bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biochemical studies of the multicopper oxidase (small laccase) from Streptomyces coelicolor using bioactive phytochemicals and site‐directed mutagenesis
Authors: Sherif Mohammed , Waung Debbie , Korbeci Bihter , Mavisakalyan Valentina , Flick Robert , Brown Greg , Abou‐Zaid Mamdouh , Yakunin Alexander F. , Master Emma R. 
Published: July 2013

SummaryMulticopper oxidases can act on a broad spectrum of phenolic and non‐phenolic compounds. These enzymes include laccases, which are widely distributed in plants and fungi, and were more recently identified in bacteria. Here, we present the results of biochemical and mutational studies of small laccase (SLAC), a multicopper oxidase from Streptomyces coelicolor (SCO6712). In addition to typical laccase substrates, SLAC was tested using phenolic compounds that exhibit antioxidant activity. SLAC showed oxidase activity against 12 of 23 substrates tested, including caffeic acid, ferulic acid, resveratrol, quercetin, morin, kaempferol and myricetin. The kinetic parameters of SLAC were determined for 2,2′‐azino‐bis(3‐ethylbenzthiazoline‐6‐sulphonic acid), 2,6‐dimethoxyphenol, quercetin, morin and myricetin, and maximum reaction rates were observed with myricetin, where kcat and Km values at 60°C were 8.1 (± 0.8) s−1 and 0.9 (± 0.3) mM respectively. SLAC had a broad pH optimum for activity (between pH 4 and 8) and temperature optimum at 60–70°C. It demonstrated remarkable thermostability with a half‐life of over 10 h at 80°C and over 7 h at 90°C. Site‐directed mutagenesis revealed 17 amino acid residues important for SLAC activity including the 10 His residues involved in copper coordination. Most notably, the Y229A and Y230A mutant proteins showed over 10‐fold increase in activity compared with the wild‐type SLAC, which was correlated to higher copper incorporation, while kinetic analyses with S929A predicts localization of this residue near the meta‐position of aromatic substrates.
Solid focal liver lesion characterisation with apparent diffusion coefficient ratios
Authors: Sutherland Tom , Steele Emma , van Tonder Frans , Yap Kelvin 
Published: July 2013

AbstractIntroductionNon‐invasive characterisation of focal liver lesions using diffusion‐weighted imaging (DWI) has been heavily investigated and has shown substantial overlap between benign and malignant lesions. We have calculated a ratio of lesion to normal liver to determine if it improves accuracy for correct categorisation.MethodAll hepatic MRI studies performed between 1st April 2009 and 26th September 2011 were retrospectively reviewed. Patients with solid focal liver lesions in whom a diagnosis could be established and had lesions over 10 mm were included. Haemangiomas, cysts and patients with chronic liver disease were excluded. Apparent diffusion coefficient (ADC) values were calculated for each lesion and adjacent normal liver on breath hold DWI.ResultsTwo hundred fifty‐eight studies were performed and 206 were excluded leaving 52 scans and 58 lesions of which 47 were benign and 11 were malignant. The mean ADC value for benign lesions was 1196.6 (two standard deviations (2SD) = ±399.9) and of benign liver 1101.5 (2SD = ±329.8) with a ratio of benign lesion to benign liver of 1.1005 (2SD = ±0.3783). The mean ADC of malignant lesions was 1153.0 (2SD = ±604.9) and malignant liver of 1080.7 (2SD = ±533.4) giving a malignant lesion to malignant liver ratio of 1.0890 (2SD = ±0.4975). None of these results were statistically significant (all P > 0.5).ConclusionDWI is unable to reliably differentiate solid benign lesions from solid malignant lesions.
Options for African agriculture in an era of high food and energy prices
Authors: Hazell Peter B. R. 
Published: July 2013

