Clinical application of genomics- and phosphoproteomics-based selection of targeted therapy in patients with advanced solid tumors

Precision oncology has come a long way since the introduction of the first targeted drug (trastuzumab) in 1999. Broad molecular testing of tumor tissue has vastly expanded our knowledge of the biology of cancer, leading to a steep increase in the number of approved targeted drugs and an expansion of the labeled indications of these drugs. Off-label use of these new classes of targeted drugs is nowadays better documented and often performed in clinical trials to maximize the learning potential of these experimental treatments for the medical community. As long as no “cure for cancer” exists, there will be room for improvement of our knowledge and approach to treating patients with cancer. General improvements in the logistics, availability of targeted drugs and access to diagnostics and expertise will likely have the greatest impact on direct benefit for patients. In the future, standardized processing and conservation of tumor tissue/biopsies should be possible in all healthcare facilities, and collaborations and sharing of knowledge and resources with the academic institutes will be viable to delivering precision oncology to all patients. If these conditions are met, more patients may potentially benefit from the knowledge and new treatment options resulting from the precision oncology trials. Also, medical oncologists may learn more about molecular testing and interpreting test results from participation in MTBs. To maximize the impact of precision oncology, international collaborations are of utmost importance and research groups throughout the world are encouraged to share best practices and creative solutions to overcome the hurdles that still hamper new initiatives in the field today. Future clinical research may focus on prospective therapy selection using molecular information from other –omics fields, such as phosphoproteomics, especially in patients where no clear monogenetic driver mutations is identified and a comprehensive pathway analysis may give more direction for potential therapeutic strategies. More knowledge on the best method of prioritizing targets for treatments will be essential, as well as clinical trials investigating new combinations of targeted agents. With an increasing understanding of cancer biology and improved strategies for treatment selection, precision oncology will be accessible for patients with advanced cancer and more patients will benefit from the knowledge that we gain today and tomorrow. In the future, treatments based on histology alone may be considered old-fashioned, and multi-omics diagnostics may result in a comprehensible report that can be easily interpreted, and will directly guide treatment decisions for individual patients

Early ADMET profiling of anti-inflammatory alkaloids using validated LC-MS/MS methods

Natural products provide an important and unique source of new lead compounds for drug discovery. Approximately 50% of all new chemical entities are inspired by nature. In the search of novel anti-inflammatory compounds in the ancient medicinal plant Isatis tinctoria, tryptanthrin, indirubin, and (E,Z)-3-(4-hydroxy-3,5-dimethoxybenzylidene)indolin-2-one (indolinone) were identified as pharmacologically active constituents. They inhibit, at low µM to nM concentrations, cyclo-oxygenase-2  (COX-2), 5-lipoxygenase (5-LOX) catalyzed leukotriene synthesis, cyclin-dependent kinase (CDK), glycogensynthase kinase-3b (GSK), and mast cell degranulation. While the molecular modes of action of these alkaloids are not yet fully understood, their unique pharmacological profiles, structural drug-like properties, and low cytotoxicity render these molecules promising anti-inflammatory leads. To further evaluate the potential of these alkaloids as novel anti-inflammatory and anti-allergic leads, an assessment of their ADMET properties was warranted. For exact quantification of the compounds, LC-MS/MS methods were developed and validated according to current regulatory guidelines. To get a first prognostic picture for the in vivo performance of our compounds, a pilot PK study was performed in male Sprague Dawley rats after intravenous administration at a concentration of 2 mg/kg b.w.. Tryptanthrin and indirubin showed a half-life (t1/2) of around 40 min, while indolinone was quickly eliminated (t1/2 = 4 min). As most of the drugs are preferentially administered orally, the gastrointestinal tract (GIT) represents the major site of drug absorption. Human colon carcinoma cells (Caco-2 cells) serve as the method of choice to predict human drug absorption across the intestinal wall in vitro. To study the permeability of the three compounds across the epithelial monolayer, the alkaloids were screened at concentrations of 5-10 µM in the Caco-2 assay. As efflux transporters can greatly impact the in vivo absorption and, thus, the bioavailability of a drug candidate, the compounds were tested for possible P-glycoprotein (P-gp) interaction. Therefore, the alkaloids were co-incubated with the P-gp inhibitor verapamil (50 µM). Active efflux was assessed by calculating the efflux ratio (ER) from bidirectional assays. Due to high lipophilicity of indirubin, the compound precipitated in the transporter buffer and was thus excluded for further investigations in aqueous solutions. Tryptanthrin displayed a high permeability (Papp > 32.0 x 10-6 cm/s) across the cell monolayer. The efflux ratio below 2 (< 1.12) and the unchanged Papp values in presence of the P-glycoprotein (P-gp) inhibitor verapamil indicated that tryptanthrin was not involved in P-gp mediated efflux. In the Caco-2 assay, the recovery of indolinone was low, pointing to possibly extensive phase II metabolism. Further investigation by a high-resolution mass spectrometry (HR-MS) system revealed the formation of two sulfate and two glucuronide conjugates for indolinone. Another well-known biological barrier in the human body is the blood-brain barrier (BBB). To evaluate the BBB permeation potential of tryptanthrin and indolinone, the compounds were tested in three cell-based human and animal BBB models. Data obtained with the human and animal BBB models showed good correlation and were indicative of a high BBB permeation potential of tryptanthrin and indolinone. Furthermore, active-mediated efflux was evaluated by calculating the ER from bidirectional assays. The ERs below 2 suggested that both compounds were not involved in active-mediated efflux. Besides P-gp, another critical anti-target in drug development is the human ether-a-go-go (hERG) potassium channel. In the late 1990s, an increasing number of non-cardiovascular drugs have been withdrawn from the market due to cardiotoxic side-effects linked to hERG blocking. Since then, regulatory agencies insist on acquiring experimental hERG data of drug candidates before moving into clinical trials. Possible cardiotoxic liability of the compounds was assessed in vitro, by measurement of an inhibitory effect on hERG tail currents in stably transfected HEK 293 cells using the patch-clamp technique. Slight hERG inhibition was found for tryptanthrin (IC50 of 22 µM) and indolinone (IC50 of 25 µM). Data obtained from the in vitro assays were corroborated by in silico predictions. For tryptanthrin and indolinone, all criteria for high human oral absorption and passive BBB penetration were met. In addition, the slight hERG inhibition found for tryptanthrin and indolinone in vitro could be confirmed by in silico predictions

