Miracle-dz/UniFAR-FTUs huggingface dataset:
Coherence of XUV Laser Sources

This article reviews recent developments in research on coherence properties of femtosecond XUV and x-ray lasers. Coherence is one of the most conspicuous features of laser sources. It describes how an electromagnetic wave field is correlated at different times and at different points in space. Coherence is a property that enables stationary interferences and thereby enables holographic and diffractive or lens less imaging. While a large number of different laser systems radiating in the infrared, visible and UV spectral range have been developed in the past five decades since the invention of the laser, the generation of intense and coherent XUV and x-ray radiation is still a formidable goal of basic research. Developed first in the mid and far infrared spectral region free electron lasers (FEL) provide a new means to generate widely tunable coherent radiation [Madey, 1971; Deacon et al., 1977; Oepts et al., 1995]. In the XUV and soft x-ray spectral region the present lack of appropriate mirrors prevent the construction of optical resonators, essential for a laser with well-defined mode properties. Therefore in this spectral region free-electron lasers have to rely on the principle of self-amplified spontaneous emission (SASE), where in a single path enough gain is accumulated to evolve a pulse from shot noise. These machines then provide pulsed XUV and x-ray radiation which shows only partial coherence (Kondratenko & Saldin, 1980; Bonifacio et al., 1984; Murphy & Pellegrini, 1985). A characterisation of the coherence properties of SASE FEL radiation is not only important for the understanding and improvement of the SASE process. With the concomitant development of coherent diffraction imaging it is also of great practical importance in a broad field of fundamental scientific applications, like holographic imaging of artificial magnetic structures or single pulse imaging of large biomolecules. The theoretical description of the coherence properties of SASE FEL has made tremendous progress in the recent years. In this chapter we will briefly review measurement methods and description of partially coherent optical fields. The considerations will be applied to characterize the spatial and temporal coherence of pulses from the SASE free electron laser in Hamburg (FLASH) and of high harmonic radiation.
Technological Environment - International Marketing Strategy Relationship

International trade involves both large and small f irms engaged in business overseas. Possible drivers tha t force companies to enter international markets include increasing c ompetition at the domestic market, maturing domestic markets, and lim ited domestic market opportunities. Technology is an important dr iving factor in shaping international marketing strategy as well as in driving force towards a more global marketplace, especially techn ology in communication. It includes telephones, the interne t, computer systems and e-mail. There are three main marketing s rategy choices, namely standardization approach, adaptation approac h and middleof-the-road approach that companies implement to ov erseas markets. The decision depends on situations and factors faci ng the companies in the international markets. In this paper, the co ntingency concept is considered that no single strategy can be effective in all contexts. The effect of strategy on performance depends on sp ecific situational variables. Strategic fit is employed to investigat e export marketing strategy adaptation under certain environmental con diti s, which in turn can lead to superior performance. Keywords—Contingency approach, international marketing strategy, strategic fit, technological environment
SHARE @ Children's Mercy SHARE @ Children's Mercy

Background: Unsupervised clustering represents one of the most widely applied methods in analysis of high-throughput ‘ omics data. A variety of unsupervised model-based or parametric clustering methods and non-parametric clustering methods have been proposed for RNA-seq count data, most of which perform well for large samples, e.g. N ≥ 500. A common issue when analyzing limited samples of RNA-seq count data is that the data follows an over-dispersed distribution, and thus a Negative Binomial likelihood model is often used. Thus, we have developed a Negative Binomial model-based (NBMB) clustering approach for application to RNA-seq studies. Results: We have developed a Negative Binomial Model-Based (NBMB) method to cluster samples using a stochastic version of the expectation-maximization algorithm. A simulation study involving various scenarios was completed to compare the performance of NBMB to Gaussian model-based or Gaussian mixture modeling (GMM). NBMB was also applied for the clustering of two RNA-seq studies; type 2 diabetes study ( N = 96) and TCGA study of ovarian cancer ( N = 295). Simulation results showed that NBMB outperforms GMM applied with different transformations in majority of scenarios with limited sample size. Additionally, we found that NBMB outperformed GMM for small clusters distance regardless of sample size. Increasing total number of genes with fixed proportion of differentially expressed genes does not change the outperformance of NBMB, but improves the overall performance of GMM. Analysis of type 2 diabetes and ovarian cancer tumor data with NBMB found good agreement with the reported disease subtypes and the gene expression patterns. This method is available in an R package on CRAN named NB.MClust . Conclusion: Use of Negative Binomial model based clustering is advisable
Redesigning the message logging model for high performance