AbstractIn a world of high food and energy prices, Africa has an imperative to do a better job feeding itself and ensuring that its people are food secure. At the same time, there is a new business opportunity to work with the private sector in developing the continent's potential to produce significantly more food, raw materials, and biofuels for regional and world markets. A challenge for African policy makers is to find the right balance between a food security and a business agenda, and to ensure that the business agenda engages with large numbers of small farms. Agricultural development requires many things, but the fundamentals for Africa are developing markets, increasing agricultural productivity, and managing volatility. This cannot happen at sufficient scale and speed without strong public sector leadership, enabling policies and investments, and well‐focused implementation strategies.
Climate change, weather shocks, and violent conflict: a critical look at the evidence
Authors: Klomp Jeroen , Bulte Erwin 
Published: July 2013

AbstractWe use cross‐country data to explore whether temperature and rainfall shocks trigger violent conflict, or not. We include a wide range of country and time samples, and explore whether the impact of weather shocks is conditional on income or political regimes. Our overall conclusion is sobering. Notwithstanding the attention this topic has attracted from the media and policy makers, we find little robust evidence linking weather shocks to the onset of conflict.
Long‐term care insurance and market for aged care in Japan: Focusing on the status of care service providers by locality and organisational nature based on survey results
Authors: Kubo Makoto 
Published: July 2013

AimThe purpose of this paper is to examine the status of care service providers by locality and organisational nature.MethodQuestionnaires were sent to 9505 home‐based care service providers registered in the databases of 17 prefectures. The prefectures were selected according to population size.Results Numerous for‐profit providers have newly entered the aged care service market and are operating selectively in Tokyo, a typical example of a metropolitan area. Furthermore, both for‐profit and non‐profit providers have suffered from a shortage of care workers and difficult management conditions, which tend to be more pronounced in Tokyo.ConclusionThe market under long‐term care insurance was successful in terms of the volume of services, but most providers were sceptical as to whether competition in the market could facilitate quality care services.
Women's experience of induction of labor: a mixed methods study
Authors: Henderson Jane , Redshaw Maggie 
Published: July 2013

AbstractObjectiveTo investigate women's experience of induction of labor.DesignMixed methods study.SettingEnglish maternity units.SampleWomen who gave birth in a two‐week period in late 2009, excluding women aged less than 16 years and women whose baby had died.MethodsThis study involved secondary analysis of data from questionnaires relating to care in childbirth. Women's experience of induction of labor was compared with that of women who had spontaneous labor by analysis of responses to structured survey questions. Responses to open questions relating to induction were analysed qualitatively.Main outcome measuresSatisfaction with care, mode of delivery, experience of induction of labor.ResultsThe response rate to the survey was 55.1% representing 5333 women, 20% of whom were induced. Nulliparous women, those with long‐term health problems, or specific pregnancy‐related problems were significantly more likely to be induced. Women who were induced were generally less satisfied with aspects of their care and significantly less likely to have a normal delivery. In the qualitative analysis the main themes that emerged concerned delay, staff shortages, neglect, pain and anxiety in relation to getting the induction started and once it was underway; and in relation to failed induction, the main themes were plans not being followed, wasted effort and pain, and feeling let down and disappointed.ConclusionsWomen having an induction were generally less satisfied with their care, suggesting the need for a focused service for these women to address their additional needs.
Factors attributing to the failure of endometrial sampling in women with postmenopausal bleeding
Authors: Visser Nicole C.M. , Breijer Maria C. , Herman Malou C. , Bekkers Ruud L.M. , Veersema Sebastiaan , Opmeer Brent C. , Mol Ben W.J. , Timmermans Anne , Pijnenborg Johanna M.A. 
Published: July 2013