Statistical Challenges and Methods for Missing and Imbalanced Data

Missing data remains a prevalent issue in every area of research. The impact of missing data, if not carefully handled, can be detrimental to any statistical analysis. Some statistical challenges associated with missing data include, loss of information, reduced statistical power and non-generalizability of findings in a study. It is therefore crucial that researchers pay close and particular attention when dealing with missing data. This multi-paper dissertation provides insight into missing data across different fields of study and addresses some of the above mentioned challenges of missing data through simulation studies and application to real datasets. The first paper of this dissertation addresses the dropout phenomenon in single-cell RNA (scRNA) sequencing through a comparative analyses of some existing scRNA sequencing techniques. The second paper of this work focuses on using simulation studies to assess whether it is appropriate to address the issue of non-detects in data using a traditional substitution approach, imputation, or a non-imputation based approach. The final paper of this dissertation presents an efficient strategy to address the issue of imbalance in data at any degree (whether moderate or highly imbalanced) by combining random undersampling with different weighting strategies. We conclude generally, based on findings from this dissertation that, missingness is not always lack of information but interestingness that needs to investigated

Risk prediction models for cardiovascular disease and overall mortality

Prediction or prognostication is at the core of modern evidence-based medicine. Prediction of overall mortality and cardiovascular disease can be improved by a systematic evaluation of measurements from large-scale epidemiological studies or by using nested sampling designs to discover new markers from omics technologies. In study I, we investigated if prediction measures such as calibration, discrimination and reclassification could be calculated within traditional sampling designs and which of these designs were the most efficient. We found that is possible to calculate prediction measures by using a proper weighting system and that a stratified casecohort design is a reasonable choice both in terms of efficiency and simplicity. In study II, we investigated the clinical utility of several genetic scores for incident coronary heart disease. We found that genetic information could be of clinical value in improving the allocation of patients to correct risk strata and that the assessment of a genetic risk score among intermediate risk subjects could help to prevent about one coronary heart disease event every 318 people screened. In study III, we explored the association between circulating metabolites and incident coronary heart disease. We found four new metabolites associated with coronary heart disease independently of established cardiovascular risk factors and with evidence of clinical utility. By using genetic information we determined a potential causal effect on coronary heart disease of one of these novel metabolites. In study IV, we compared a large number of demographics, health and lifestyle measurements for association with all-cause and cause-specific mortality. By ranking measurements in terms of their predictive abilities we could provide new insights about their relative importance, as well as reveal some unexpected associations. Moreover we developed and validated a prediction score for five-year mortality with good discrimination ability and calibrated it for the entire UK population. In conclusion, we applied a translational approach spanning from the discovery of novel biomarkers to their evaluation in terms of clinical utility. We combined this effort with methodological improvements aimed to expand prediction measures in settings that were not previously explored. We identified promising novel metabolomics markers for cardiovascular disease and supported the potential clinical utility of a genetic score in primary prevention. Our results might fuel future studies aimed to implement these findings in clinical practice

The responsive reply chain: the influence of the positioning of decoupling points

Manufacturing supply chains have been challenged by high competition, dynamic, and stochastic conditions. They have to be constantly responsive in today’s ever-changing manufacturing environment. The proper positioning of decoupling points for material flow and information flow has a significant potential for increasing responsiveness in a supply chain. Positioning the material decoupling point as close to the end consumer as possible whilst the information decoupling point is positioned upstream is the key to the industries’ ability to reduce lead time and enhance performance in the dynamic behaviour of the supply chain. [Continues.

