bluuebunny/crossref_metadata_2025_split huggingface dataset:
A dynamically reconfigurable Fano metamaterial through graphene tuning for switching and sensing applications
Authors: Amin M. , Farhat M. , Baǧcı H. 
Published: July 2013

AbstractWe report on a novel electrically tunable hybrid graphene-gold Fano resonator. The proposed metamaterial consists of a square graphene patch and a square gold frame. The destructive interference between the narrow- and broadband dipolar surface plasmons, which are induced respectively on the surfaces of the graphene patch and the gold frame, leads to the plasmonic equivalent of electromagnetically induced transparency (EIT). The response of the metamaterial is polarization independent due to the symmetry of the structure and its spectral features are shown to be highly controllable by changing a gate voltage applied to the graphene patch. Additionally, effective group index of the device is retrieved and is found to be very high within the EIT window suggesting its potential use in slow light applications. Potential outcomes such as high sensing ability and switching at terahertz frequencies are demonstrated through numerical simulations with realistic parameters.
Composting and Compost
Authors: Stentiford Ed 
Published: July 2013

Composting is a complex biological process which, when engineered and controlled, can deliver a high quality product which returns nutrients to the soil and improves its structure. This chapter looks at the fundamental processes which drive the composting process and then the key features which the process needs to deliver a quality product.
The biological degradation process can be represented by a series of exponential decay terms, each one representing a different component of the feedstock. Researchers have found that, in practice, the decay of most material mixtures can be represented by using two components, one of which has a ‘fast’ rate, e.g. starch and sugars, and the other having a ‘slow’ rate, e.g. cellulose. The decay of typical wastes used in composting, such as domestic refuse and mixtures of sewage sludge and woodchips, can be represented by using two rate constants. The degradation releases heat, the use of which is the key to effective composting, producing pile core temperatures in the 55 to 70°C range. The elevated temperature serves two purposes, firstly to sanitise the material (kill off most of the pathogens) and secondly to maximise the rate of degradation. Each 10°C increase in temperature, up to around 55°C, effectively doubles the reaction rate, making the process far more rapid than if it occurred at ambient temperatures. The key requirements to produce these conditions in a practical situation, i.e. pile structure (to facilitate aeration), available nutrients (primarily the C : N ratio) and the appropriate moisture content, are considered.
Tamoxifen inhibits macrophage FABP4 expression through the combined effects of the GR and PPARγ pathways
Authors: Jiang Meixiu , Zhang Ling , Ma Xingzhe , Hu Wenquan , Chen Yuanli , Yu Miao , Wang Qixue , Li Xiaoju , Yin Zhinan , Zhu Yan , Gao Xiumei , Hajjar David P. , Duan Yajun , Han Jihong 
Published: July 2013

Macrophage adipocyte fatty acid-binding protein (FABP4) plays an important role in foam cell formation and development of atherosclerosis. Tamoxifen inhibits this disease process. In the present study, we determined whether the anti-atherogenic property of tamoxifen was related to its inhibition of macrophage FABP4 expression. We initially observed that tamoxifen inhibited macrophage/foam cell formation, but the inhibition was attenuated when FABP4 expression was selectively inhibited by siRNA. We then observed that tamoxifen and 4-hydroxytamoxifen inhibited FABP4 protein expression in primary macrophages isolated from both the male and female wild-type mice, suggesting that the inhibition is sex-independent. Tamoxifen and 4-hydroxytamoxifen inhibited macrophage FABP4 protein expression induced either by activation of GR (glucocorticoid receptor) or PPARγ (peroxisome-proliferator-activated receptor γ). Associated with the decreased protein expression, Fabp4 mRNA expression and promoter activity were also inhibited by tamoxifen and 4-hydroxytamoxifen, indicating transcriptional regulation. Analysis of promoter activity and EMSA/ChIP assays indicated that tamoxifen and 4-hydroxytamoxifen activated the nGRE (negative glucocorticoid regulatory element), but inhibited the PPRE (PPARγ regulatory element) in the Fabp4 gene. In vivo, administration of tamoxifen to ApoE (apolipoprotein E)-deficient (apoE−/−) mice on a high-fat diet decreased FABP4 expression in macrophages and adipose tissues as well as circulating FABP4 levels. Tamoxifen also inhibited FABP4 protein expression by human blood monocyte-derived macrophages. Taken together, the results of the present study show that tamoxifen inhibited FABP4 expression through the combined effects of GR and PPARγ signalling pathways. Our findings suggest that the inhibition of macrophage FABP4 expression can be attributed to the anti-atherogenic properties of tamoxifen.
Metabolic potential of the organic‐solvent tolerant Pseudomonas putida DOT‐T1E deduced from its annotated genome
Authors: Udaondo Zulema , Molina Lazaro , Daniels Craig , Gómez Manuel J. , Molina‐Henares María A. , Matilla Miguel A. , Roca Amalia , Fernández Matilde , Duque Estrella , Segura Ana , Ramos Juan Luis 
Published: July 2013

