bluuebunny/crossref_metadata_2025_split huggingface dataset:
Managing for Coexistence of Kokanee and Trophy Lake Trout in a Montane Reservoir
Authors: Pate William M. , Johnson Brett M. , Lepak Jesse M. , Brauch Daniel 
Published: October 2014

Abstract
Kokanee Oncorhynchus nerka and Lake Trout Salvelinus namaycush are stocked for sportfishing in lakes and reservoirs throughout the western United States and Canada. However, where the two species co-occur, unsustainable levels of predation by Lake Trout can lead to declines in kokanee abundance and declines in Lake Trout growth and body condition. Such declines occurred in Blue Mesa Reservoir, Colorado. In 2009, managers began removing Lake Trout (&lt;740 mm TL) in an attempt to sustain the hatchery-dependent kokanee population while still providing a trophy Lake Trout fishery. To evaluate this and other strategies for achieving the dual management goals, we developed age-structured kokanee and Lake Trout population models and linked them to a bioenergetics model of Lake Trout predation. We found that the existing level of Lake Trout removal (0.23; ages 4–9) is insufficient to prevent further decline and ultimately the extirpation of the kokanee population. If removal of age-4–9 Lake Trout is intensified to 0.38, the kokanee population would persist; however, removal would have to be increased to 0.63 to allow a return to historic kokanee abundance. Focusing removal on age-4 Lake Trout (0.78) would allow for persistence of kokanee and would leave more trophy Lake Trout for anglers, suggesting that the two goals are compatible under some circumstances. However, management costs of balancing kokanee with trophy Lake Trout are high and put both fisheries at risk unless Lake Trout abundance is controlled.
Received October 31, 2013; accepted May 5, 2014
A probabilistic model for analysing the effect of performance levels on visual behaviour patterns of young sailors in simulated navigation
Authors: Manzanares Aarón , Menayo Ruperto , Segado Francisco , Salmerón Diego , Cano Juan Antonio 
Published: October 2014

AbstractThe visual behaviour is a determining factor in sailing due to the influence of the environmental conditions. The aim of this research was to determine the visual behaviour pattern in sailors with different practice time in one star race, applying a probabilistic model based on Markov chains. The sample of this study consisted of 20 sailors, distributed in two groups, top ranking (n = 10) and bottom ranking (n = 10), all of them competed in the Optimist Class. An automated system of measurement, which integrates the VSail‐Trainer® sail simulator and the Eye Tracking SystemTM was used. The variables under consideration were the sequence of fixations and the fixation recurrence time performed on each location by the sailors. The event consisted of one of simulated regatta start, with stable conditions of wind, competitor and sea. Results show that top ranking sailors perform a low recurrence time on relevant locations and higher on irrelevant locations while bottom ranking sailors make a low recurrence time in most of the locations. The visual pattern performed by bottom ranking sailors is focused around two visual pivots, which does not happen in the top ranking sailor's pattern. In conclusion, the Markov chains analysis has allowed knowing the visual behaviour pattern of the top and bottom ranking sailors and its comparison.
Making Time for Agricultural and Life Science Research: Technical Change and Productivity Gains
Authors: Prager Daniel L. , Foltz Jeremy D. , Barham Bradford L. 
Published: October 2014

AbstractThis work analyzes the research productivity of agricultural and life science faculty in U.S. Land Grant research universities from 1975 to 2005. Production function estimations that control for inputs and demographic characteristics reveal significant improvements after 1980 in faculty research productivity per unit time, especially in the non‐top ten universities. Because, however, time available to faculty for research has decreased substantially in the past three decades, overall journal article output per faculty did not increase after the 1980s. Our findings demonstrate large productivity increases but raise concerns about the optimal allocation of faculty time.
Visual workflows for
13
C-metabolic flux analysis
Authors: Nöh Katharina , Droste Peter , Wiechert Wolfgang 
Published: October 2014

