Angiogenic activity of breast cancer patients' monocytes reverted by combined use of systems modeling and experimental approaches.

Angiogenesis plays a key role in tumor growth and cancer progression. TIE-2-expressing monocytes (TEM) have been reported to critically account for tumor vascularization and growth in mouse tumor experimental models, but the molecular basis of their pro-angiogenic activity are largely unknown. Moreover, differences in the pro-angiogenic activity between blood circulating and tumor infiltrated TEM in human patients has not been established to date, hindering the identification of specific targets for therapeutic intervention. In this work, we investigated these differences and the phenotypic reversal of breast tumor pro-angiogenic TEM to a weak pro-angiogenic phenotype by combining Boolean modelling and experimental approaches. Firstly, we show that in breast cancer patients the pro-angiogenic activity of TEM increased drastically from blood to tumor, suggesting that the tumor microenvironment shapes the highly pro-angiogenic phenotype of TEM. Secondly, we predicted in silico all minimal perturbations transitioning the highly pro-angiogenic phenotype of tumor TEM to the weak pro-angiogenic phenotype of blood TEM and vice versa. In silico predicted perturbations were validated experimentally using patient TEM. In addition, gene expression profiling of TEM transitioned to a weak pro-angiogenic phenotype confirmed that TEM are plastic cells and can be reverted to immunological potent monocytes. Finally, the relapse-free survival analysis showed a statistically significant difference between patients with tumors with high and low expression values for genes encoding transitioning proteins detected in silico and validated on patient TEM. In conclusion, the inferred TEM regulatory network accurately captured experimental TEM behavior and highlighted crosstalk between specific angiogenic and inflammatory signaling pathways of outstanding importance to control their pro-angiogenic activity. Results showed the successful in vitro reversion of such an activity by perturbation of in silico predicted target genes in tumor derived TEM, and indicated that targeting tumor TEM plasticity may constitute a novel valid therapeutic strategy in breast cancer.

A survey of transposable element classification systems--a call for a fundamental update to meet the challenge of their diversity and complexity.

The increase of publicly available sequencing data has allowed for rapid progress in our understanding of genome composition. As new information becomes available we should constantly be updating and reanalyzing existing and newly acquired data. In this report we focus on transposable elements (TEs) which make up a significant portion of nearly all sequenced genomes. Our ability to accurately identify and classify these sequences is critical to understanding their impact on host genomes. At the same time, as we demonstrate in this report, problems with existing classification schemes have led to significant misunderstandings of the evolution of both TE sequences and their host genomes. In a pioneering publication Finnegan (1989) proposed classifying all TE sequences into two classes based on transposition mechanisms and structural features: the retrotransposons (class I) and the DNA transposons (class II). We have retraced how ideas regarding TE classification and annotation in both prokaryotic and eukaryotic scientific communities have changed over time. This has led us to observe that: (1) a number of TEs have convergent structural features and/or transposition mechanisms that have led to misleading conclusions regarding their classification, (2) the evolution of TEs is similar to that of viruses by having several unrelated origins, (3) there might be at least 8 classes and 12 orders of TEs including 10 novel orders. In an effort to address these classification issues we propose: (1) the outline of a universal TE classification, (2) a set of methods and classification rules that could be used by all scientific communities involved in the study of TEs, and (3) a 5-year schedule for the establishment of an International Committee for Taxonomy of Transposable Elements (ICTTE).

Plant Mating Systems: Female Sterility in the Driver's Seat.

Violation of Mendel's Law of Segregation by selfish X chromosomes that favour their own transmission is known for a number of organisms. Now, a new study reveals sex-ratio distortion favouring males and explains previously puzzling sex ratios in a Mediterranean shrub.

Searching electronic marketplaces

The main objective of this thesis was to analyze the usability of registers and indexes of electronic marketplaces. The work is focused on UDDI-based electronic marketplaces, which are standardized by the W3C. UDDI-registers are usable in intranets, extranets and in Internet. Using UDDI-registers Web-services can be searched in many ways, including alphabetical and domain specific searches. Humans and machines can use the features UDDI-registers. The thesis deals the design principles, architectures and specifications of UDDI-registers. In addition, the thesis includes the design and the specifications of an electronic marketplace developed for supporting electronic logistics services.

Managing the Sick Child in the Era of Declining Malaria Transmission: Development of ALMANACH, an Electronic Algorithm for Appropriate Use of Antimicrobials.