AbstractObjectiveTo determine which doctor‐ and patient‐related factors affect failure of outpatient endometrial sampling in women with postmenopausal bleeding, and to develop a multivariable prediction model to select women with a high probability of failed sampling.DesignProspective multicenter cohort study.SettingThree teaching hospitals in the Netherlands.PopulationWomen presenting with postmenopausal bleeding with an indication for endometrial sampling.MethodsMultivariable logistic regression was performed to evaluate the impact of doctor's training level and patient's characteristics on failure of sampling.Main outcome measuresFailure of endometrial sampling, classified as technical failure or insufficient tissue for diagnosis.ResultsIn 74 (20.8%) of the 356 included women, sampling technically failed, and in 84 (29.8%) the amount of tissue was insufficient for diagnosis. Nulliparity [odds ratio (OR) 3.8, 95% confidence interval (CI) 1.8–7.9] and advanced age (OR 1.03 per year, 95% CI 1.00–1.06) were associated with technical failure. Advanced age was associated with insufficient sampling (OR 1.04 per year, 95% CI 1.01–1.07), and endometrial thickness >12 mm decreased the chance of insufficient sampling (OR 0.3, 95%CI 0.1–0.8). The prediction model for total failure had an area under the ROC curve of 0.64 (95% CI 0.58–0.70).ConclusionsIn women with postmenopausal bleeding, the failure rate of endometrial sampling is relatively high and is associated with nulliparity and advanced age. Endometrial thickness >12 mm decreased the chance of failure. A multivariable prediction model for total failure based on patient characteristics has a moderate capacity to discriminate between women at high or low risk of failure.
Feasibility and safety of laparoscopic total proctocolectomy with ileal pouch‐anal anastomosis for severe ulcerative colitis
Authors: Kawamura Junichiro , Hasegawa Suguru , Kawada Kenji , Yamaguchi Takashi , Nagayama Satoshi , Matsusue Ryo , Nomura Akinari , Sakai Yoshiharu 
Published: July 2013

AbstractIntroductionThe laparoscopic approach is accepted as a treatment option for patients with ulcerative colitis (UC) who are otherwise in good health. However, its application for patients with severe UC remains controversial. The purpose of this study was to evaluate the feasibility of the laparoscopic approach for severe UC cases. Short‐ and long‐term clinical outcomes after laparoscopic total proctocolectomy with ileal pouch‐anal anastomosis were compared between severe and mild‐to‐intermediate UC patients.MethodsCases treated between March 2002 and September 2010 were retrieved retrospectively from the database of Kyoto Medical Center and Kyoto University Hospital. Intraoperative complications and short‐ and long‐term clinical outcomes were compared.ResultsA total of 31 patients underwent laparoscopic total proctocolectomy with ileal pouch‐anal anastomosis. A comparison of short‐ and long‐term clinical outcomes after one‐ or two‐stage laparoscopic ileal pouch‐anal anastomosis between severe (n = 7) and mild‐to‐intermediate (n = 21) UC patients revealed no significant differences. The proportion of patients with restoration of intestinal continuity did not differ between the groups (severe: 86%, mild to intermediate: 95%; P = 0.69).ConclusionThe present findings suggest that laparoscopic total proctocolectomy with ileal pouch‐anal anastomosis for severe UC patients could be a good alternative approach when performed by an experienced hand.
Evaluation of Attention‐Guiding Video Visualization
Authors: Kurzhals K. , Höferlin M. , Weiskopf D. 
Published: July 2013

AbstractWe investigate four different variants of attention‐guiding video visualization techniques that aim to help users distribute their attention equally among potential objects of interest: bounding box visualization, force‐directed visualization, top‐down visualization, grid visualization. Objects of interest are highlighted by rectangular shapes and then we concentrate on the manipulation of color, motion, and size. We conducted a controlled laboratory user study (n=25) to compare the four visualization techniques and the unmodified video material as baseline. We evaluated task performance and distribution of attention in a search task. These two properties become especially important when video material with numerous objects has to be observed. The distribution of attention was measured by eye tracking. Our results show that a more even distribution of attention between the objects can be achieved by attention‐guiding visualization, compared to unmodified video. Many participants feel more comfortable when they look at bounding boxes and the grid, but improvements in search task performance could not be confirmed.
Visual Analysis of Set Relations in a Graph
Authors: Xu Panpan , Du Fan , Cao Nan , Shi Conglei , Zhou Hong , Qu Huamin 
Published: July 2013