Abstract
Motivation: The precise quantification of intracellular metabolic flow rates is of fundamental importance in bio(techno)logy and medical research. The gold standard in the field is metabolic flux analysis (MFA) with 13 C-labeling experiments. 13 C-MFA workflows orchestrate several, mainly human-in-the-loop, software applications, integrating them with plenty of heterogeneous information. In practice, this had posed a major practical barrier for evaluating, interpreting and understanding isotopic data from carbon labeling experiments.
Results: Graphical modeling, interactive model exploration and visual data analysis are the key to overcome this limitation. We have developed a first-of-its-kind graphical tool suite providing scientists with an integrated software framework for all aspects of 13 C-MFA. Almost 30 modules (plug-ins) have been implemented for the Omix visualization software. Several advanced graphical workflows and ergonomic user interfaces support major domain-specific modeling and proofreading tasks. With that, the graphical suite is a productivity enhancing tool and an original educational training instrument supporting the adoption of 13 C-MFA applications in all life science fields.
Availability: The Omix Light Edition is freely available at http://www.omix-visualization.com
Contact: k.noeh@fz-juelich.de , p.droste@omix-visualization.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Quantifying tumor heterogeneity in whole-genome and whole-exome sequencing data
Authors: Oesper Layla , Satas Gryte , Raphael Benjamin J. 
Published: October 2014

Abstract
Motivation: Most tumor samples are a heterogeneous mixture of cells, including admixture by normal (non-cancerous) cells and subpopulations of cancerous cells with different complements of somatic aberrations. This intra-tumor heterogeneity complicates the analysis of somatic aberrations in DNA sequencing data from tumor samples.
Results: We describe an algorithm called THetA2 that infers the composition of a tumor sample—including not only tumor purity but also the number and content of tumor subpopulations—directly from both whole-genome (WGS) and whole-exome (WXS) high-throughput DNA sequencing data. This algorithm builds on our earlier Tumor Heterogeneity Analysis (THetA) algorithm in several important directions. These include improved ability to analyze highly rearranged genomes using a variety of data types: both WGS sequencing (including low ∼7× coverage) and WXS sequencing. We apply our improved THetA2 algorithm to WGS (including low-pass) and WXS sequence data from 18 samples from The Cancer Genome Atlas (TCGA). We find that the improved algorithm is substantially faster and identifies numerous tumor samples containing subclonal populations in the TCGA data, including in one highly rearranged sample for which other tumor purity estimation algorithms were unable to estimate tumor purity.
Availability and implementation: An implementation of THetA2 is available at http://compbio.cs.brown.edu/software
Contact: layla@cs.brown.edu or braphael@brown.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
ExomeAI: detection of recurrent allelic imbalance in tumors using whole-exome sequencing data
Authors: Nadaf Javad , Majewski Jacek , Fahiminiya Somayyeh 
Published: October 2014

Abstract
Summary: Whole-exome sequencing (WES) has extensively been used in cancer genome studies; however, the use of WES data in the study of loss of heterozygosity or more generally allelic imbalance (AI) has so far been very limited, which highlights the need for user-friendly and flexible software that can handle low-quality datasets. We have developed a statistical approach, ExomeAI, for the detection of recurrent AI events using WES datasets, specifically where matched normal samples are not available.
Availability: ExomeAI is a web-based application, publicly available at: http://genomequebec.mcgill.ca/exomeai .
Contact: JavadNadaf@gmail.com or somayyeh.fahiminiya@mcgill.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
Application of Process Improvement Principles to Increase the Frequency of Complete Airway Management Documentation
Authors: McCarty L. Kelsey , Saddawi-Konefka Daniel , Gargan Lauren M. , Driscoll William D. , Walsh John L. , Peterfreund Robert A. 
Published: October 2014

Abstract

Background:
Process improvement in healthcare delivery settings can be difficult, even when there is consensus among clinicians about a clinical practice or desired outcome. Airway management is a medical intervention fundamental to the delivery of anesthesia care. Like other medical interventions, a detailed description of the management methods should be documented. Despite this expectation, airway documentation is often insufficient. The authors hypothesized that formal adoption of process improvement methods could be used to increase the rate of “complete” airway management documentation.