SummaryPseudomonas putida DOT‐T1E is an organic solvent tolerant strain capable of degrading aromatic hydrocarbons. Here we report the DOT‐T1E genomic sequence (6 394 153 bp) and its metabolic atlas based on the classification of enzyme activities. The genome encodes for at least 1751 enzymatic reactions that account for the known pattern of C, N, P and S utilization by this strain. Based on the potential of this strain to thrive in the presence of organic solvents and the subclasses of enzymes encoded in the genome, its metabolic map can be drawn and a number of potential biotransformation reactions can be deduced. This information may prove useful for adapting desired reactions to create value‐added products. This bioengineering potential may be realized via direct transformation of substrates, or may require genetic engineering to block an existing pathway, or to re‐organize operons and genes, as well as possibly requiring the recruitment of enzymes from other sources to achieve the desired transformation.
Comparative genome analysis of Lactobacillus casei strains isolated from Actimel and Yakult products reveals marked similarities and points to a common origin
Authors: Douillard François P. , Kant Ravi , Ritari Jarmo , Paulin Lars , Palva Airi , de Vos Willem M. 
Published: July 2013

SummaryThe members of the Lactobacillus genus are widely used in the food and feed industry and show a remarkable ecological adaptability. Several Lactobacillus strains have been marketed as probiotics as they possess health‐promoting properties for the host. In the present study, we used two complementary next‐generation sequencing technologies to deduce the genome sequences of two Lactobacillus casei strains LcA and LcY, which were isolated from the products Actimel and Yakult, commercialized as probiotics. The LcA and LcY draft genomes have, respectively, an estimated size of 3067 and 3082 Mb and a G+C content of 46.3%. Both strains are close to identical to each other and differ by no more than minor chromosomal re‐arrangements, substitutions, insertions and deletions, as evident from the verified presence of one insertion‐deletion (InDel) and only 29 single‐nucleotide polymorphisms (SNPs). In terms of coding capacity, LcA and LcY are predicted to encode a comparable exoproteome, indicating that LcA and LcY are likely to establish similar interactions with human intestinal cells. Moreover, both L. casei LcA and LcY harboured a 59.6 kb plasmid that shared high similarities with plasmids found in other L. casei strains, such as W56 and BD‐II. Further analysis revealed that the L. casei plasmids constitute a good evolution marker within the L. casei species. The plasmids of the LcA and LcY strains are almost identical, as testified by the presence of only three verified SNPs, and share a 3.5 kb region encoding a remnant of a lactose PTS system that is absent from the plasmids of W56 and BD‐II but conserved in another smaller L. casei plasmid (pLC2W). Our observations imply that the results obtained in animal and human experiments performed with the Actimel and Yakult strains can be compared with each other as these strains share a very recent common ancestor.
Liver diseases and aging: friends or foes?
Authors: Sheedfar Fareeba , Biase Stefano Di , Koonen Debby , Vinciguerra Manlio 
Published: July 2013