OBJECTIVE: To review the available knowledge on epidemiology and diagnoses of acute infections in children aged 2 to 59 months in primary care setting and develop an electronic algorithm for the Integrated Management of Childhood Illness to reach optimal clinical outcome and rational use of medicines. METHODS: A structured literature review in Medline, Embase and the Cochrane Database of Systematic Review (CDRS) looked for available estimations of diseases prevalence in outpatients aged 2-59 months, and for available evidence on i) accuracy of clinical predictors, and ii) performance of point-of-care tests for targeted diseases. A new algorithm for the management of childhood illness (ALMANACH) was designed based on evidence retrieved and results of a study on etiologies of fever in Tanzanian children outpatients. FINDINGS: The major changes in ALMANACH compared to IMCI (2008 version) are the following: i) assessment of 10 danger signs, ii) classification of non-severe children into febrile and non-febrile illness, the latter receiving no antibiotics, iii) classification of pneumonia based on a respiratory rate threshold of 50 assessed twice for febrile children 12-59 months; iv) malaria rapid diagnostic test performed for all febrile children. In the absence of identified source of fever at the end of the assessment, v) urine dipstick performed for febrile children <2 years to consider urinary tract infection, vi) classification of 'possible typhoid' for febrile children >2 years with abdominal tenderness; and lastly vii) classification of 'likely viral infection' in case of negative results. CONCLUSION: This smartphone-run algorithm based on new evidence and two point-of-care tests should improve the quality of care of <5 year children and lead to more rational use of antimicrobials.

Comparison of Inoculation with the InoqulA and WASP Automated Systems with Manual Inoculation.

The quality of sample inoculation is critical for achieving an optimal yield of discrete colonies in both monomicrobial and polymicrobial samples to perform identification and antibiotic susceptibility testing. Consequently, we compared the performance between the InoqulA (BD Kiestra), the WASP (Copan), and manual inoculation methods. Defined mono- and polymicrobial samples of 4 bacterial species and cloudy urine specimens were inoculated on chromogenic agar by the InoqulA, the WASP, and manual methods. Images taken with ImagA (BD Kiestra) were analyzed with the VisionLab version 3.43 image analysis software to assess the quality of growth and to prevent subjective interpretation of the data. A 3- to 10-fold higher yield of discrete colonies was observed following automated inoculation with both the InoqulA and WASP systems than that with manual inoculation. The difference in performance between automated and manual inoculation was mainly observed at concentrations of >10(6) bacteria/ml. Inoculation with the InoqulA system allowed us to obtain significantly more discrete colonies than the WASP system at concentrations of >10(7) bacteria/ml. However, the level of difference observed was bacterial species dependent. Discrete colonies of bacteria present in 100- to 1,000-fold lower concentrations than the most concentrated populations in defined polymicrobial samples were not reproducibly recovered, even with the automated systems. The analysis of cloudy urine specimens showed that InoqulA inoculation provided a statistically significantly higher number of discrete colonies than that with WASP and manual inoculation. Consequently, the automated InoqulA inoculation greatly decreased the requirement for bacterial subculture and thus resulted in a significant reduction in the time to results, laboratory workload, and laboratory costs.

Asymmetrical nature of the Trollius-Chiastocheta interaction: insights into the evolution of nursery pollination systems

The mutualistic versus antagonistic nature of an interaction is defined by costs and benefits of each partner, which may vary depending on the environment. Contrasting with this dynamic view, several pollination interactions are considered as strictly obligate and mutualistic. Here, we focus on the interaction between Trollius europaeus and Chiastocheta flies, considered as a specialized and obligate nursery pollination system - the flies are thought to be exclusive pollinators of the plant and their larvae develop only in T.europaeus fruits. In this system, features such as the globelike flower shape are claimed to have evolved in a coevolutionary context. We examine the specificity of this pollination system and measure traits related to offspring fitness in isolated T.europaeus populations, in some of which Chiastocheta flies have gone extinct. We hypothesize that if this interaction is specific and obligate, the plant should experience dramatic drop in its relative fitness in the absence of Chiastocheta. Contrasting with this hypothesis, T.europaeus populations without flies demonstrate a similar relative fitness to those with the flies present, contradicting the putative obligatory nature of this pollination system. It also agrees with our observation that many other insects also visit and carry pollen among T.europaeus flowers. We propose that the interaction could have evolved through maximization of by-product benefits of the Chiastocheta visits, through the male flower function, and selection on floral traits by the most effective pollinator. We argue this mechanism is also central in the evolution of other nursery pollination systems.