Over the past decade the number of processors used in high performance computing has increased to hundreds of thousands. As a direct consequence, and while the computational power follows the trend, the mean time between failures (MTBF) has suffered and is now being counted in hours. In order to circumvent this limitation, a number of fault‐tolerant algorithms as well as execution environments have been developed using the message passing paradigm. Among them, message logging has been proved to achieve a better overall performance when the MTBF is low, mainly due to a faster failure recovery. However, message logging suffers from a high overhead when no failure occurs. Therefore, in this paper we discuss a refinement of the message logging model intended to improve the failure‐free message logging performance. The proposed approach simultaneously removes useless memory copies and reduces the number of logged events. We present the implementation of a pessimistic message logging protocol in Open MPI and compare it with the previous reference implementation MPICH‐V2. The results outline a several order of magnitude improvement on the performance and a zero overhead for most messages. Published in 2010 by John Wiley & Sons, Ltd.
Parallel deterministic annealing clustering and its application to LC-MS data analysis

We present a scalable parallel deterministic annealing formalism for clustering with cutoffs and position-dependent variances. We apply it to the “peak matching" problem of the precise identification of the common LC-MS peaks across a cohort of multiple biological samples in proteomic biomarker discovery. We reliably and automatically find tens of thousands of clusters starting with a single one that is split recursively as distance resolution is sharpened. We parallelize the algorithm and compare unconstrained and trimmed clusters using data from a human tuberculosis cohort.
Attribute-aware Collaborative Filtering: Survey and Classification

Attribute-aware CF models aims at rating prediction given not only the historical rating from users to items, but also the information associated with users (e.g. age), items (e.g. price), or even ratings (e.g. rating time). This paper surveys works in the past decade developing attribute-aware CF systems, and discovered that mathematically they can be classified into four different categories. We provide the readers not only the high level mathematical interpretation of the existing works in this area but also the mathematical insight for each category of models. Finally we provide in-depth experiment results comparing the effectiveness of the major works in each category.
The New Normal 1

The Great Recession has caused many Americans to reevaluate their consumption-rich way of life. In response to the shrinking economy, they have spent less, saved more, and simplified their lives. This essay asks whether people will seek a return to their prerecession lifestyles—in particular a return to making the acquisition and consumption of consumer goods a major source of meaning and contentment—as soon as their economic condition allows or whether they will make their more austere lives their ‘‘new normal. ’’ It evaluates existing research on contentment and suggests that if instead of choosing to return to their ‘‘old normal,’’ Americans learn to derive satisfaction from nonconsumerist sources, in particular social relations and transcendental activities (i.e., religious, contemplative, and cultural activities), they may find the new normal quite acceptable.
Improved Feature Selection and Redundance Computing - THUIR at TREC 2004 Novelty Track.

This is the third years that Tsinghua University Information Retrieval Group (THUIR) participates in Novelty task of TREC. Our research on this year’s novelty track mainly focused on four aspects: (1) text feature selection and reduction; (2) improved sentence classification in finding relevant information; (3)efficient sentence redundancy computing; (4) effective result filtering. All experiments have been performed on TMiner IR system, developed by THU IR group last year.
11-11-2009 Computer-Aided Assessment of Diagnostic Images for Epidemiological Research

Background: Diagnostic images are often assessed for clinical outcomes using subjective methods, which are limited by the skill of the reviewer. Computer-aided diagnosis (CAD) algorithms that assist reviewers in their decisions concerning outcomes have been developed to increase sensitivity and specificity in the clinical setting. However, these systems have not been well utilized in research settings to improve the measurement of clinical endpoints. Reductions in bias through their use could have important implications for etiologic research. Methods: Using the example of cortical cataract detection, we developed an algorithm for assisting a reviewer in evaluating digital images for the presence and severity of lesions. Available image processing and statistical methods that were easily implementable were used as the basis for the CAD algorithm. The performance of the system was compared to the subjective assessment of five reviewers using 60 simulated images. Cortical cataract severity scores from 0 to 16 were assigned to the images by the reviewers and the CAD system, with each image assessed twice to obtain a measure of variability. Image characteristics that affected reviewer bias were also assessed by systematically varying the appearance of the simulated images. Results: The algorithm yielded severity scores with smaller bias on images where cataract severity was mild to moderate (approximately ≤ 6/16ths). On high severity images, the bias of the CAD system exceeded that of the reviewers. The variability of the CAD system was zero on repeated images but ranged from 0.48 to 1.22 for the reviewers. The direction and magnitude of the bias exhibited by the reviewers was a function of the number of cataract opacities, the shape and the contrast of the lesions in the simulated images. Conclusion: CAD systems are feasible to implement with available software and can be valuable when medical images contain exposure or outcome information for etiologic research. Our results indicate that such systems have the potential to decrease bias and discriminate very small changes in disease severity. Simulated images are a tool that can be used to assess performance of a CAD system when a gold standard is not available. Published: 11 November 2009 BMC Medical Research Methodology 2009, 9:74 doi:10.1186/1471-2288-9-74 Received: 23 April 2009 Accepted: 11 November 2009 This article is available from: http://www.biomedcentral. com/1471-2288/9/74 © 2009 Abraham et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. BMC Medical Research Methodology 2009, 9:74 http://www.biomedcentral. com/1471-2288/9/74
Expected Performances of the Copernicus Imaging Microwave Radiometer (CIMR) for an All‐Weather and High Spatial Resolution Estimation of Ocean and Sea Ice Parameters