Methods:
The authors defined a set of criteria as a local practice standard of “complete” airway management documentation. The authors then employed selected process improvement methodologies over 13 months in three iterative and escalating phases to increase the percentage of records with complete documentation. The criteria were applied retrospectively to determine the baseline frequency of complete records, and prospectively to measure the impact of process improvements efforts over the three phases of implementation.

Results:
Immediately before the initial intervention, a retrospective review of 23,011 general anesthesia cases over 6 months showed that 13.2% of patient records included complete documentation. At the conclusion of the 13-month improvement effort, documentation improved to a completion rate of 91.6% (P < 0.0001). During the subsequent 21 months, the completion rate was sustained at an average of 90.7% (SD, 0.9%) across 82,571 general anesthetic records.

Conclusion:
Systematic application of process improvement methodologies can improve airway documentation and may be similarly effective in improving other areas of anesthesia clinical practice.
Intestinal and Gastric Permeability in Children With Eosinophilic Esophagitis and Reflux Esophagitis
Authors: Leung Aldrich J.T. , Persad Sujata , Slae Mordechai , Abdelradi Amr , Kluthe Cheryl , Shirton Leanne , Danchuk Ronda , Persad Rabin , Meddings Jon , Huynh Hien Q. 
Published: October 2014

ABSTRACTObjectives:Eosinophilic esophagitis (EoE) is an allergic and immune‐mediated entity that leads to a characteristic inflammation of esophageal mucosa. Patients complain of dysphagia and reflux‐like symptoms. As many as 80% of patients with EoE may also have a history of atopy, and patients with asthma and eczema have previously been shown to have increased intestinal permeability. This study was designed to assess small intestinal and gastric permeability in patients with EoE and to see whether it differed from healthy individuals and patients with reflux esophagitis (RE).Methods:Gastric and small intestinal permeability was measured using sugar probe tests containing lactulose, mannitol, and sucrose. Lactulose‐to‐mannitol (L/M) ratios in the patient's urine were a measure for intestinal permeability, and total sucrose was a measure for gastric permeability.Results:We analyzed samples from 23 patients with EoE, 20 RE, 14 normal upper endoscopy with gastrointestinal symptoms, and 26 healthy controls. All of the 4 groups had L/M ratios less than the upper limit of normal (<0.025). There was no statistically significant difference in gastric permeability between the 4 groups (L/M P = 0.26, sucrose P = 0.46).Conclusions:Our data suggest that an alteration in gastric and intestinal permeability does not play a role in EoE or RE pathogenesis.
Recurrence-Based Information Processing in Gene Regulatory Networks
Authors: Gabalda-Sagarra Marçal , Carey Lucas , Garcia-Ojalvo Jordi 
Published: October 2014

