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The set S n of n × n permutation matrices forms a ranked partially ordered set under the Bruhat order. The Bruhat order on S n can be equivalently defined by means of an entrywise partial order on an associated matrix. Lascoux and Schützenberger proved that the MacNeille completion (the unique smallest lattice containing a partially ordered set) of the Bruhat order on S n is the set A n of n × n alternating sign matrices (ASMs) with a partial order defined by this same entrywise order giving a ranked lattice. We continue investigations of the structure of this lattice. We show that the lattice contains some special dense ASMs defining intervals which are Boolean lattices which together span (in terms of hitting all ranks) the lattice from its minimal element to its maximal element. We also show that the number of ASMs of a given rank is a polynomial in n of degree r and obtain a natural maximal saturated chain. The Hasse diagram of a poset can be regarded as a (directed) graph, and we determine the maximal indegree, outdegree, and total degree of ASMs in A n ; a similar determination was done by Adin and Roichman for the Bruhat order on S n . The join-irreducible permutations in P n are the bigrassmanians, that is, permutations σ such that both σ and its inverse σ − 1 have exactly one descent. The bigrassmanians are also the join-irreducible elements of the lattice on A n . We determine the minimal set of bigrassmanians whose joins are the special dense ASMs. [ABSTRACT FROM AUTHOR]

A flexible one-dimensional model was created in Python to determine the periodic steady state cooling power of an active magnetocaloric regenerator. Several features of the model provide advantages when performing large parametric studies. Geometry, material properties, and operation parameters are read in as input. Fluid flow and magnetization profiles are parameterized, and thermodynamic consistency is forced in magnetocaloric material properties. A dynamic time step is used, and three associated model constants are set to work over a wide range of input parameter combinations. Derivative gain is adjusted to minimize convergence time resulting in an average convergence time reduction of approximately 50%. [ABSTRACT FROM AUTHOR]

The existence of symmetric Hamilton cycle decompositions for complete graphs and cocktail party graphs has been defined and explored in recent work by Akiyama et al., Brualdi and Schroeder, and others. In these works, the notion of symmetry in cocktail party graphs K 2 m − F was integrally tied to the missing 1-factor. In this paper, we generalize the notion of symmetric decompositions in two ways. First, we require only that F is symmetric and show that if F is not the invariant 1-factor under the symmetry action, then K 2 m − F has a symmetric Hamilton cycle decomposition for every m ≥ 2 . Second, we consider other actions as symmetry, apply such definitions to appropriate complete graphs and complete multipartite graphs, and classify the existence of Hamilton cycle decompositions with such symmetry. [ABSTRACT FROM AUTHOR]

Abstract: The definition of edge-adjacency can be generalized in multiple ways to hypergraphs, and extended from that, cycles and Hamilton cycles. One such generalization of a Hamilton cycle is attributed to Kierstead and Katona. In a recent paper by Kuhl and Schroeder, Hamilton cycle decompositions of complete -partite -uniform hypergraphs are discussed, a conjecture was made that the necessary numerical conditions are sufficient, and was shown true for some cases. In this paper, the conjecture is proved using constructions involving Hamming codes, comparisons between the two constructions are made, and a classification of when they are equivalent is shown. [Copyright &y& Elsevier]

Abstract: The purpose of this study was to investigate the effect of parameter changes that can potentially lead to unreliable measurements in fat quantification. Chemical shift imaging was performed using spoiled gradient echo sequences with systematic variations in the following: two-dimensional/three-dimensional sequence, number of echoes, delta echo time, fractional echo factor, slice thickness, repetition time, flip angle, bandwidth, matrix size, flow compensation and field strength. Results indicated no significant (or significant but small) changes in fat fraction with parameter. The significant changes can be attributed to the known effects of T1 bias and two forms of noise bias. [Copyright &y& Elsevier]

