Distributed Augmentation, Hypersweeps, and Branch Decomposition of Contour Trees for Scientific Exploration.

Contour trees describe the topology of level sets in scalar fields and are widely used in topological data analysis and visualization. A main challenge of utilizing contour trees for large-scale scientific data is their computation at scale using highperformance computing. To address this challenge, recent work has introduced distributed hierarchical contour trees for distributed computation and storage of contour trees.

A major role of coumarin-dependent ferric iron reduction in strategy I-type iron acquisition in Arabidopsis.

Many non-graminaceous species release various coumarins in response to iron (Fe) deficiency. However, the physiological relevance of these coumarins remains poorly understood. Here, we show that the three enzymes leading to sideretin biosynthesis co-exist in Arabidopsis (Arabidopsis thaliana) epidermal and cortical cells and that the shift to fraxetin at alkaline pH depends on MYB72-mediated repression of CYTOCHROME P450, FAMILY 82, SUBFAMILY C, POLYPEPTIDE 4 (CYP82C4).

ExTreeM: Scalable Augmented Merge Tree Computation via Extremum Graphs.

Over the last decade merge trees have been proven to support a plethora of visualization and analysis tasks since they effectively abstract complex datasets. This paper describes the ExTreeM-Algorithm: A scalable algorithm for the computation of merge trees via extremum graphs. The core idea of ExTreeM is to first derive the extremum graph G of an input scalar field f defined on a cell complex K, and subsequently compute the unaugmented merge tree of f on G instead of K; which are equivalent.

Deep Learning Segmentation of Complex Features in Atomic-Resolution Phase-Contrast Transmission Electron Microscopy Images.

Phase-contrast transmission electron microscopy (TEM) is a powerful tool for imaging the local atomic structure of materials. TEM has been used heavily in studies of defect structures of two-dimensional materials such as monolayer graphene due to its high dose efficiency. However, phase-contrast imaging can produce complex nonlinear contrast, even for weakly scattering samples.

Optimization and Augmentation for Data Parallel Contour Trees.

Contour trees are used for topological data analysis in scientific visualization. While originally computed with serial algorithms, recent work has introduced a vector-parallel algorithm. However, this algorithm is relatively slow for fully augmented contour trees which are needed for many practical data analysis tasks.

Importance of oxidation products in coumarin-mediated Fe(hydr)oxide mineral dissolution.

Due to the low iron solubility in alkaline soils, plants have evolved different iron acquisition strategies, which are either based on ferric iron reduction (strategy I) or complexation by phytosiderophores (strategy II). Recently, a prominent role of coumarins for iron acquisition has been discovered, but details of the respective mechanism remain unclear. Since coumarins may act as iron-binding ligands but also as reductants, various reaction sequences are possible, resulting in different iron species and oxidized coumarins.

Potassium and Calcium Channel Complexes as Novel Targets for Cancer Research.

The intracellular Ca concentration is mainly controlled by Ca channels. These channels form complexes with K channels, which function to amplify Ca flux. In cancer cells, voltage-gated/voltage-dependent Ca channels and non-voltage-gated/voltage-independent Ca channels have been reported to interact with K channels such as Ca-activated K channels and voltage-gated K channels.

Scalable Contour Tree Computation by Data Parallel Peak Pruning.

As data sets grow to exascale, automated data analysis and visualization are increasingly important, to intermediate human understanding and to reduce demands on disk storage via in situ analysis. Trends in architecture of high performance computing systems necessitate analysis algorithms to make effective use of combinations of massively multicore and distributed systems. One of the principal analytic tools is the contour tree, which analyses relationships between contours to identify features of more than local importance.

Dynamic Nested Tracking Graphs.

This work describes an approach for the interactive visual analysis of large-scale simulations, where numerous superlevel set components and their evolution are of primary interest. The approach first derives, at simulation runtime, a specialized Cinema database that consists of images of component groups, and topological abstractions. This database is processed by a novel graph operation-based nested tracking graph algorithm (GO-NTG) that dynamically computes NTGs for component groups based on size, overlap, persistence, and level thresholds.

