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Search Results: 1 - 10 of 152072 matches for " Barnett William K "
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Collaborative software for traditional and translational research
Berman Ari E,Barnett William K,Mooney Sean D
Human Genomics , 2012, DOI: 10.1186/1479-7364-6-21
Abstract: Biomedical research has entered a period of renewed vigor with the introduction and rapid development of genomic technologies and next-generation sequencing methods. This research paradigm produces extremely large datasets that are both difficult to store and challenging to mine for relevant data. Additionally, the thorough exploration of such datasets requires more resources, personnel, and multidisciplinary expertise to properly analyze and interpret the data. As a result, modern biomedical research practices are increasingly designed to include multi-laboratory collaborations that effectively distribute the scientific workload and expand the pool of expertise within a project. The scope of biomedical research is further complicated by increased efforts in translational research, which mandates the translation of basic laboratory research results into the human medical application space, adding to the complexity of potential collaborations. This increase in multidisciplinary, multi-laboratory, and biomedical translational research identifies a specific need for formalized collaboration practices and software applications that support such efforts. Here, we describe formal technological requirements for such efforts and we review several software solutions that can effectively improve the organization, communication, and formalization of collaborations in biomedical research today.
Initial Findings from a Study of Best Practices and Models for Cyberinfrastructure Software Sustainability
Craig A. Stewart,Julie Wernert,Eric A. Wernert,William K. Barnett,Von Welch
Computer Science , 2013,
Abstract: We present a set of common themes and recommendations extracted from in depth interviews with the leaders of 12 distinct cyberinfrastructure software projects. These interviews were conducted as part of a larger study to identify and elucidate the best practices and management models that lead to sustainability for cyberinfrastructure software. Respondents in a formal survey of cyberinfrastructure users identified these projects as good examples of sustained software initiatives. While there is clearly no single method or plan that will guarantee sustainability for all projects, we can draw general guidance from these exemplars. This paper presents the common themes, ideas, and recommendations that emerged from those interviews.
A Codimension-2 Bifurcation Controlling Endogenous Bursting Activity and Pulse-Triggered Responses of a Neuron Model
William H. Barnett, Gennady S. Cymbalyuk
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0085451
Abstract: The dynamics of individual neurons are crucial for producing functional activity in neuronal networks. An open question is how temporal characteristics can be controlled in bursting activity and in transient neuronal responses to synaptic input. Bifurcation theory provides a framework to discover generic mechanisms addressing this question. We present a family of mechanisms organized around a global codimension-2 bifurcation. The cornerstone bifurcation is located at the intersection of the border between bursting and spiking and the border between bursting and silence. These borders correspond to the blue sky catastrophe bifurcation and the saddle-node bifurcation on an invariant circle (SNIC) curves, respectively. The cornerstone bifurcation satisfies the conditions for both the blue sky catastrophe and SNIC. The burst duration and interburst interval increase as the inverse of the square root of the difference between the corresponding bifurcation parameter and its bifurcation value. For a given set of burst duration and interburst interval, one can find the parameter values supporting these temporal characteristics. The cornerstone bifurcation also determines the responses of silent and spiking neurons. In a silent neuron with parameters close to the SNIC, a pulse of current triggers a single burst. In a spiking neuron with parameters close to the blue sky catastrophe, a pulse of current temporarily silences the neuron. These responses are stereotypical: the durations of the transient intervals–the duration of the burst and the duration of latency to spiking–are governed by the inverse-square-root laws. The mechanisms described here could be used to coordinate neuromuscular control in central pattern generators. As proof of principle, we construct small networks that control metachronal-wave motor pattern exhibited in locomotion. This pattern is determined by the phase relations of bursting neurons in a simple central pattern generator modeled by a chain of oscillators.