AbstractMany applications can be modeled as a graph with additional attributes attached to the nodes. For example, a graph can be used to model the relationship of people in a social media website or a bibliographical dataset. Meanwhile, additional information is often available, such as the topics people are interested in and the music they listen to. Based on this additional information, different set relationships may exist among people. Revealing the set relationships in a network can help people gain social insight and better understand their roles within a community. In this paper, we present a visualization system for exploring set relations in a graph. Our system is designed to reveal three different relationships simultaneously: the social relationship of people, the set relationship among people's items of interest, and the similarity relationship of the items. We propose two novel visualization designs: a) a glyph‐based visualization to reveal people's set relationships in the context of their social networks; b) an integration of visual links and a contour map to show people and their items of interest which are clustered into different groups. The effectiveness of the designs has been demonstrated by the case studies on two representative datasets including one from a social music service website and another from an academic collaboration network.
An Interactive Analysis and Exploration Tool for Epigenomic Data
Authors: Younesy H. , Nielsen C.B. , Möller T. , Alder O. , Cullum R. , Lorincz M.C. , Karimi M.M. , Jones S.J.M. 
Published: July 2013

AbstractIn this design study, we present an analysis and abstraction of the data and tasks related to the domain of epigenomics, and the design and implementation of an interactive tool to facilitate data analysis and visualization in this domain. Epigenomic data can be grouped into subsets either by k‐means clustering or by querying for combinations of presence or absence of signal (on/off) in different epigenomic experiments. These steps can easily be interleaved and the comparison of different workflows is explicitly supported. We took special care to contain the exponential expansion of possible on/off combinations by creating a novel querying interface. An interactive heat map facilitates the exploration and comparison of different clusters. We validated our iterative design by working closely with two groups of biologists on different biological problems. Both groups quickly found new insight into their data as well as claimed that our tool would save them several hours or days of work over using existing tools.
Complexity Plots
Authors: Thiyagalingam Jeyarajan , Walton Simon , Duffy Brian , Trefethen Anne , Chen Min 
Published: July 2013

AbstractIn this paper, we present a novel visualization technique for assisting the observation and analysis of algorithmic complexity. In comparison with conventional line graphs, this new technique is not sensitive to the units of measurement, allowing multivariate data series of different physical qualities (e.g., time, space and energy) to be juxtaposed together conveniently and consistently. It supports multivariate visualization as well as uncertainty visualization. It enables users to focus on algorithm categorization by complexity classes, while reducing visual impact caused by constants and algorithmic components that are insignificant to complexity analysis. It provides an effective means for observing the algorithmic complexity of programs with a mixture of algorithms and black‐box software through visualization. Through two case studies, we demonstrate the effectiveness of complexity plots in complexity analysis in research, education and application.
TAMRESH – Tensor Approximation Multiresolution Hierarchy for Interactive Volume Visualization
Authors: Suter S.K. , Makhynia M. , Pajarola R. 
Published: July 2013

AbstractInteractive visual analysis of large and complex volume datasets is an ongoing and challenging problem. We tackle this challenge in the context of state‐of‐the‐art out‐of‐core multiresolution volume rendering by introducing a novel hierarchical tensor approximation (TA) volume visualization approach. The TA framework allows us (a) to use a rank‐truncated basis for compact volume representation, (b) to visualize features at multiple scales, and (c) to visualize the data at multiple resolutions. In this paper, we exploit the special properties of the TA factor matrix bases and define a novel multiscale and multiresolution volume rendering hierarchy. Different from previous approaches, to represent one volume dataset we use but one set of global bases (TA factor matrices) to reconstruct at all resolution levels and feature scales. In particular, we propose a coupling of multiscalable feature visualization and multiresolution DVR through the properties of global TA bases. We demonstrate our novel TA multiresolution hierarchy based volume representation and visualization on a number of μCT volume datasets.
Gestaltlines
Authors: Brandes Ulrik , Nick Bobo , Rockstroh Brigitte , Steffen Astrid 
Published: July 2013