Sulfated Glycoaminoglycans and Proteoglycan Syndecan-4 Are Involved in Membrane Fixation of LL-37 and Its Pro-Migratory Effect in Breast Cancer Cells.

Initially characterized by its antimicrobial activities, LL-37 has also been shown to significantly contribute to tumor development. On breast cancer cell lines, LL-37 increases intracellular calcium via the TRPV2 channel and their migration via the activation of PI3K/AKT signaling. Its all-d enantiomer d-LL-37 induces similar effects, which excludes a protein-protein interaction of LL-37 in a classic ligand-receptor manner.

Multi-scale visual analysis of time-varying electrocorticography data via clustering of brain regions.

Background: There exists a need for effective and easy-to-use software tools supporting the analysis of complex Electrocorticography (ECoG) data. Understanding how epileptic seizures develop or identifying diagnostic indicators for neurological diseases require the in-depth analysis of neural activity data from ECoG. Such data is multi-scale and is of high spatio-temporal resolution.

Apply or Die: On the Role and Assessment of Application Papers in Visualization.

Application-oriented papers provide an important way to invigorate and cross-pollinate the visualization field, but the exact criteria for judging an application paper's merit remain an open question. This article builds on a panel at the 2016 IEEE Visualization Conference entitled "Application Papers: What Are They, and How Should They Be Evaluated?" that sought to gain a better understanding of prevalent views in the visualization community. This article surveys current trends that favor application papers, reviews the benefits and contributions of this paper type, and discusses their assessment in the review process.

Brain Modulyzer: Interactive Visual Analysis of Functional Brain Connectivity.

We present Brain Modulyzer, an interactive visual exploration tool for functional magnetic resonance imaging (fMRI) brain scans, aimed at analyzing the correlation between different brain regions when resting or when performing mental tasks. Brain Modulyzer combines multiple coordinated views-such as heat maps, node link diagrams and anatomical views-using brushing and linking to provide an anatomical context for brain connectivity data. Integrating methods from graph theory and analysis, e.

SK3/TRPC1/Orai1 complex regulates SOCE-dependent colon cancer cell migration: a novel opportunity to modulate anti-EGFR mAb action by the alkyl-lipid Ohmline.

Background: Barely 10-20% of patients with metastatic colorectal cancer (mCRC) receive a clinical benefit from the use of anti-EGFR monoclonal antibodies (mAbs). We hypothesized that this could depends on their efficiency to reduce Store Operated Calcium Entry (SOCE) that are known to enhance cancer cells.

Results: In the present study, we demonstrate that SOCE promotes migration of colon cancer cell following the formation of a lipid raft ion channel complex composed of TRPC1/Orai1 and SK3 channels.

Activation of TRPV2 and BKCa channels by the LL-37 enantiomers stimulates calcium entry and migration of cancer cells.

Expression of the antimicrobial peptide hCAP18/LL-37 is associated to malignancy in various cancer forms, stimulating cell migration and metastasis. We report that LL-37 induces migration of three cancer cell lines by activating the TRPV2 calcium-permeable channel and recruiting it to pseudopodia through activation of the PI3K/AKT pathway. Ca2+ entry through TRPV2 cooperated with a K+ efflux through the BKCa channel.

and in-transit analysis of cosmological simulations.

Modern cosmological simulations have reached the trillion-element scale, rendering data storage and subsequent analysis formidable tasks. To address this circumstance, we present a new MPI-parallel approach for analysis of simulation data while the simulation runs, as an alternative to the traditional workflow consisting of periodically saving large data sets to disk for subsequent 'offline' analysis. We demonstrate this approach in the compressible gasdynamics/-body code Nyx, a hybrid code based on the BoxLib framework, used for large-scale cosmological simulations.