SummaryThe liver is the only internal human organ capable of natural regeneration of lost tissue, as little as 25% of a liver can regenerate into a whole liver. The process of aging predisposes to hepatic functional and structural impairment and metabolic risk. Therefore, understanding how aging could affect the molecular pathology of liver diseases is particularly important, and few studies to date have tackled this complex process. The most common liver disease, affecting one‐third of the overall population, is nonalcoholic fatty liver disease (NAFLD), characterized by an intrahepatic accumulation of lipids. NAFLD can evolve into nonalcoholic steatohepatitis (NASH) in the presence of oxidative stress and inflammation. NASH is a serious risk factor for disabling and deadly liver diseases such as cirrhosis and hepatocellular carcinoma (HCC). Old age seems to favor NAFLD, NASH, and ultimately HCC, in agreement with the inflamm‐aging theory, according to which aging accrues inflammation. However, the incidence of HCC drops significantly in the very elderly (individuals aged more than 70) and the relationship between the progression of NAFLD/NASH/HCC and very old age is obscure. In this review, we discuss the literature and we argue that there might be an age window in which the liver becomes resistant to the development of injury; this needs to be studied to understand fully the interaction between age and liver diseases from a therapeutic perspective.
The Caenorhabditis elegans LET‐418/Mi2 plays a conserved role in lifespan regulation
Authors: De Vaux Véronique , Pfefferli Catherine , Passannante Myriam , Belhaj Khaoula , von Essen Alina , Sprecher Simon G. , Müller Fritz , Wicky Chantal 
Published: July 2013

SummaryThe evolutionarily conserved nucleosome‐remodeling protein Mi2 is involved in transcriptional repression during development in various model systems, plays a role in embryonic patterning and germ line development, and participates in DNA repair and cell cycle progression. It is the catalytic subunit of the nucleosome remodeling and histone deacetylase (NuRD) complex, a key determinant of differentiation in mammalian embryonic stem cells. In addition, the Drosophila and C. elegans Mi2 homologs participate in another complex, the MEC complex, which also plays an important developmental role in these organisms. Here we show a new and unexpected feature of the C. elegans Mi2 homolog, LET‐418/Mi2. Lack of LET‐418/Mi2 results in longevity and enhanced stress resistance, a feature that we found to be conserved in Drosophila and in Arabidopsis. The fact that depletion of other components of the NuRD and the MEC complexes did not result in longevity suggests that LET‐418 may regulate lifespan in a different molecular context. Genetic interaction studies suggest that let‐418 could act in the germ‐cell‐loss pathway, downstream of kri‐1 and tcer‐1. On the basis of our data and on previous findings showing a role for let‐418 during development, we propose that LET‐418/Mi2 could be part of a system that drives development and reproduction with concomitant life‐reducing effects later in life.
Robot‐assisted laparoscopic vs open radical cystectomy: comparison of complications and perioperative oncological outcomes in 200 patients
Authors: Kader A. Karim , Richards Kyle A. , Krane L. Spencer , Pettus Joseph A. , Smith John J. , Hemal Ashok K. 
Published: July 2013

ObjectiveTo compare perioperative morbidity and oncological outcomes of robot‐assisted laparoscopic radical cystectomy (RARC) to openRC(ORC) at a single institution.Patients and MethodsA retrospective analysis was performed on a consecutive series of patients undergoingRC(100RARCand 100ORC) atWakeForestUniversity with curative intent from 2006 until 2010.Complication data using theClavien system were collected for 90 days postoperatively.Complications and other perioperative outcomes were compared between patient groups.ResultsPatients in both groups had comparable preoperative characteristics.The overall and major complication (Clavien ≥3) rates were lower forRARCpatients at 35 vs 57% (P= 0.001) and 10 vs 22% (P= 0.019), respectively.There were no significant differences between groups for pathological outcomes, including stage, number of nodes harvested or positive margin rates.ConclusionOur data suggest that patients undergoingRARChave perioperative oncological outcomes comparable withORC, with fewer overall or major complications.Definitive claims about comparative outcomes withRARCrequire results from larger, randomised controlled trials.
Can the Leibovich score for clear cell renal cell carcinoma (ccRCC) be accurately reported by a general pathologist?
Authors: Vasdev Nikhil , Altal Yaman , Mafeld Sebastian , Wong Kevin , Chadwick David , Gowda Basavaraj D.R. , Mutton Adrienne , Nagarajan Srikantiah , Bhatti Aftab 
Published: July 2013