Granger causality for state space models
Lionel Barnett,Anil K. Seth
Statistics , 2015, DOI: 10.1103/PhysRevE.91.040101
Abstract: Granger causality, a popular method for determining causal influence between stochastic processes, is most commonly estimated via linear autoregressive modeling. However, this approach has a serious drawback: if the process being modeled has a moving average component, then the autoregressive model order is theoretically infinite, and in finite sample large empirical model orders may be necessary, resulting in weak Granger-causal inference. This is particularly relevant when the process has been filtered, downsampled, or observed with (additive) noise - all of which induce a moving average component and are commonplace in application domains as diverse as econometrics and the neurosciences. By contrast, the class of autoregressive moving average models - or, equivalently, linear state space models - is closed under digital filtering, downsampling (and other forms of aggregation) as well as additive observational noise. Here, we show how Granger causality, conditional and unconditional, in both time and frequency domains, may be calculated simply and directly from state space model parameters, via solution of a discrete algebraic Riccati equation. Numerical simulations demonstrate that Granger causality estimators thus derived have greater statistical power and smaller bias than pure autoregressive estimators. We conclude that the state space approach should be the default for (linear) Granger causality estimation.
Selective Population of Edge States in a 2D Topological Band System
Bogdan Galilo,Derek K. K. Lee,Ryan Barnett
Physics , 2015, DOI: 10.1103/PhysRevLett.115.245302
Abstract: We consider a system of interacting spin-one atoms in a hexagonal lattice under the presence of a synthetic gauge field. Quenching the quadratic Zeeman field is shown to lead to a dynamical instability of the edge modes. This, in turn, leads to a spin current along the boundary of the system which grows exponentially fast in time following the quench. Tuning the magnitude of the quench can be used to selectively populate edge modes of different momenta. Implications of the intrinsic symmetries of Hamiltonian on the dynamics are discussed. The results hold for atoms with both antiferromagnetic and ferromagnetic interactions.
Residency and Spatial Use by Reef Sharks of an Isolated Seamount and Its Implications for Conservation
Adam Barnett, Kátya G. Abrantes, Jamie Seymour, Richard Fitzpatrick
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0036574
Abstract: Although marine protected areas (MPAs) are a common conservation strategy, these areas are often designed with little prior knowledge of the spatial behaviour of the species they are designed to protect. Currently, the Coral Sea area and its seamounts (north-east Australia) are under review to determine if MPAs are warranted. The protection of sharks at these seamounts should be an integral component of conservation plans. Therefore, knowledge on the spatial ecology of sharks at the Coral Sea seamounts is essential for the appropriate implementation of management and conservation plans. Acoustic telemetry was used to determine residency, site fidelity and spatial use of three shark species at Osprey Reef: whitetip reef sharks Triaenodon obesus, grey reef sharks Carcharhinus amblyrhynchos and silvertip sharks Carcharhinus albimarginatus. Most individuals showed year round residency at Osprey Reef, although five of the 49 individuals tagged moved to the neighbouring Shark Reef (~14 km away) and one grey reef shark completed a round trip of ~250 km to the Great Barrier Reef. Additionally, individuals of white tip and grey reef sharks showed strong site fidelity to the areas they were tagged, and there was low spatial overlap between groups of sharks tagged at different locations. Spatial use at Osprey Reef by adult sharks is generally restricted to the north-west corner. The high residency and limited spatial use of Osprey Reef suggests that reef sharks would be highly vulnerable to targeted fishing pressure and that MPAs incorporating no-take of sharks would be effective in protecting reef shark populations at Osprey and Shark Reef.
