, chemistry and/or materials science. The additional information gained from the diffraction signal by x-ray diffraction and computed tomography (XRD-CT) can give this method a distinct advantage in materials science applications compared to classical tomography. Its active development over the last decade revealed structural details in a non-destructive way with unprecedented sensitivity. In the current contribution an attempt to adopt the well-established XRD-CT technique for neutron diffraction computed tomography (ND-CT) is reported. A specially designed \u27phantom\u27, an object displaying adaptable contrast sufficient for both XRD-CT and ND-CT, was used for method validation. The feasibility of ND-CT is demonstrated, and it is also shown that the ND-CT technique is capable to provide a non-destructive view into the interior of the \u27phantom\u27 delivering structural information consistent with a reference XRD-CT experiment