Incorporating standardised drift-tube ion mobility to enhance non-targeted assessment of the wine metabolome (LC×IM-MS)

Liquid chromatography with drift-tube ion mobility spectrometry-mass spectrometry (LCxIM-MS) is emerging as a powerful addition to existing LC-MS workflows for addressing a diverse range of metabolomics-related questions [1,2]. Importantly, excellent precision under repeatability and reproducibility conditions of drift-tube IM separations [3] supports the development of non-targeted approaches for complex metabolome assessment such as wine characterisation [4]. In this work, fundamentals of this new analytical metabolomics approach are introduced and application to the analysis of 90 authentic red and white wine samples originating from Macedonia is presented. Following measurements, intersample alignment of metabolites using non-targeted extraction and three-dimensional alignment of molecular features (retention time, collision cross section, and high-resolution mass spectra) provides confidence for metabolite identity confirmation. Applying a fingerprinting metabolomics workflow allows statistical assessment of the influence of geographic region, variety, and age. This approach is a state-of-the-art tool to assess wine chemodiversity and is particularly beneficial for the discovery of wine biomarkers and establishing product authenticity based on development of fingerprint libraries

Improving the Performance of Wireless LANs

This book quantifies the key factors of WLAN performance and describes methods for improvement. It provides theoretical background and empirical results for the optimum planning and deployment of indoor WLAN systems, explaining the fundamentals while supplying guidelines for design, modeling, and performance evaluation. It discusses environmental effects on WLAN systems, protocol redesign for routing and MAC, and traffic distribution; examines emerging and future network technologies; and includes radio propagation and site measurements, simulations for various network design scenarios, numerous illustrations, practical examples, and learning aids

Modelling the impact of port-centric logistics cluster on inter-firm competition

Port-centric logistics clusters are considered as intermodal gateways of international trade, which connect national economies with global production networks. Globalization and the resultant interdependency between producers and the markets they serve have thus increased the vitality of sophisticated global seaport hubs and networks. These clusters are a spatial aggregation of logistics-related interconnected and interdependent companies that assist in smooth port operations. Singapore, Rotterdam, and Dubai ports are world-class models of port-centric logistics clusters. The formation of these clusters is a derivative of regional growth and offer a conducive business environment within a geographically contained area. Despite the increasing popularity of cluster theory, there seems a lack of unified theoretical framework, and identification methods of the cluster because of the divergent approaches by which it has been proposed including but not limited to agglomeration economies, industrial districts, knowledge spillover, regional development, innovation system, and network, etc. There has been insufficient evidence to empirically evaluate the prevalence of port-centric logistics cluster, assess the functionality and characteristics of port-centric logistics clusters. There is also disagreement on three key questions: what industry types port-centric logistics clusters constitute, what methods are appropriate to delineate the boundary of port-centric logistics cluster and do the logistics firms within-cluster demonstrate higher inter-firm competition through competitive rivalry near port than away from port vicinity. In this study, a spatial approach is adopted to geographically delineate the spatial congregation of port-centric logistics employment using Melbourne as a case. Using the Census data from Australian Bureau of Statistics, this study aims to identify the industrial sectors that characterize port-centric logistics cluster followed by delineating the geographic boundary of cluster around Melbourne port that represents the area from where the seaport draws its workers in different port-related industries.&amp;nbsp; Using the information about where people live and work, and what industry they work in, the total workforce employed in port-related industries within the close vicinity of Port of Melbourne is estimated. Areas, where port-related employment is above nation&#039;s logistics employment average and spatially adjacent, are categorized as part of the port-centric logistics cluster. The employment gradient mapped in GIS illustrates the territorial representation of port-centric logistics cluster. The establishment of Melbourne port-centric logistics cluster could mean the opportunities for organizations to achieve agglomeration economies, increase rivalry among organizations to promote competition, closer proximity between customers and supplier, shared resources, increased inter-firm interactions, and knowledge sharing. Further, this study adopts a quantitative approach to model the relationship between the cluster and inter-firm competition. An online and paper-based survey was administered to 379 logistics firms within and outside the cluster. The constructs were adopted from previous studies and validated items were used. A pilot test was conducted to assess constructs reliability and validity. The measurement and structural models were tested using structural equation modelling. The results show a significant impact of clustering of logistics firms on inter-firm competition through competitive rivalry among firms. A multi-group analysis reveals a significant difference between two groups in relation to the impact of clustering around port geography and away from port on inter-firm competition. The study found that the logistics firms demonstrate accentuated competition near the port in a clustered environment than away from port geography. This shows the impact of land use consolidation by the State Government in its effort to boost transport and warehousing employment closer to the port. The contributions this study offer includes validated conceptual framework to evaluate the impact of clustering of logistics firms on inter-firm competition. From managerial perspective this study offers on the opportunity for the manager on how to make a locational decision to provide the services. The decision is based on considering the potential benefits of collocating into the clustered environment to enhance their capabilities through spill over effect which is inherited within the cluster. Moreover, the knowledge created through this study can be utilized to draft policies regarding transportation planning and urban land use to support the geographical area around the port which may, in turn, stimulate the logistics firms to work in the designated zone. The major limitation of the study is using the data only from Melbourne. A future study may consider comparing the data from two different cities or country to validate the results of this study of the positive impact of clustering on the competitive rivalry