Comparative study of the oxidation behavior of sulfur-containing amino acids and glutathione by electrochemistry-mass spectrometry in the presence and absence of cisplatin.

Small sulfur-containing compounds are involved in several important biochemical processes, including-but not limited to-redox regulation and drug conjugation/detoxification. While methods for stable redox pairs of such compounds (thiols/disulfides) are available, analytical data on more labile and short-lived redox intermediates are scarce, due to highly challenging analytical requirements. In this study, we employ the direct combination of reagentless electrochemical oxidation and mass spectrometric (EC-MS) identification for monitoring oxidation reactions of cysteine, N-acetylcysteine, methionine, and glutathione under simulated physiological conditions (pH 7.

Antimicrobial Peptide LL-37 Is Both a Substrate of Cathepsins S and K and a Selective Inhibitor of Cathepsin L.

Lung cysteine cathepsins B, K, L, and S contribute to physiological and pathological processes including degradation of antimicrobial peptides/proteins (AMPs) such as surfactant protein SP-A, lactoferrin, secretory leukocyte peptidase inhibitor, and beta-defensins-2 and -3. Substantial amounts of uncleaved LL-37, a 37-mer cationic AMP, were observed in the sputum of patients with cystic fibrosis (CF). Nevertheless LL-37 was degraded after prolonged incubation in CF sputum, and the hydrolysis was blocked by E-64, a selective inhibitor of cysteine proteases.

Optimized sample preparation strategy for the analysis of low molecular mass adducts of a fluorescent cisplatin analogue in cancer cell lines by CE-dual-LIF.

Pt-based anticancer drugs, such as cisplatin, are known to undergo several (bio-)chemical transformation steps after administration. Hydrolysis and adduct formation with small nucleophiles and larger proteins are their most relevant reactions on the way to the final reaction site (DNA), but there are still many open questions regarding the identity and pharmacological relevance of various proposed adducts and intermediates. Furthermore, the role of buffer components or additives, which are inevitably added to samples during any type of analytical measurement, has been frequently neglected in previous studies.

Lipid rafts, KCa/ClCa/Ca2+ channel complexes and EGFR signaling: Novel targets to reduce tumor development by lipids?

Membrane lipid rafts are distinct plasma membrane nanodomains that are enriched with cholesterol, sphingolipids and gangliosides, with occasional presence of saturated fatty acids and phospholipids containing saturated acyl chains. It is well known that they organize receptors (such as Epithelial Growth Factor Receptor), ion channels and their downstream acting molecules to regulate intracellular signaling pathways. Among them are Ca2+ signaling pathways, which are modified in tumor cells and inhibited upon membrane raft disruption.

[Definitions, decision-making and documentation in end of life situations in the intensive care unit].

The present work provides assistance for physicians concerning decision making in clinical borderline situations in the ICU. Based on a structured checklist the two fundamental aspects of any medical decision, the medical indication and the patient's preference are queried in a systematic way. Four possible steps of withholding and/or withdrawing therapy are discussed.

Senescence-induced iron mobilization in source leaves of barley (Hordeum vulgare) plants.

• Retranslocation of iron (Fe) from source leaves to sinks requires soluble Fe binding forms. As much of the Fe is protein-bound and associated with the leaf nitrogen (N) status, we investigated the role of N in Fe mobilization and retranslocation under N deficiency- vs dark-induced leaf senescence. • By excluding Fe retranslocation from the apoplastic root pool, Fe concentrations in source and sink leaves from hydroponically grown barley (Hordeum vulgare) plants were determined in parallel with the concentrations of potential Fe chelators and the expression of genes involved in phytosiderophore biosynthesis.

Visualizing nD point clouds as topological landscape profiles to guide local data analysis.

Analyzing high-dimensional point clouds is a classical challenge in visual analytics. Traditional techniques, such as projections or axis-based techniques, suffer from projection artifacts, occlusion, and visual complexity. We propose to split data analysis into two parts to address these shortcomings.