Climate change resulting in ocean warming, sea level rise, and sea ice melting has consequences for the global economy, navigation, and security. The Copernicus Imaging Microwave Radiometer (CIMR) mission is a high priority candidate mission within the European Copernicus Expansion program. CIMR is designed to observe the ocean and sea ice and more particularly the Arctic environment. Sea surface temperature (SST), ocean wind speed, sea surface salinity (SSS), and sea ice concentration (SIC) are fundamental variables for understanding, monitoring, and predicting the state of the ocean and sea ice. CIMR is a conically scanning microwave radiometer imager that includes channels at 1.4, 6.9, 10.65, 18.7, and 36.5 GHz, in a Sun-synchronous polar orbit, to provide SST, ocean wind speed, SSS, and SIC with an increased accuracy and/or spatial resolution. Here we analyze the performances of the CIMR mission in terms of theoretical retrieval precision and spatial resolution on the SST, SSS, and SIC products. A careful information content analysis is conducted. The CIMR performances are compared with the Advanced Microwave Scanning Radiometer 2 and the Soil Moisture Active Passive current missions. Maps of the retrieval precision based on realistic conditions are computed. CIMR will provide SST, SSS, and SIC with a spatial resolution of 15, 55, and 5 km and a precision of 0.2 K, 0.3 psu, and 5%, respectively. The SST and SIC will be retrieved at better than 30 km from the coast. CIMR is currently in preparatory phase, and if selected, it is for a launch in the 2025+ time frame. Plain Language Summary Climate change resulting in ocean warming, sea level rise, and sea ice melting has consequences for the global economy, navigation, and security. The Copernicus Imaging Microwave Radiometer mission is a high priority candidate satellite mission within the European Copernicus Expansion program. It is designed to observe the ocean and sea ice and more particularly the Arctic environment. Sea surface temperature, ocean wind speed, sea surface salinity, and sea ice concentration are fundamental variables for understanding, monitoring, and predicting the state of the ocean and sea ice. Here we analyze the performances of this new satellite mission in terms of precision and spatial resolution on the sea surface temperature, sea surface salinity, and sea ice concentration and compare it with current missions. The Copernicus Imaging Microwave Radiometer will provide sea surface temperature, sea surface salinity, and sea ice concentration with a spatial resolution of 15, 55, and 5 km and a precision of 0.2 K, 0.3 psu, and 5%, respectively. This satellite mission is currently in preparatory phase, and if selected, it is for a launch in the 2025 time frame.
Minimal Graphics

The problem of producing a photorealistic rendering of a graphical model continues to be the focus of considerable research effort in the computer graphics community. However, photorealism is not the only possible criteria for judging the value of an image. In this paper we step back from the physically–based model that underlies many of the existing approaches to rendering, and instead consider the rendering problem from a more fundamental view: how is graphical information processed by the user? Using differences in artistic traditions as our initial motivation, we identify the need for an approach to rendering that is based fundamentally on cognitive theory. Existing work on non–photorealistic rendering has started to take steps that address this need, but using a model of cognitive information processing we identify a significant research problem: the quest for a minimal rendering process. 1991 Computing Reviews Classification System: H.1. 2, H.5. 0, I.3. 3, I.3. 6, I.3. 7, I.3. m, J.4, J.5
Optimizing the nitrogen supply of prairie organic agriculture with green manures and grazing

Cicek, Harun. PhD. , The University of Manitoba, November, 2013. Optimizing the Nitrogen Supply of Prairie Organic Agriculture with Green Manures and Grazing. Major Professor; Martin H. Entz. There is a need to design green manure systems that can supply optimum Nitrogen (N) to cash crops and that are compatible with intensive annual crop production. Grazing and no-till management in organic systems have been recently proposed tools to improve nutrient cycling and sustainability. From 2008 to 2012, a series of field experiments were conducted to i) identify green manure species and ii) green manure management options to maximize N benefit to following cash crops and explore the opportunities to reduce tillage during the green manure phase of an organic rotation. A total of four green manure systems (double-cropped green manures, relay-cropped green manures, full season green manures, and catch crops after grazed full season green manures), three green manure management options (soil incorporation, grazing and no-till), and 10 green manure species, as well as, three green manure mixtures were tested. Among the relay and double crops tested, relay-cropped red clover (Trifolium pratense) and double-cropped pea were the greatest biomass producers and N suppliers. Double-cropped pea (Pisum sativum cv. 40-10) and relay-cropped red clover produced around 900 kg ha and 2000 kg ha of dry matter biomass respectively. Overall, relay crops were more productive than the double crops. The greatest biomass producing full season green manures were hairy vetch (Vicia villosa L.), pea/oat (Avena sativa cv. Leggett) and sweet clover (Mellilotus officinalis cv. Norgold). Pea/oat and hairy vetch were the most weed competitive species and on
Drivers with limited perception: model and application to traffic simulation

