Protein Three Dimensional Nano-Crystallography by Imaging and Diffraction

In this thesis the prospects of electron diffraction and imaging techniques are discussed to solve the structure of three dimensional nano-crystals. These crystals are beyond the scope of current X-ray techniques.Biophysical Structural Chemistr

From correlation to causation: the cruciality of a collectivity in the context of collective action

This paper discusses a longitudinal field study on collective action which aims to move beyond student samples and enhance mundane realism. First we provide a historical overview of the literature on the what (i.e., antecedents of collective action) and the how (i.e., the methods employed) of the social psychology of protest. This historical overview is substantiated with meta-analytical evidence on how these antecedents and methods changed over time. After the historical overview, we provide an empirical illustration of a longitudinal field study in a natural setting―a newly-built Dutch neighbourhood. We assessed changes in informal embeddedness, efficacy, identification, emotions, and grievances over time. Between t0 and t1 the residents protested against the plan to allow a mosque to carrying out their services in a community building in the neighbourhood. We examined the antecedents of protest before [t0] and after [t1] the protests, and whether residents participated or not. We show how a larger social network functions as a catalyst in steering protest participation. Our longitudinal field study replicates basic findings from experimental and survey research. However, it also shows that one antecedent in particular, which is hard to manipulate in the lab (i.e., the size of someone’s social network), proved to be of great importance. We suggest that in overcoming our most pertinent challenge―causality―we should not only remain in our laboratories but also go out and examine real-life situations with people situated in real-life social networks

Spotting Trees with Few Leaves

We show two results related to the Hamiltonicity and $k$-Path algorithms in undirected graphs by Bj\"orklund [FOCS'10], and Bj\"orklund et al., [arXiv'10]. First, we demonstrate that the technique used can be generalized to finding some $k$-vertex tree with $l$ leaves in an $n$-vertex undirected graph in $O^*(1.657^k2^{l/2})$ time. It can be applied as a subroutine to solve the $k$-Internal Spanning Tree ($k$-IST) problem in $O^*(\min(3.455^k, 1.946^n))$ time using polynomial space, improving upon previous algorithms for this problem. In particular, for the first time we break the natural barrier of $O^*(2^n)$. Second, we show that the iterated random bipartition employed by the algorithm can be improved whenever the host graph admits a vertex coloring with few colors; it can be an ordinary proper vertex coloring, a fractional vertex coloring, or a vector coloring. In effect, we show improved bounds for $k$-Path and Hamiltonicity in any graph of maximum degree $\Delta=4,\ldots,12$ or with vector chromatic number at most 8

Coke formation in the oxidative dehydrogenation of ethylbenzene to styrene by TEOM

A packed bed microbalance reactor setup (TEOM-GC) is used to investigate the formation of coke as a function of time-on-stream on gamma-Al2O3 and 3P/SiO2 catalyst samples under different conditions for the ODH reaction of ethylbenzene to styrene. All samples show a linear correlation of the styrene selectivity and yield with the initial coverage of coke. The COX production increases with the coverage of coke. On the 3 wt% P/SiO2 sample, the initial coke build-up is slow and the coke deposition rate increases with time. On alumina-based catalyst samples, a fast initial coke build-up takes place, decreasing with time-on-stream, but the amount of coke does not stabilize. A higher O-2 : EB feed ratio results in more coke, and a higher temperature results in less coke. This coking behaviour of Al2O3 can be described by existing "monolayer-multilayer" models. Further, the coverage of coke on the catalyst varies with the position in the bed. For maximal styrene selectivity, the optimal coverage of coke should be sufficient to convert all O-2, but as low as possible to prevent selectivity loss by COX production. This is in favour of high temperature and low O-2 : EB feed ratios. The optimal coke coverage depends in a complex way on all the parameters: temperature, the O-2 : EB feed ratio, reactant concentrations, and the type of starting material.</p

A 2k2k-Vertex Kernel for Maximum Internal Spanning Tree

We consider the parameterized version of the maximum internal spanning tree problem, which, given an $n$-vertex graph and a parameter $k$, asks for a spanning tree with at least $k$ internal vertices. Fomin et al. [J. Comput. System Sci., 79:1-6] crafted a very ingenious reduction rule, and showed that a simple application of this rule is sufficient to yield a $3k$-vertex kernel. Here we propose a novel way to use the same reduction rule, resulting in an improved $2k$-vertex kernel. Our algorithm applies first a greedy procedure consisting of a sequence of local exchange operations, which ends with a local-optimal spanning tree, and then uses this special tree to find a reducible structure. As a corollary of our kernel, we obtain a deterministic algorithm for the problem running in time $4^k \cdot n^{O(1)}$

