A method for matching patients to advanced prostate cancer clinical trials

Objective: To illustrate a new method for simplifying patient recruitment for advanced prostate cancer clinical trials using natural language processing techniques. Background: The identification of eligible participants for clinical trials is a critical factor to increase patient recruitment rates and an important issue for discovery of new treatment interventions. The current practice of identifying eligible participants is highly constrained due to manual processing of disparate sources of unstructured patient data. Informatics-based approaches can simplify the complex task of evaluating patient’s eligibility for clinical trials. We show that an ontology-based approach can address the challenge of matching patients to suitable clinical trials. Methods: The free-text descriptions of clinical trial criteria as well as patient data were analysed. A set of common inclusion and exclusion criteria was identified through consultations with expert clinical trial coordinators. A research prototype was developed using Unstructured Information Management Architecture (UIMA) that identified SNOMED CT concepts in the patient data and clinical trial description. The SNOMED CT concepts model the standard clinical terminology that can be used to represent and evaluate patient’s inclusion/exclusion criteria for the clinical trial. Results: Our experimental research prototype describes a semi-automated method for filtering patient records using common clinical trial criteria. Our method simplified the patient recruitment process. The discussion with clinical trial coordinators showed that the efficiency in patient recruitment process measured in terms of information processing time could be improved by 25%. Conclusion: An UIMA-based approach can resolve complexities in patient recruitment for advanced prostate cancer clinical trials.

Mixture models of nucleotide sequence evolution that account for heterogeneity in the substitution process across sites and across lineages

Molecular phylogenetic studies of homologous sequences of nucleotides often assume that the underlying evolutionary process was globally stationary, reversible, and homogeneous (SRH), and that a model of evolution with one or more site-specific and time-reversible rate matrices (e.g., the GTR rate matrix) is enough to accurately model the evolution of data over the whole tree. However, an increasing body of data suggests that evolution under these conditions is an exception, rather than the norm. To address this issue, several non-SRH models of molecular evolution have been proposed, but they either ignore heterogeneity in the substitution process across sites (HAS) or assume it can be modeled accurately using the distribution. As an alternative to these models of evolution, we introduce a family of mixture models that approximate HAS without the assumption of an underlying predefined statistical distribution. This family of mixture models is combined with non-SRH models of evolution that account for heterogeneity in the substitution process across lineages (HAL). We also present two algorithms for searching model space and identifying an optimal model of evolution that is less likely to over- or underparameterize the data. The performance of the two new algorithms was evaluated using alignments of nucleotides with 10 000 sites simulated under complex non-SRH conditions on a 25-tipped tree. The algorithms were found to be very successful, identifying the correct HAL model with a 75% success rate (the average success rate for assigning rate matrices to the tree's 48 edges was 99.25%) and, for the correct HAL model, identifying the correct HAS model with a 98% success rate. Finally, parameter estimates obtained under the correct HAL-HAS model were found to be accurate and precise. The merits of our new algorithms were illustrated with an analysis of 42 337 second codon sites extracted from a concatenation of 106 alignments of orthologous genes encoded by the nuclear genomes of Saccharomyces cerevisiae, S. paradoxus, S. mikatae, S. kudriavzevii, S. castellii, S. kluyveri, S. bayanus, and Candida albicans. Our results show that second codon sites in the ancestral genome of these species contained 49.1% invariable sites, 39.6% variable sites belonging to one rate category (V1), and 11.3% variable sites belonging to a second rate category (V2). The ancestral nucleotide content was found to differ markedly across these three sets of sites, and the evolutionary processes operating at the variable sites were found to be non-SRH and best modeled by a combination of eight edge-specific rate matrices (four for V1 and four for V2). The number of substitutions per site at the variable sites also differed markedly, with sites belonging to V1 evolving slower than those belonging to V2 along the lineages separating the seven species of Saccharomyces. Finally, sites belonging to V1 appeared to have ceased evolving along the lineages separating S. cerevisiae, S. paradoxus, S. mikatae, S. kudriavzevii, and S. bayanus, implying that they might have become so selectively constrained that they could be considered invariable sites in these species.

SnO2 decorated graphene nanocomposite anode materials prepared via an up-scalable wet-mechanochemical process for sodium ion batteries

A facile and up-scalable wet-mechanochemical process is designed for fabricating ultra-fine SnO2 nanoparticles anchored on graphene networks for use as anode materials for sodium ion batteries. A hierarchical structure of the SnO2@graphene composite is obtained from the process. The resultant rechargeable SIBs achieved high rate capability and good cycling stability.