AbstractCellular information processing is generally attributed to the complex networks of genes and proteins that regulate cell behavior. It is still unclear, however, what are the main features of those networks that allow a cell to encode and interpret its ever changing environment. Here we address this question by studying the computational capabilities of the transcriptional regulatory networks of five evolutionary distant organisms. We identify in all cases a cyclic recurrent structure, formed by a small core of genes, that is essential for dynamical encoding and information integration. The recent history of the cell is encoded by the transient dynamics of this recurrent reservoir of nodes, while the rest of the network forms a readout layer devoted to decode and interpret the high-dimensional dynamical state of the recurrent core. This separation of roles allows for the integration of temporal information, while facilitating the learning of new environmental conditions and preventing catastrophic interference between those new inputs and the previously stored information. This resembles the reservoir-computing paradigm recently proposed in computational neuroscience and machine learning. Our results reveal that gene regulatory networks act as echo-state networks that perform optimally in standard memory-demanding tasks, and confirms that most of their memory resides in the recurrent reservoir. We also show that the readout layer can learn to decode the information stored in the reservoir via standard evolutionary strategies. Our work thus suggests that recurrent dynamics is a key element for the processing of complex time-dependent information by cells.SummaryCells must monitor the dynamics of their environment continuously, in order to adapt to present conditions and anticipate future changes. But anticipation requires processing temporal information, which in turn requires memory. Here we propose that cells can perform such dynamical information processing via the reservoir computing paradigm. According to this concept, a structure with recurrent (cyclic) paths, known as the reservoir, stores in its dynamics a record of the cell’s recent history. A much simpler feedforward structure then reads and decodes that information. We show that the transcriptional gene regulatory networks of five evolutionary distant organisms are organized in this manner, allowing them to store complex time-dependent signals entering the cell in a biologically realistic manner.
Cost benefit analysis on SVC and UPFC in a dynamic economic dispatch problem
Authors: Sreejith Sekharan , P. Simon Sishaj 
Published: October 2014

Purpose
– The aim of this paper is to compare the performance of static VAR compensator (SVC) and unified power flow controller (UPFC) in dynamic economic dispatch (DED) problem. DED schedules the online generator outputs with the predicted load demands over a certain period so that the electric power system is operated most economically. During last decade, flexible alternating current transmission systems (FACTS) devices are broadly used for maximizing the loadability of existing power system transmission networks. However, based on the literature survey, the performance of SVC and UPFC incorporated in the DED problem and its cost–benefit analysis are not discussed earlier in any of the literature.

Design/methodology/approach
– Here, the DED problem is solved applying ABC algorithm incorporating SVC and UPFC. The following conditions are investigated with the incorporation of SVC and UPFC into DED problem: the role of SVC and UPFC for improving the power flow and voltage profile and the approximate analysis on cost recovery and payback period with SVC and UPFC in DED problem.

Findings
– The incorporation of FACTS devices reduces the generation cost and improves the stability of the system. The percentage cost recovered with FACTS devices is estimated approximately using equated monthly installment (EMI) and non-EMI scheme. It is clear from the illustrations that the installation of FACTS devices is profitable after a certain period.

Research limitations/implications
– In this research work, the generation cost with FACTS devices is only taken into account while calculating the profit. The other benefits like congestion management, cost gained due to land and cost due to stability issues are not considered. For future work, these things can be considered while calculating the benefit.

Originality/value
– The originality of the work is incorporation of FACTS devices in DED problem and approximate estimation of recovery cost with FACTS devices in DED problem.
Sector size, technical change and stability in the USA (1957-2006): a Schumpeterian approach
Authors: Konstantakis Konstantinos , G. Michaelides Panayotis , Papageorgiou Theofanis 
Published: October 2014

Purpose– The purpose of this paper is to investigate two famous postulates of the Schumpeterian doctrine and its implications for the US economy.Design/methodology/approach– Analytically, the authors investigate whether sector size matters for sectoral: technological change and stability, as expressed through the relevant quantitative measures and variables. To this end, the authors test a number of relevant models that express the various forms of this relationship. More precisely, the authors use panel data for the 14 main sectors of economic activity in the USA over the period 1957-2006, just before the first signs of the US and global recession made their appearance.Findings– The results seem to be in line with the Schumpeterian postulate that market size matters for technological change and economic stability, for the US economy (1957-2006). Clearly, further research would be of great interest.Originality/value– This work contributes to the literature in the following ways: first, it provides an extensive review of the literature on the subject and adopts two relevant methodological approaches. Second, based on these quantitative approaches, the paper offers a complete investigation of two famous postulates of the Schumpeterian theory for the US economy, and it is the first, to the best of the authors’ knowledge, to do so by sector of economic activity, in a panel data framework. Third, the paper uses a wide data set (1957-2006) to examine the US economy up until the first signs of the US and global economic recession made their appearance.
Student engagement with sustainability: understanding the value–action gap
Authors: Chaplin Gareth , Wyton Paul 
Published: October 2014

Purpose
– The purpose of this paper is to present the findings of research that aimed to determine what university students living in Unite accommodation in the UK understand about the concept of sustainable living. It considers what barriers they perceive to be standing in the way of following sustainable living practices. In particular, the research aimed to explore any value–action gap for the student population with a view to informing future actions to help close any gap.