Finding and counting vertex-colored subtrees

The problems studied in this article originate from the Graph Motif problem introduced by Lacroix et al. in the context of biological networks. The problem is to decide if a vertex-colored graph has a connected subgraph whose colors equal a given multiset of colors $M$. It is a graph pattern-matching problem variant, where the structure of the occurrence of the pattern is not of interest but the only requirement is the connectedness. Using an algebraic framework recently introduced by Koutis et al., we obtain new FPT algorithms for Graph Motif and variants, with improved running times. We also obtain results on the counting versions of this problem, proving that the counting problem is FPT if M is a set, but becomes W[1]-hard if M is a multiset with two colors. Finally, we present an experimental evaluation of this approach on real datasets, showing that its performance compares favorably with existing software.Comment: Conference version in International Symposium on Mathematical Foundations of Computer Science (MFCS), Brno : Czech Republic (2010) Journal Version in Algorithmic

A straightforward and robust method for introducing human hair as a nucleant into high throughput crystallization trials

Biophysical Structural Chemistr

The cost of emission mitigation by legume crops in French agriculture

Transplantation and immunomodulatio

Performance of factor IX extended half-life product measurements in external quality control assessment programs

Background: Patients with hemophilia B are increasingly treated with extended half-life (EHL) factor IX (FIX) concentrates. For the laboratory, introduction of these EHL concentrates presents a major challenge. To understand the variation in FIX activity levels, all available diagnostic assays need to be directly compared. Methods: The ECAT, UKNEQAS, and RCPAQAP have collaboratively performed a global survey to evaluate the quality of FIX measurements using FIX deficient plasma samples spiked with recombinant FIX (rFIX), rFIXFP, rFIXFc, and N9-GP to levels at typical FIX trough (6 IU/dL) and peak levels (60 IU/dL). Participants were asked to use their routine protocols, using one-stage assays (OSA) or chromogenic assays (CA). Results: In samples spiked with 6 IU/dL product, median (25%-75% range) FIX activity levels (OSA), were 8.0 IU/dL (7.0-9.2) for rFIX, 6.0 IU/dL (4.0-7.1) for rFIXFP, 6.6 IU/dL (5.5-8.0) for rFIXFc, and 4.9 IU/dL (3.5-8.4) for N9-GP. In samples spiked with 60 IU/dL, FIX activity levels measured (using OSA) was 63.0 IU/dL (59.9-67.0) for rFIX, 42.5 IU/dL (28.2-47.0) for rFIXFP, 50.0 IU/dL (45.0-55.0) for rFIXFc, and 34.0 IU/dL (24.8-67.5) for N9-GP. Considerable differences were observed between reagents for all samples. With CA, there was also quite some variation, but no differences between reagents. Conclusion: Large variation is observed in the measurement of FIX activity levels after administration of rFIX and EHL FIX products. For N9-GP, most silica-based assays show especially high levels. It is essential to standardize and improve reliability of measurements of these concentrates as diagnosis and treatment monitoring is based on these results

Comprehensive routine diagnostic screening to identify predictive mutations, gene amplifications, and microsatellite instability in FFPE tumor material

Background: Sensitive and reliable molecular diagnostics is needed to guide therapeutic decisions for cancer patients. Although less material becomes available for testing, genetic markers are rapidly expanding. Simultaneous detection of predictive markers, including mutations, gene amplifications and MSI, will save valuable material, time and costs. Methods: Using a single-molecule molecular inversion probe (smMIP)-based targeted next-generation sequencing (NGS) approach, we developed an NGS panel allowing detection of predictive mutations in 33 genes, gene amplifications of 13 genes and microsatellite instability (MSI) by the evaluation of 55 microsatellite markers. The panel was designed to target all clinically relevant single and multiple nucleotide mutations in routinely available lung cancer, colorectal cancer, melanoma, and gastro-intestinal stromal tumor samples, but is useful for a broader set of tumor types. Results: The smMIP-based NGS panel was successfully validated and cut-off values were established for reliable gene amplification analysis (i.e. relative coverage ≥3) and MSI detection (≥30% unstable loci). After validation, 728 routine diagnostic tumor samples including a broad range of tumor types were sequenced with sufficient sensitivity (2.4% drop-out), including samples with low DNA input (< 10 ng; 88% successful), low tumor purity (5-10%; 77% successful), and cytological material (90% successful). 75% of these tumor samples showed ≥1 (likely) pathogenic mutation, including targetable mutations (e.g. EGFR, BRAF, MET, ERBB2, KIT, PDGFRA). Amplifications were observed in 5.5% of the samples, comprising clinically relevant amplifications (e.g. MET, ERBB2, FGFR1). 1.5% of the tumor samples were classified as MSI-high, including both MSI-prone and non-MSI-prone tumors. Conclusions: We developed a comprehensive workflow for predictive analysis of diagnostic tumor samples. The smMIP-based NGS analysis was shown suitable for limited amounts of histological and cytological material. As smMIP technology allows easy adaptation of panels, this approach can comply with the rapidly expanding molecular markers