Objectives
To evaluate the accuracy of reporting of the Leibovich score (LS) by general pathologists at our centre by comparing the LS in their initial reports with the LS in subsequent review reports by our specialist urological pathologists.
We also assessed whether a revision in the LS subsequently altered the risk group.
Patients and Methods
In all, 54 consecutive patients had had their initial histology after nephrectomy reported by a general pathologist between August 2008 and March 2012.
The histological slides were subsequently re‐reviewed by the two specialist urological pathologists and revised LS were given if appropriate. The cases were then discussed at the Uro‐oncology Multi disciplinary meeting (MDT) and the reason for the revised LS was discussed with the participating panel and reviewed by the uropathologist.
Results
The general pathologists allocated the 54 patients into low‐ (13 patients), intermediate‐ (25) and high‐risk (16) categories.
After a review of the slides by the specialist urological pathologists and discussion at the MDT meeting the LS was revised in 23 patients (42.6%).
The 23 patients who had their LS revised were divided into two groups for the purpose of the present study. On revision of the LS a total of eight patients (14.8%) changed their prognostic group.
The change in the prognostic group in the eight patients was increased from intermediate‐ to high‐risk in four patients.
There was a reduction in the LS in four patients, which was from high‐ to intermediate‐risk category in one patient and intermediate‐ to low‐risk in three patients.
Conclusion
In the present study, histopathology review by a specialist urological pathologist led to a change in LS in 42.6% of cases leading a change in risk grouping in 14.8% of cases. This level of discrepancy is not insignificant. However, the few cases evaluated in the present study does limit robust conclusions and further studies are needed to investigate this issue, so that recommendations can be made to enhance diagnostic accuracy and reproducibility.
Progressive High‐Quality Response Surfaces for Visually Guided Sensitivity Analysis
Authors: Demir I. , Westermann R. 
Published: July 2013

AbstractIn this paper we present a technique which allows us to perform high quality and progressive response surface prediction from multidimensional input samples in an efficient manner. We utilize kriging interpolation to estimate a response surface which minimizes the expectation value and variance of the prediction error. High computational efficiency is achieved by employing parallel matrix and vector operations on the GPU. Our approach differs from previous kriging approaches in that it uses a novel progressive updating scheme for new samples based on blockwise matrix inversion. In this way we can handle very large sample sets to which new samples are continually added. Furthermore, we can monitor the incremental evolution of the surface, providing a means to early terminate the computation when no significant changes have occurred. When the generation of input samples is fast enough, our technique enables steering this generation process interactively to find relevant dependency relations.
Nonparametric Models for Uncertainty Visualization
Authors: Pöthkow Kai , Hege Hans‐Christian 
Published: July 2013

AbstractAn uncertain (scalar, vector, tensor) field is usually perceived as a discrete random field with a priori unknown probability distributions. To compute derived probabilities, e.g. for the occurrence of certain features, an appropriate probabilistic model has to be selected. The majority of previous approaches in uncertainty visualization were restricted to Gaussian fields. In this paper we extend these approaches to nonparametric models, which are much more flexible, as they can represent various types of distributions, including multimodal and skewed ones. We present three examples of nonparametric representations: (a) empirical distributions, (b) histograms and (c) kernel density estimates (KDE). While the first is a direct representation of the ensemble data, the latter two use reconstructed probability density functions of continuous random variables. For KDE we propose an approach to compute valid consistent marginal distributions and to efficiently capture correlations using a principal component transformation. Furthermore, we use automatic bandwidth selection, obtaining a model for probabilistic local feature extraction. The methods are demonstrated by computing probabilities of level crossings, critical points and vortex cores in simulated biofluid dynamics and climate data.
Mass‐Dependent Integral Curves in Unsteady Vector Fields
Authors: Günther Tobias , Kuhn Alexander , Kutz Benjamin , Theisel Holger 
Published: July 2013