AbstractWe propose a general technique to visualize multivariate data sequences. It is based on a symbiotic combination of three powerful concepts from information visualization: sparklines, glyphs and gestalt theory. By visualizing several well‐known data sets in new ways we first demonstrate how explicit consideration of gestalt principles can be used to leverage visual perception capabilities for the identification of patterns such as trends, periodicities, change points, or outliers. A more detailed case study with complex and noisy data from a psychological experiment then demonstrates how basic design ideas for gestaltlines can be applied in less controlled, and thus more realistic, situations. The case study is complemented with reports on feedback from domain experts and a user study, both indicating that gestaltlines can be a convenient and valid means to explore and communicate patterns in micro‐visualizations.
Comparative Visualization of Tracer Uptake in In Vivo Small Animal PET/CT Imaging of the Carotid Arteries
Authors: Diepenbrock S. , Hermann S. , Schäfers M. , Kuhlmann M. , Hinrichs K. 
Published: July 2013

AbstractCardiovascular diseases are the main cause of death in the western world. Medical research on atherosclerosis is therefore of great interest and a very active research topic. We present a visualization system that supports scientists in exploring plaque development and evaluating the applicability of PET tracers for early diagnosis of cardiovascular diseases. In our application case a cone shaped cuff has been implanted around the carotid artery of ApoE knockout mice, fed with a high cholesterol western type diet. As a result, vascular lesions develop upstream and downstream from the cuff. Tracer uptake induced by these lesions needs to be analyzed in order to evaluate the effectiveness of different PET tracers. We discuss the approach previously utilized to perform this kind of analysis, the problems arising from in vivo image acquisition (in contrast to ex vivo) and the design process of our application. In close cooperation with domain experts we have developed new visualization techniques that display PET activity in the vessel wall and surrounding tissue in a single image. We use the vessel wall detected in the CT image to perform a normalized circular projection which allows the user to judge PET signal distribution in relation to the deformed vessel. Based on this projection a quantitative analysis of a defined region adjacent to the vessel wall can be performed and compared to the artery without the cuff.
Streamlines for Illustrative Real‐Time Rendering
Authors: Lawonn K. , Moench T. , Preim B. 
Published: July 2013

AbstractLine drawing techniques are important methods to illustrate shapes. Existing feature line methods, e.g., suggestive contours, apparent ridges, or photic extremum lines, solely determine salient regions and illustrate them with separate lines. Hatching methods convey the shape by drawing a wealth of lines on the whole surface. Both approaches are often not sufficient for a faithful visualization of organic surface models, e.g., in biology or medicine. In this paper, we present a novel object‐space line drawing algorithm that conveys the shape of such surface models in real‐time. Our approach employs contour‐ and feature‐based illustrative streamlines to convey surface shape (ConFIS). For every triangle, precise streamlines are calculated on the surface with a given curvature vector field. Salient regions are detected by determining maxima and minima of a scalar field. Compared with existing feature lines and hatching methods, ConFIS uses the advantages of both categories in an effective and flexible manner. We demonstrate this with different anatomical and artificial surface models. In addition, we conducted a qualitative evaluation of our technique to compare our results with exemplary feature line and hatching methods.
Interactive Extraction and Tracking of Biomolecular Surface Features
Authors: Krone M. , Reina G. , Schulz C. , Kulschewski T. , Pleiss J. , Ertl T. 
Published: July 2013

AbstractWe present a coordinated‐view application for the analysis of molecular surface features like cavities, channels and pockets. Our tool employs object‐space ambient occlusion for the detection of such features and tracks them over time. It offers time‐dependent graphs of metrics concerning those features and allows analyzing the temporal relationship of the features, i.e. when they (dis)appear, split or merge and which features participate in each of these events. The automated analysis process is performed in real time while the user interactively explores a dynamic data set. The system supports linking and brushing to allow for a user‐guided visual analysis based on different aspects of the data. We demonstrate the effectiveness of our approach by applying it to data sets from biochemistry and report the insights that can be gained. We also evaluate the benefits of our method with respect to recent advancements in the field. The algorithmic pipeline leverages the computing power of modern GPUs, thus achieving interactive frame rates without any precomputation for fully dynamic data sets.