1,721,129 research outputs found
DASH: a novel analysis method for molecular dynamics simulation data. Analysis of ligands of PPAR-gamma
No full textA novel molecular dynamics (MD) analysis algorithm, DASH, is introduced in this paper. DASH has been developed to utilize the sequential nature of MD simulation data. By adjusting a set of parameters, the sensitivity of DASH can be controlled, allowing molecular motions of varying magnitudes to be detected or ignored as desired, with no knowledge of the number of conformations required being prerequisite. MD simulations of three synthetic ligands of the orphan nuclear receptor PPARgamma were generated in vacuo using Tripos's SYBYL and used as the training set for DASH. Two X-ray crystal structures of PPARgamma complexed with Rosiglitazone were compared to gain knowledge of the pharmacophoric conformation; this showed that the conformation of the ligand is significantly different between the two structures, indicating that there is no distinct conformation in which rosiglitazone binds to PPARgamma but multiple binding modes. An investigation into simulation length was carried out. A simulation of 5 ns was found to give highly variable results, whereas a simulation of 25 ns gave a representative window of motion for molecules of this size. DASH was compared with Ward's hierarchical cluster analysis method. The results show that DASH analysis is as good as Ward analysis in some areas (e.g. conformation identification) and is superior in others (e.g. speed and input size).</p
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Recommended from our members
Standard Testing Protocols for CO2 Sensors and CO2-based Demand Control
Full text linkCarbon dioxide (CO2)-based demand control ventilation (DCV) automatically adjusts building ventilation rates based on indoor CO2 concentration. Since the indoor CO2 concentration is directly related to the occupancy, the purpose of CO2-based DCV is to conserve energy by reducing the ventilation rates during periods of low occupancy. In this work, two standard testing protocols for CO2 sensors and CO2-based DCV system controllers are developed and performed on several currently available CO2 sensors and DCV system controllers. Test results are provided and discussed
Recommended from our members
Control-Enabled Approaches for Active Detection of Cyberattacks on Process Control Systems
Full text linkIncreasing reliance on wireless communication and complexity of cyberattacks have rendered industrial control systems (ICSs) such as process control systems (PCSs) (which are ICSs that operate chemical manufacturing processes) vulnerable to cyberattacks by malicious agents. In the past decade, several highly sophisticated cyberattacks (e.g., Stuxnet virus (2010), German steel mill attack (2014), Ukrainian power grid attack (2015), TRITON (2017)) have demonstrated that information technology (IT) infrastructure-based solutions to handling cyberattacks on control systems are insufficient on their own. An increasing body of research has focused on developing operational technology (OT)-based approaches to enhance the cyberattack resilience of PCSs. Cyberattack resilience here is defined as the ability of a PCS to minimize the impact of a cyberattack and recover from it. Research on cyberattack resilience of PCSs involves approaches that range from designing PCSs that are inherently attack-resilient to developing cyberattack detection, identification and mitigation schemes. Cyberattack detection schemes are OT-based anomaly detection schemes that reveal the presence of a cyberattack on a PCS by monitoring the process operational data for anomalies and are an important component of a cyberattack resilient PCS. The motivating realization behind the work presented in this dissertation is that the influence of PCS design parameters may be exploited to reveal the presence of an ongoing cyberattack on a PCS. In the chapters that follow, several approaches for cyberattack detection are presented. First, a control screening approach that may be used to incorporate attack detectability within the conventional PCS design considerations is presented. The screening algorithm is based on a characterization of the interdependence between the PCS design parameters, and the ability of the detection scheme to detect the attack (attack detectability). Next, for a certain class of detection schemes monitoring a process, the relationship between the PCS design parameters, the closed-loop stability of the attacked process, and the detectability of certain attacks is rigorously characterized. Based on the characterization, for attack detection, it may be preferred to operate the process under performance degrading ``attack-sensitive'' parameters. To manage a potential tradeoff between attack detection and closed-loop performance, an active detection method utilizing switching between two control modes is developed. Under the active detection method, extended process operation is under a first (nominal) mode, the control parameters (called nominal parameters) for which are selected to meet traditional control design criteria. Under the second (attack-sensitive) mode, the process is operated with attack-sensitive parameters. The process is operated under the attack-sensitive mode intermittently to probe the process for an ongoing attack. Control parameter switching on a process under steady-state operation may induce transient behavior, which may trigger false alarms in the class of detection schemes. For processes with an invertible output matrix, a switching condition is imposed to select control parameter switching instances such that false alarms in the system are minimized. To eliminate false alarms due to control switching on processes with a non-invertible output matrix, a reachable set-based detection scheme is developed. The reachable set-based cyberattack detection scheme guarantees a zero false alarm rate during transient attack-free process operation by tracking the evolution of the monitoring variable values with respect to their reachable sets of the attack-free process at each time step. Following this, a switching-enabled active detection method that utilizes the reachable set-based detection scheme to enable attack detection with a zero false alarm rate is presented. Furthermore, the control parameter switching instances between the nominal to attack-sensitive modes are randomized, thereby preserving the confidentiality of the detection method. Destabilization of a process for attack detection (as with operation under attack-sensitive mode) may not always be preferred. Two different alternate control modes that may be used to induce perturbations for active attack detection without destabilizing the attacked process are presented. To guarantee attack detection, the alternate control mode selected must induce ``attack-revealing'' perturbations in the process. Reachability analysis is used to present a set-based condition that if satisfied means that the control mode selected induces attack-revealing perturbations. Different models of false data injection attacks are considered. A screening algorithm that may be used to select an attack-revealing control mode for the active detection of attacks is presented. The application of all methods are applied to simulations of different illustrative processes to demonstrate their attack detection capabilities
- …