Factors determining patients' intentions to use point-of-care testing medical devices for self-monitoring: the case of international normalized ratio self-testing
Shah SG, Barnett J, Kuljis J, Hone K, Kaczmarski R
Patient Preference and Adherence , 2013, DOI: http://dx.doi.org/10.2147/PPA.S38328
Abstract: ctors determining patients' intentions to use point-of-care testing medical devices for self-monitoring: the case of international normalized ratio self-testing Original Research (1116) Total Article Views Authors: Shah SG, Barnett J, Kuljis J, Hone K, Kaczmarski R Published Date December 2012 Volume 2013:7 Pages 1 - 14 DOI: http://dx.doi.org/10.2147/PPA.S38328 Received: 20 September 2012 Accepted: 30 October 2012 Published: 28 December 2012 Syed Ghulam Sarwar Shah,1 Julie Barnett,1 Jasna Kuljis,2 Kate Hone,2 Richard Kaczmarski3 1Multidisciplinary Assessment of Technology Centre for Healthcare, 2Department of Information Systems and Computing, Brunel University London, Uxbridge, Middlesex, UK; 3Department of Haematology, Hillingdon Hospital, Uxbridge, Middlesex, UK Purpose: To identify factors that determine patients' intentions to use point-of-care medical devices, ie, portable coagulometer devices for self-testing of the international normalized ratio (INR) required for ongoing monitoring of blood-coagulation intensity among patients on long-term oral anticoagulation therapy with vitamin K antagonists, eg, warfarin. Methods: A cross-sectional study that applied the technology-acceptance model through a self-completed questionnaire, which was administered to a convenience sample of 125 outpatients attending outpatient anticoagulation services at a district general hospital in London, UK. Data were analyzed using descriptive statistics, factor analyses, and structural equation modeling. Results: The participants were mainly male (64%) and aged ≥ 71 years (60%). All these patients were attending the hospital outpatient anticoagulation clinic for INR testing; only two patients were currently using INR self-testing, 84% of patients had no knowledge about INR self-testing using a portable coagulometer device, and 96% of patients were never offered the option of the INR self-testing. A significant structural equation model explaining 79% of the variance in patients’ intentions to use INR self-testing was observed. The significant predictors that directly affected patients' intention to use INR self-testing were the perception of technology (β = 0.92, P < 0.001), trust in doctor (β = 0.24, P = 0.028), and affordability (β = 0.15, P = 0.016). In addition, the perception of technology was significantly affected by trust in doctor (β = 0.43, P = 0.002), age (β = 0.32, P < 0.001), and affordability (β = 0.23, P = 0.013); thereby, the intention to use INR self-testing was indirectly affected by trust in doctor (β = 0.40), age (β = 0.29), and affordability (β = 0.21) via the perception of technology. Conclusion: Patients’ intentions to use portable coagulometers for INR self-testing are affected by patients' perceptions about the INR testing device, the cost of device, trust in doctors/clinicians, and the age of the patient, which need to be considered prior to any intervention involving INR self-testing by patients. Manufacturers should focus on increasi
Factors determining patients' intentions to use point-of-care testing medical devices for self-monitoring: the case of international normalized ratio self-testing
Shah SG,Barnett J,Kuljis J,Hone K
Patient Preference and Adherence , 2012,
Abstract: Syed Ghulam Sarwar Shah,1 Julie Barnett,1 Jasna Kuljis,2 Kate Hone,2 Richard Kaczmarski31Multidisciplinary Assessment of Technology Centre for Healthcare, 2Department of Information Systems and Computing, Brunel University London, Uxbridge, Middlesex, UK; 3Department of Haematology, Hillingdon Hospital, Uxbridge, Middlesex, UKPurpose: To identify factors that determine patients' intentions to use point-of-care medical devices, ie, portable coagulometer devices for self-testing of the international normalized ratio (INR) required for ongoing monitoring of blood-coagulation intensity among patients on long-term oral anticoagulation therapy with vitamin K antagonists, eg, warfarin.Methods: A cross-sectional study that applied the technology-acceptance model through a self-completed questionnaire, which was administered to a convenience sample of 125 outpatients attending outpatient anticoagulation services at a district general hospital in London, UK. Data were analyzed using descriptive statistics, factor analyses, and structural equation modeling.Results: The participants were mainly male (64%) and aged ≥ 71 years (60%). All these patients were attending the hospital outpatient anticoagulation clinic for INR testing; only two patients were currently using INR self-testing, 84% of patients had no knowledge about INR self-testing using a portable coagulometer device, and 96% of patients