AbstractRecent research in flow visualization is focusing on the analysis of time‐dependent, but mass‐less particles. However, in many application scenarios, the mass of particles – and their resulting inertia – is essential in understanding fluid mechanics. This includes critical processes, such as dust particles interacting with aircraft (e.g., brown‐or white‐out effects) and particle separation based on density variation. In this paper, we contribute a generalized description of mass‐dependent particle trajectories and apply existing unsteady flow visualization methods to the mass‐dependent case. This comprises the extension of common concepts, i.e., path lines, streak lines, and time lines. Furthermore, we introduce a new class of integral curves, called mass lines that effectively visualizes mass separation and captures mass‐related features in unsteady flow fields that are inaccessible using traditional methods. We demonstrate the applicability of our method, using a number of real‐world and artificial data sets, in which mass is a crucial parameter. In particular, we focus on the analysis of brown‐out conditions, introduced by a helicopter in forward flight close to the ground.
Vessel Visualization using Curvicircular Feature Aggregation
Authors: Mistelbauer G. , Morar A. , Varchola A. , Schernthaner R. , Baclija I. , Köchl A. , Kanitsar A. , Bruckner S. , Gröller E. 
Published: July 2013

AbstractRadiological investigations are common medical practice for the diagnosis of peripheral vascular diseases. Existing visualization methods such as Curved Planar Reformation (CPR) depict calcifications on vessel walls to determine if blood is still able to flow. While it is possible with conventional CPR methods to examine the whole vessel lumen by rotating around the centerline of a vessel, we propose Curvicircular Feature Aggregation (CFA), which aggregates these rotated images into a single view. By eliminating the need for rotation, vessels can be investigated by inspecting only one image. This method can be used as a guidance and visual analysis tool for treatment planning. We present applications of this technique in the medical domain and give feedback from radiologists.
AmniVis – A System for Qualitative Exploration of Near‐Wall Hemodynamics in Cerebral Aneurysms
Authors: Neugebauer M. , Lawonn K. , Beuing O. , Berg P. , Janiga G. , Preim B. 
Published: July 2013

AbstractThe qualitative exploration of near‐wall hemodynamics in cerebral aneurysms provides important insights for risk assessment. For instance, a direct relation between complex flow patterns and aneurysm formation could be observed. Due to the high complexity of the underlying time‐dependent flow data, the exploration is challenging, in particular for medical researchers not familiar with such data. We present the AmniVis‐Explorer, a system that is designed for the preparation of a qualitative medical study. The provided features were developed in close collaboration with medical researchers involved in the study. This comprises methods for a purposeful selection of surface regions of interest and a novel approach to provide a 2D overview of flow patterns that are represented by streamlines at these regions. Furthermore, we present a specialized interface that supports binary classification of patterns and temporal exploration as well as methods for selection, highlighting and automatic 3D navigation to particular patterns. Based on eight representative datasets, we conducted informal interviews with two bord‐certified radiologists and a flow expert to evaluate the system. It was confirmed that the AmniVis‐Explorer allows for an easy selection, qualitative exploration and classification of near‐wall flow patterns that are represented by streamlines.
AOI Rivers for Visualizing Dynamic Eye Gaze Frequencies
Authors: Burch Michael , Kull Andreas , Weiskopf Daniel 
Published: July 2013

AbstractIt is difficult to explore and analyze eye gaze trajectories for commonly applied visual task solution strategies because such data shows complex spatio‐temporal structure. In particular, the traditional eye gaze plots of scan paths fail for a large number of study participants since these plots lead to much visual clutter. To address this problem we introduce the AOI Rivers technique as a novel interactive visualization method for investigating time‐varying fixation frequencies, transitions between areas of interest (AOIs), and the sequential order of gaze visits to AOIs in a visual stimulus of an eye tracking experiment. To this end, we extend the ThemeRiver technique by influents, effluents, and transitions similar to the concept of Sankey diagrams. The AOI Rivers visualization is complemented by linked spatial views of the data in the form of heatmaps, gaze plots, or display of the visual stimulus. The usefulness of our technique is demonstrated for gaze trajectory data recorded in a previously conducted eye tracking experiment.