We propose a model of the driver perception suited for microscopic, agent-based traffic simulations. The model includes both top-down and bottom-up perception, and takes into account the limited amount of perceptive resource which gain access to short-term memory. The driving task is split into sub-tasks, which can be activated in parallel (e.g. car following and crossroads passing). Perceived entities (percepts) as well as subtasks are ranked with respect to their subjective value, and due to the bounded perception, only the more "valuable" percepts are sent to the decision module of the cognitive model. The competition among percepts to gain access to the short-term memory simulates attentional processes. A computational implementation of the model is proposed for the driver, using agent-based modeling. It is implemented in a traffic simulation environment and allows the driver-agent to manage the conflicts and the longitudinal space in the middle of the crossroads. This way, we improve the realism of the simulation. Furthermore, this model can lead to a new way of identifying and explaining near accidents. We illustrate some benefits for a microscopic traffic simulation at crossroads in two situations . The first scenario explores the traffic parameters at a crossroads, simulating various distributions of the driver's age. The second one demonstrates the adaptive behavior of simulated drivers facing a dangerous (e.g. hypo-vigilant) driver.
The thermal threshold of the Atlantic meridional overturning circulation and its control by wind stress forcing during glacial climate

Paleo proxy data suggest that the Atlantic meridional overturning circulation (AMOC) was shallower and weaker at the Last Glacial Maximum (LGM) than at present. In this study, we have identified the existence of a thermal threshold of the AMOC which may explain why many coupled climate models fail to simulate the weaker AMOC during the LGM. By using results obtained from a coupled climate model and conducting sensitivity simulations with an ocean general circulation model, we found that the sudden transition from the present‐day AMOC to the weaker glacial AMOC occurs when we gradually change the degree of surface cooling from present‐day to glacial conditions. This result is related to response of deep convection in the northern North Atlantic Ocean; moderate cooling enhances deep convection whereas sufficient cooling results in total covering of sea ice there and suppression of deep convection. The findings indicate the existence of a thermal threshold controlling the AMOC, where the present‐day‐type AMOC suddenly shifts to the weaker glacial AMOC once the surface cooling exceeds this threshold. We also demonstrate that wind stress forcing plays a critical role in controlling the value of the thermal threshold. Our study suggests that slight differences in the degree of surface cooling or wind stress forcing for LGM simulations could lead to the very different response of the AMOC during the LGM as reported in previous LGM simulations.
Evaluating gold standard corpora against gene / protein tagging solutions and lexical resources

Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources Journal of Biomedical Semantics 2013, 4:28 doi:10.1186/2041-1480-4-28 Dietrich Rebholz-Schuhmann (rebholz@ifi.uzh.ch) Senay Kafkas (kafkas@ebi.ac.uk) Jee-Hyub Kim (jhkim@ebi.ac.uk) Chen Li (chenli@ebi.ac.uk) Antonio Jimeno Yepes (antonio.jimeno@gmail.com) Robert Hoehndorf (leechuck@leechuck.de) Rolf Backofen (backofen@informatik.uni-freiburg.de) Ian Lewin (ian.lewin@linguamatics.com)
Slope failures within and upstream of Lake Quinault, Washington, as uneven responses to Holocene earthquakes along the Cascadia subduction zone

Abstract Investigation of Lake Quinault in western Washington, including a reflection seismic survey, analysis of piston cores, and preliminary mapping in the steep, landslide-prone Quinault River catchment upstream of the lake, reveals evidence for three episodes of earthquake disturbance in the past 3000 yr. These earthquakes triggered failures on the lake’s underwater slopes and delta front, as well as subaerial landsliding, partial channel blockage, and forced fluvial sediment aggradation. The ages of the three Lake Quinault disturbance events overlap with those of coseismically subsided, coastal marsh soils nearby in southwest Washington that are interpreted to record ruptures of the Cascadia megathrust. Absent from Lake Quinault, however, are signals of obvious disturbance from five additional subduction earthquakes inferred to have occurred during the period of record. The lack of evidence for these events may reflect the limitations of the data set derived from the detrital, river-dominated lake stratigraphy but may also have bearing on debates about segmentation and the distribution of slip along the Cascadia subduction zone during prior earthquakes.