Abstract: Degradation of microstructure and phase composition of perovskite-structured Ba0.5Sr0.5Co0.8Fe0.2O3−δ membrane was investigated after exposure to CO2-containing atmospheres in the temperature range of 800–900°C. A carbonate surface layer was formed on the treated membrane. Adjacent to the carbonate layer is an intermediate decomposed zone, consisting of mainly CoO and a Ba–Sr–Co–Fe oxide compound as well as (Ba, Sr)CO3 carbonate. Three different carbonate phases were observed, depending on the annealing conditions. The growth of both the carbonate top layer and the decomposed zone obeys a parabolic rate law, indicating a diffusion-controlled growth mechanism. The growth kinetics and mechanism are insusceptible to the change of partial pressure of oxygen and carbon dioxide under the given conditions. Deviation from the nominal composition was observed in this decomposed zone, which becomes more pronounced closer to the carbonate top layer. The carbonate layer was found to grow outward, which indicates outward diffusion of barium and strontium cations under their respective chemical potential gradient. Full substitution of Co by Fe in this material leads to reduced degradation rate in CO2, which is consistent with the lowering of the chemical potential of the A-site cations. The adverse effect of CO2 was found to be more pronounced at the grain boundaries of the membrane. [Copyright &y& Elsevier]

Abstract: Predicting protein interaction interfaces and protein complexes are two important related problems. For interface prediction, there are a number of tools, such as PPI–Pred, PPISP, PINUP, Promate, and SPPIDER, which predict enzyme–inhibitor interfaces with success rates of 23% to 55% and other interfaces with 10% to 28% on a benchmark dataset of 62 complexes. Here, we develop, metaPPI, a meta server for interface prediction. It significantly improves prediction success rates to 70% for enzyme–inhibitor and 44% for other interfaces. As shown with Promate, predicted interfaces can be used to improve protein docking. Here, we follow this idea using the meta server instead of individual predictions. We confirm that filtering with predicted interfaces significantly improves candidate generation in rigid-body docking based on shape complementarity. Finally, we show that the initial ranking of candidate solutions in rigid-body docking can be further improved for the class of enzyme–inhibitor complexes by a geometrical scoring which rewards deep pockets. A web server of metaPPI is available at scoppi.tu-dresden.de/metappi. The source code of our docking algorithm BDOCK is also available at www.biotec.tu-dresden.de/~bhuang/bdock. [Copyright &y& Elsevier]

Summary Large efforts dedicated to detect somatic alterations across tumor genomes/exomes are expected to produce significant improvements in precision cancer medicine. However, high inter-tumor heterogeneity is a major obstacle to developing and applying therapeutic targeted agents to treat most cancer patients. Here, we offer a comprehensive assessment of the scope of targeted therapeutic agents in a large pan-cancer cohort. We developed an in silico prescription strategy based on identification of the driver alterations in each tumor and their druggability options. Although relatively few tumors are tractable by approved agents following clinical guidelines (5.9%), up to 40.2% could benefit from different repurposing options, and up to 73.3% considering treatments currently under clinical investigation. We also identified 80 therapeutically targetable cancer genes. [ABSTRACT FROM AUTHOR]

Abstract: Corrosion in CO2 and recovery in CO2-free gas of BaCo1−x−y Fe x Nb y O3−δ (x=0.2–0.8, y=0.1–0.5) perovskite membranes were studied at 800–1000°C for potential application in oxyfuel combustion. The oxygen permeation fluxes decreased during exposure to CO2, which became less pronounced with increasing content of Fe and/or Nb. No significant degradation was observed for the cobalt-free composition with high Fe/Nb contents, BaFe0.55Nb0.45O3−δ . A combined analysis of XRD, IR, TGA, and SEM-EDS revealed that degradation in both the phase composition and microstructure with carbonate formation occurred during annealing in CO2, particularly for samples of low Fe/Nb content. The enhanced CO2 resistance of the perovskite due to Fe/Nb doping was found to accord with an increasing average metal–oxygen bonding. The loss of oxygen permeability caused by CO2 was rapidly recovered by switching the sweep gas back to a CO2-free inert gas. Decomposition of carbonate and formation of Ba(Co, Fe) x O y phases took place during the recovery both on the surface and in the decomposed zone. However, the original perovskite phase and dense grain structure was not regenerated. [Copyright &y& Elsevier]