Design/methodology/approach
– The study was completed through an online questionnaire survey of students living in halls of residence operated by provider The Unite Group Plc. The survey informed semi-structured interviews and focus groups that explored the issues raised in greater detail.

Findings
– It was found that students living in Unite properties believed sustainable living to be important, yet levels of understanding were very low and there appeared to be a wide value–action gap. Reasons for this are varied; however, an unexpected theme emerged around the association of effort and importance. There was a very strong association between sustainable living and recycling, which, therefore, saw the lack of adequate recycling facilities as a significant barrier to sustainable living. There were also issues around a lack of information, cost and respondents’ flatmates as further barriers. However, the most significant barrier was the displacement of responsibility for sustainable living to other people or organisations.

Originality/value
– Gaining an insight into the complexity of attitude and behaviour of students with the sustainability agenda will enable understanding that can be applied to activities that promote sustainability.
Cognitive styles and the use of electronic journals in a mobile context
Authors: Chan Chu-Han , Hsieh Chen-Wei , Y. Chen Sherry 
Published: October 2014

Purpose– The purpose of this paper is to examine how different cognitive style groups use electronic journals via mobile devices, with an emphasis on the use of search mechanisms, the approaches to judge the relevance and to refine the results, the use of horizontal screens, and on the influence of negative emotions.Design/methodology/approach– Participants’ cognitive styles were identified as Holists and Serialists with Ford's Study Preference Questionnaire. The behaviour of the participants interacting with theScienceDirectwas observed and was analysed with both traditional statistics and data mining.Findings– Holists prefer to use multiple searches when undertaking the Expert Search only, which is a complex search mechanism. Conversely, Serialists have a tendency to use multiple searches, irrespective of the complexity of search mechanisms. Additionally, the Expert Search may be helpful for Serialists while the Basic Search seems beneficial to Holists. Regarding the judgement of relevance, Holists tend to use a variety of approaches while Serialists prefer to use a single approach. In general, the major results of this study confirm those of Vilar and Žumer (2008).Originality/value– The novelty of this study covers two aspects. One is to examine the behaviour of Holists and Serialists in the mobile context of electronic journals and the other is to analyse data with an integrative approach that combines both traditional statistics and data mining. The former contributes to the understandings of how to design mobile electronic journals that can accommodate the needs of different cognitive style groups. The latter can not only strengthen the reliability of the results obtained from traditional statistics, but also discover findings neglected by traditional statistics.
Prestack exploding reflector modelling and migration for anisotropic media
Authors: Alkhalifah T. 
Published: October 2014

ABSTRACTThe double‐square‐root equation is commonly used to image data by downward continuation using one‐way depth extrapolation methods. A two‐way time extrapolation of the double‐square‐root‐derived phase operator allows for up and downgoing wavefields but suffers from an essential singularity for horizontally travelling waves. This singularity is also associated with an anisotropic version of the double‐square‐root extrapolator. Perturbation theory allows us to separate the isotropic contribution, as well as the singularity, from the anisotropic contribution to the operator. As a result, the anisotropic residual operator is free from such singularities and can be applied as a stand alone operator to correct for anisotropy. We can apply the residual anisotropy operator even if the original prestack wavefield was obtained using, for example, reverse‐time migration. The residual correction is also useful for anisotropic parameter estimation. Applications to synthetic data demonstrate the accuracy of the new prestack modelling and migration approach. It also proves useful in approximately imaging the Vertical Transverse Isotropic Marmousi model.