Business process management as the 'killer app' for Petri nets

Since their inception in 1962, Petri nets have been used in a wide variety of application domains. Although Petri nets are graphical and easy to understand, they have formal semantics and allow for analysis techniques ranging from model checking and structural analysis to process mining and performance analysis. Over time Petri nets emerged as a solid foundation for Business Process Management (BPM) research. The BPM discipline develops methods, techniques, and tools to support the design, enactment, management, and analysis of operational business processes. Mainstream business process modeling notations and workflow management systems are using token-based semantics borrowed from Petri nets. Moreover, state-of-the-art BPM analysis techniques are using Petri nets as an internal representation. Users of BPM methods and tools are often not aware of this. This paper aims to unveil the seminal role of Petri nets in BPM.

Authorisation management in business process environments: An authorisation model and a policy model

This thesis provides two main contributions. The first one is BP-TRBAC, a unified authorisation model that can support legacy systems as well as business process systems. BP-TRBAC supports specific features that are required by business process environments. BP-TRBAC is designed to be used as an independent enterprise-wide authorisation model, rather than having it as part of the workflow system. It is designed to be the main authorisation model for an organisation. The second contribution is BP-XACML, an authorisation policy language that is designed to represent BPM authorisation policies for business processes. The contribution also includes a policy model for BP-XACML. Using BP-TRBAC as an authorisation model together with BP-XACML as an authorisation policy language will allow an organisation to manage and control authorisation requests from workflow systems and other legacy systems.

Nitrogen-doped graphene films from chemical vapor deposition of pyridine: Influence of process parameters on the electrical and optical properties

Graphene films were produced by chemical vapor deposition (CVD) of pyridine on copper substrates. Pyridine-CVD is expected to lead to doped graphene by the insertion of nitrogen atoms in the growing sp2 carbon lattice, possibly improving the properties of graphene as a transparent conductive film. We here report on the influence that the CVD parameters (i.e., temperature and gas flow) have on the morphology, transmittance, and electrical conductivity of the graphene films grown with pyridine. A temperature range between 930 and 1070 °C was explored and the results were compared to those of pristine graphene grown by ethanol-CVD under the same process conditions. The films were characterized by atomic force microscopy, Raman and X-ray photoemission spectroscopy. The optical transmittance and electrical conductivity of the films were measured to evaluate their performance as transparent conductive electrodes. Graphene films grown by pyridine reached an electrical conductivity of 14.3 × 105 S/m. Such a high conductivity seems to be associated with the electronic doping induced by substitutional nitrogen atoms. In particular, at 930 °C the nitrogen/carbon ratio of pyridine-grown graphene reaches 3%, and its electrical conductivity is 40% higher than that of pristine graphene grown from ethanol-CVD.

Wave propagation in elastic solids undergoing damage and growth process

Modeling and analysis of wave propagation in elastic solids undergoing damage and growth process are reported in this paper. Two types of diagnostic problems, (1) the propagation of waves in the presence of a slow growth process and (2) the propagation of waves in the presence of a fast growth process, are considered. The proposed model employs a slow and a fast time scale and a homogenization technique in the wavelength scale. A detailed analysis of wave dispersion is carried out. A spectral analysis reveals certain low-frequency bands, where the interaction between the wave and the growth process produces acoustic metamaterial-like behavior. Various practical issues in designing an efficient method of acousto-ultrasonic wave based diagnostics of the growth process are discussed. Diagnostics of isotropic damage in a ductile or quasi-brittle solid by using a micro-second pulsating signal is considered for computer simulations, which is to illustrate the practical application of the proposed modeling and analysis. The simulated results explain how an estimate of signal spreading can be effectively employed to detect the presence of a steady-state damage or the saturation of a process.

BPMN process views construction

Process view technology is catching more attentions in modern business process management, as it enables the customisation of business process representation. This capability helps improve the privacy protection, authority control, flexible display, etc., in business process modelling. One of approaches to generate process views is to allow users to construct an aggregate on their underlying processes. However, most aggregation approaches stick to a strong assumption that business processes are always well-structured, which is over strict to BPMN. Aiming to build process views for non-well-structured BPMN processes, this paper investigates the characteristics of BPMN structures, tasks, events, gateways, etc., and proposes a formal process view aggregation approach to facilitate BPMN process view creation. A set of consistency rules and construction rules are defined to regulate the aggregation and guarantee the order preservation, structural and behaviour correctness and a novel aggregation technique, called EP-Fragment, is developed to tackle non-well-structured BPMN processes.