Abstract: The influence of cation substitution on the transition metal oxidation states, oxygen nonstoichiometry and oxygen transport properties of Ba(Co, Fe, Nb)O3− δ perovskites was investigated with room temperature XRD, X-ray absorption near edge structure and high temperature oxygen permeation measurements. Results show that substitution of Fe for Co is accompanied by a decrease in the lattice constant, whereas Nb substitution leads to the opposite trend. With increasing Fe and/or Nb content, the oxygen permeation flux decreases, whereas the apparent activation energy of the oxygen permeation increases. The oxidation state of Co is smaller than +3 and susceptible to the variation of cation composition. In contrast, the oxidation states of Fe and Nb are larger than +3 and close to +5, respectively, and almost independent of the composition. The influence of Fe and Nb contents on the oxygen transport properties is discussed in terms of the oxygen stoichiometry and metal–oxygen bonding. [Copyright &y& Elsevier]

Highlights: [•] TiO2 core/RuO2 shell submicron-particles were prepared via a sequential spray pyrolysis. [•] Spherical particles have the mean particle diameters between 200 and 400nm. [•] This method is promising for synthesis of core–shell and core–multishell materials. [ABSTRACT FROM AUTHOR]

Detection of remote binding site similarity in proteins plays an important role for drug repositioning and off-target effect prediction. Various non-covalent interactions such as hydrogen bonds and van-der-Waals forces drive ligands' molecular recognition by binding sites in proteins. The increasing amount of available structures of protein-small molecule complexes enabled the development of comparative approaches. Several methods have been developed to characterize and compare protein–ligand interaction patterns. Usually implemented as fingerprints, these are mainly used for post processing docking scores and (off-)target prediction. In the latter application, interaction profiles detect similarities in the bound interactions of different ligands and thus identify essential interactions between a protein and its small molecule ligands. Interaction pattern similarity correlates with binding site similarity and is thus contributing to a higher precision in binding site similarity assessment of proteins with distinct global structure. This renders it valuable for existing drug repositioning approaches in structural bioinformatics. Current methods to characterize and compare structure-based interaction patterns – both for protein-small-molecule and protein–protein interactions – as well as their potential in target prediction will be reviewed in this article. The question of how the set of interaction types, flexibility or water-mediated interactions, influence the comparison of interaction patterns will be discussed. Due to the wealth of protein–ligand structures available today, predicted targets can be ranked by comparing their ligand interaction pattern to patterns of the known target. Such knowledge-based methods offer high precision in comparison to methods comparing whole binding sites based on shape and amino acid physicochemical similarity. [ABSTRACT FROM AUTHOR]

Abstract: We initiate a study of the zero–nonzero patterns of alternating sign matrices. We characterize the row (column) sum vectors of these patterns and determine their minimum term rank. In the case of connected alternating sign matrices, we find the minimum number of nonzero entries and characterize the case of equality. We also study symmetric alternating sign matrices, in particular, those with only zeros on the main diagonal. These give rise to alternating signed graphs without loops, and we determine the maximum number of edges in such graphs. We also consider alternating sign matrices whose patterns are maximal within the class of all alternating sign matrices. [Copyright &y& Elsevier]