were never offered the option of the INR self-testing. A significant structural equation model explaining 79% of the variance in patients’ intentions to use INR self-testing was observed. The significant predictors that directly affected patients' intention to use INR self-testing were the perception of technology (β = 0.92, P < 0.001), trust in doctor (β = 0.24, P = 0.028), and affordability (β = 0.15, P = 0.016). In addition, the perception of technology was significantly affected by trust in doctor (β = 0.43, P = 0.002), age (β = 0.32, P < 0.001), and affordability (β = 0.23, P = 0.013); thereby, the intention to use INR self-testing was indirectly affected by trust in doctor (β = 0.40), age (β = 0.29), and affordability (β = 0.21) via the perception of technology.Conclusion: Patients’ intentions to use portable coagulometers for INR self-testing are affected by patients' perceptions about the INR testing device, the cost of device, trust in doctors/clinicians, and the age of the patient, which need to be considered prior to any intervention involving INR self-testing by patients. Manufacturers should focus on increasing the affordability of INR testing devices for pa
The place of quality assurance in managing animal welfare during long distance transport
John L. Barnett,Michelle K. Edge,Paul H. Hemsworth
Veterinaria Italiana , 2008,
Abstract: The authors describe the development of an animal welfare component of a quality assurance (QA) programme for the land transportation of livestock in Australia. Relationships among animal welfare practices on farms, during transport and at destinations require an approach that covers the entire production chain. The need for QA programmes includes increased awareness in the transport industry that animal welfare is an issue that engages the broader community and recognition that contentious welfare standards are discussed in the public domain and that public attitudes influence animal welfare standards. Three booklets have been produced that cover animal welfare issues in transport for the major commercial livestock species. Strategies for implementation of QA in industry have also been developed. The welfare standards have been incorporated into the transport industry's QA programme. QA programmes need to be acceptable to the community, be able to meet all customers' requirements and demonstrate to government authorities that they provide appropriate confidence that animal welfare standards have been met. The full impact of QA programmes will be fully appreciated when their ability to deliver comprehensive benefits and continual improvements in animal welfare has been evaluated.
Long-Term Changes in Species Composition and Relative Abundances of Sharks at a Provisioning Site
Juerg M. Brunnschweiler, Kátya G. Abrantes, Adam Barnett
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0086682
Abstract: Diving with sharks, often in combination with food baiting/provisioning, has become an important product of today’s recreational dive industry. Whereas the effects baiting/provisioning has on the behaviour and abundance of individual shark species are starting to become known, there is an almost complete lack of equivalent data from multi-species shark diving sites. In this study, changes in species composition and relative abundances were determined at the Shark Reef Marine Reserve, a multi-species shark feeding site in Fiji. Using direct observation sampling methods, eight species of sharks (bull shark Carcharhinus leucas, grey reef shark Carcharhinus amblyrhynchos, whitetip reef shark Triaenodon obesus, blacktip reef shark Carcharhinus melanopterus, tawny nurse shark Nebrius ferrugineus, silvertip shark Carcharhinus albimarginatus, sicklefin lemon shark Negaprion acutidens, and tiger shark Galeocerdo cuvier) displayed inter-annual site fidelity between 2003 and 2012. Encounter rates and/or relative abundances of some species changed over time, overall resulting in more individuals (mostly C. leucas) of fewer species being encountered on average on shark feeding dives at the end of the study period. Differences in shark community composition between the years 2004–2006 and 2007–2012 were evident, mostly because N. ferrugineus, C. albimarginatus and N. acutidens were much more abundant in 2004–2006 and very rare in the period of 2007–2012. Two explanations are offered for the observed changes in relative abundances over time, namely inter-specific interactions and operator-specific feeding protocols. Both, possibly in combination, are suggested to be important determinants of species composition and encounter rates, and relative abundances at this shark provisioning site in Fiji. This study, which includes the most species from a spatially confined shark provisioning site to date, suggests that long-term provisioning may result in competitive exclusion among shark species.
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