Role-based process view derivation and composition

The process view concept deploys a partial and temporal representation to adjust the visible view of a business process according to various perception constraints of users. Process view technology is of practical use for privacy protection and authorization control in process-oriented business management. Owing to complex organizational structure, it is challenging for large companies to accurately specify the diverse perception of different users over business processes. Aiming to tackle this issue, this article presents a role-based process view model to incorporate role dependencies into process view derivation. Compared to existing process view approaches, ours particularly supports runtime updates to the process view perceivable to a user with specific view merging operations, thereby enabling the dynamic tracing of process perception. A series of rules and theorems are established to guarantee the structural consistency and validity of process view transformation. A hypothetical case is conducted to illustrate the feasibility of our approach, and a prototype is developed for the proof-of-concept purpose.

A High-Resolution Transmission of the Precipitation Process in a Electron Microscopy Study Dilute Ti-N Alloy

The precipitation processes in dilute nitrogen alloys of titanium have been examined in detail by conventional transmission electron microscopy (CTEM) and high-resolution electron microscopy (HREM). The alloy Ti-2 at. pct N on quenching from its high-temperature beta phase field has been found to undergo early stages of decomposition. The supersaturated solid solution (alpha''-hcp) on decomposition gives rise to an intimately mixed, irresolvable product microstructure. The associated strong tweed contrast presents difficulties in understanding the characteristic features of the process. Therefore, HREM has been carried out with a view to getting a clear picture of the decomposition process. Studies on the quenched samples of the alloy suggest the formation of solute-rich zones of a few atom layers thick, randomly distributed throughout the matrix. On aging, these zones grow to a size beyond which the precipitate/matrix interfaces appear to become incoherent and the alpha' (tetragonal) product phase is seen distinctly. The structural details, the crystallography of the precipitation process, and the sequence of precipitation reaction in the system are illustrated.

Different phenomenological theories and their abilities to describe the interdiffusion process in a binary system during multiphase growth

There are essentially two different phenomenological models available to describe the interdiffusion process in binary systems in the olid state. The first of these, which is used more frequently, is based on the theory of flux partitioning. The second model, developed much more recently, uses the theory of dissociation and reaction. Although the theory of flux partitioning has been widely used, we found that this theory does not account for the mobility of both species and therefore is not suitable for use in most interdiffusion systems. We have first modified this theory to take into account the mobility of both species and then further extended it to develop relations or the integrated diffusion coefficient and the ratio of diffusivities of the species. The versatility of these two different models is examined in the Co-Si system with respect to different end-member compositions. From our analysis, we found that the applicability of the theory of flux partitioning is rather limited but the theory of dissociation and reaction can be used in any binary system.

Removal Of Chromium From Electroplating Effluents By The Sulfide Process

A method has been developed for the removal of chromium using ferrous sulphide generated in situ. The effects of experimental parameters such as pH, reagent dosages, interference from cations and chelating agents have been investigated. Under optimum conditions, removal efficiencies of 99 and 97% for synthetic and industrial samples have been obtained. The method offers all the advantages of sulphide precipitation process and can be adopted easily for industrial effluents.

Effects of the filling process on the evolution of the mushy zone and macrosegregation in alloy casting

A numerical model of the entire casting process starting from the mould filling stage to complete solidification is presented. The model takes into consideration any phase change taking place during the filling process. A volume of fluid method is used for tracking the metal–air interface during filling and an enthalpy based macro-scale solidification model is used for the phase change process. The model is demonstrated for the case of filling and solidification of Pb–15 wt%Sn alloy in a side-cooled two-dimensional rectangular cavity, and the resulting evolution of a mushy region and macrosegregation are studied. The effects of process parameters related to filling, namely degree of melt superheat and filling velocity on macrosegregation in the cavity, are also investigated. Results show significant differences in the progress of the mushy zone and macrosegregation pattern between this analysis and conventional analysis without the filling effect.

Temperature measurements in the boron carbide manufacturing process - A hot model study

Boron carbide is produced in a heat resistance furnace using boric oxide and petroleum coke as the raw materials. The product yield is very low. Heat transfer plays an important role in the formation of boron carbide. Temperature at the core reaches up to 2600 K. No experimental study is available in the open literature for this high temperature process particularly in terms of temperature measurement and heat transfer. Therefore, a laboratory scale hot model of the process has been setup to measure the temperatures in harsh conditions at different locations in the furnace using various temperature measurement devices such as pyrometer and various types of thermocouple. Particular attention was paid towards the accuracy and reliability of the measured data. The recorded data were analysed to understand the heat transfer process inside the reactor and the effect of it on the formation of boron carbide.