Abstract: The purpose of this study was to investigate the relationship between liver fat fraction (FF) and diffusion parameters derived from the intravoxel incoherent motion (IVIM) model. Thirty-six subjects with suspected nonalcoholic fatty liver disease underwent diffusion-weighted magnetic resonance imaging with 10 b-values and spoiled gradient recalled echo imaging with six echoes for fat quantification. Correlations were measured between FF, transverse relaxivity (R2⁎), diffusivity (D) and perfusion fraction (f). The primary finding was that no significant correlation was obtained for D vs. FF or f vs. FF. Significant correlations were obtained for D vs. R2⁎ (r=−0.490, P=.002) and f vs. D (r=−0.458, P=.005). The conclusion is that hepatic steatosis does not affect measurement of perfusion or diffusion and therefore is unlikely to confound the use of apparent diffusivity to evaluate hepatic fibrosis. [Copyright &y& Elsevier]

Abstract: For a positive integer, the -term rank of a -matrix is defined to be the largest number of s in with at most one 1 in each column and at most s in each row. Thus the -term rank is the ordinary term rank. We generalize some basic results for the term rank to the -term rank, including a formula for the maximum term rank over a nonempty class of -matrices with the same row sum and column sum vectors. We also show the surprising result that in such a class there exists a matrix which realizes all of the maximum terms ranks between 1 and . [Copyright &y& Elsevier]

Abstract: This study assesses the stability of magnetic resonance liver fat measurements against changes in T2* due to the presence of iron, which is a confound for accurate quantification. The liver T2* was experimentally shortened by intravenous infusion of a super paramagnetic iron oxide contrast agent. Low flip angle multiecho gradient echo sequences were performed before, during and after infusion. The liver fat fraction (FF) was calculated in co-localized regions-of-interest using T2* models that assumed no decay, monoexponential decay and biexponential decay. Results show that, when T2* was neglected, there was a strong underestimation of FF and with monoexponential decay there was a weak overestimation of FF. Curve-fitting using the biexponential decay was found to be problematic. The overestimation of FF may be due to remaining deficiencies in the model, although is unlikely to be important for clinical diagnosis of steatosis. [Copyright &y& Elsevier]

Abstract: In this note we investigate pairs of graphs that can be realized as the row-orthogonal and column-orthogonal graphs of a square (0,1)-matrix, and graphs that can be realized as the row- and column-orthogonal graph of a symmetric (0,1)-matrix. We provide a general construction that shows, in particular, that trees, and all bipartite graphs with a vertex of degree 1 or of diameter at least 9 have such a symmetric realization. [Copyright &y& Elsevier]

Purpose: To prove an expected benefit of concurrent radiochemotherapy (RCT), a two-arm randomized multicentric study was performed. In a subgroup analysis the influence of pretherapeutical hemoglobin level (p-Hb) on survival under locoregional control (SLC) was tested. Patients and Methods: The study included primarily untreated Stage III/IV (International Union Against Cancer [UICC]) oropharyngeal and hypopharyngeal carcinomas. Patients were randomized to receive either hyperfractionated (hf) and accelerated (acc) RCT with two cycles 5-fluorouracil (600 mg/m2/day) and carboplatin (70 mg/m2/day) on Days 1–5 and 29–33 or hf-acc radiotherapy (RT) alone. Total RT dose in both arms was 69.9 Gy in 38 days in concomitant boost technique. Results: After a median follow-up time of 57 months, SLC is significantly better in RCT than in RT (p = 0.01), with median SLC of 17 months and 11 months, respectively. Also overall survival (OS) shows a benefit for RCT (p = 0.016), with a median survival of 23 months for RCT and 16 months for RT. However, the benefit in SLC and OS is not seen in hypopharyngeal carcinomas. In a multivariate analysis of oropharyngeal cancer patients, p-Hb levels lower than 12.7 g/dL resulted in lower SLC compared with higher p-Hb levels up to 13.8 g/dL. P-Hb levels >13.8 g/dL did not further improve SLC. Conclusions: Hyperfractionated-accelerated RCT is superior to hf-acc RT in oropharyngeal carcinomas. P-Hb levels >13.8 g/dL do not further improve SLC. [Copyright &y& Elsevier]