An Advocacy for the Use of 3D Stem Cell Culture Systems for the Development of Regenerative Medicine: An Emphasis on Photoreceptor Generation

The availability of stem cells is of great promise to study early developmental stages and to generate adequate cells for cell transfer therapies. Although many researchers using stem cells were successful in dissecting intrinsic and extrinsic mechanisms and in generating specific cell phenotypes, few of the stem cells or the differentiated cells show the capacity to repair a tissue. Advances in cell and stem cell cultivation during the last years made tremendous progress in the generation of bona fide differentiated cells able to integrate into a tissue after transplantation, opening new perspectives for developmental biology studies and for regenerative medicine. In this review, we focus on the main works attempting to create in vitro conditions mimicking the natural environment of CNS structures such as the neural tube and its development in different brain region areas including the optic cup. The use of protocols growing cells in 3D organoids is a key strategy to produce cells resembling endogenous ones. An emphasis on the generation of retina tissue and photoreceptor cells is provided to highlight the promising developments in this field. Other examples are presented and discussed, such as the formation of cortical tissue, the epithelial gut or the kidney organoids. The generation of differentiated tissues and well-defined cell phenotypes from embryonic stem (ES) cells or induced pluripotent cells (iPSCs) opens several new strategies in the field of biology and regenerative medicine. A 3D organ/tissue development in vitro derived from human cells brings a unique tool to study human cell biology and pathophysiology of an organ or a specific cell population. The perspective of tissue repair is discussed as well as the necessity of cell banking to accelerate the progress of this promising field.

Déclaration et traitement des événements indésirables en médecine interne [Incident-reporting electronic-based system in internal medicine].

How to recognize, announce and analyze incidents in internal medicine units is a daily challenge that is taught to all hospital staff. It allows suggesting useful improvements for patients, as well as for the medical department and the institution. Here is presented the assessment made in the CHUV internal medicine department one year after the beginning of the institutional procedure which promotes an open process regarding communication and risk management. The department of internal medicine underlines the importance of feedback to the reporters, ensures the staff of regular follow-up concerning the measures being taken and offers to external reporters such as general practioners the possibility of using this reporting system too.

The First International Workshop on Warning Criteria for Active Slides: technical issues, problems and solutions for managing early warning systems

Early warning systems (EWSs) rely on the capacity to forecast a dangerous event with a certain amount of advance by defining warning criteria on which the safety of the population will depend. Monitoring of landslides is facilitated by new technologies, decreasing prices and easier data processing. At the same time, predicting the onset of a rapid failure or the sudden transition from slow to rapid failure and subsequent collapse, and its consequences is challenging for scientists that must deal with uncertainties and have limited tools to do so. Furthermore, EWS and warning criteria are becoming more and more a subject of concern between technical experts, researchers, stakeholders and decision makers responsible for the activation, enforcement and approval of civil protection actions. EWSs imply also a sharing of responsibilities which is often averted by technical staff, managers of technical offices and governing institutions. We organized the First International Workshop on Warning Criteria for Active Slides (IWWCAS) to promote sharing and networking among members from specialized institutions and relevant experts of EWS. In this paper, we summarize the event to stimulate discussion and collaboration between organizations dealing with the complex task of managing hazard and risk related to active slides.

Weather based warning systems for bean angular-leaf-spot and anthracnose

Data available in the literature were used to develop a warning system for bean angular leaf spot and anthracnose, caused by Phaeoisariopsis griseola and Colletotrichum lindemuthianum, respectively. The model is based on favorable environmental conditions for the infectious process such as continuous leaf wetness duration and mean air temperature during this subphase of the pathogen-host relationship cycle. Equations published by DALLA PRIA (1977) showing the interactions of those two factors on the disease severity were used. Excell spreadsheet was used to calculate the leaf wetness period needed to cause different infection probabilities at different temperature ranges. These data were employed to elaborate critical period tables used to program a computerized electronic device that records leaf wetness duration and mean temperature and automatically shows the daily disease severity value (DDSV) for each disease. The model should be validated in field experiments under natural infection for which the daily disease severity sum (DDSS) should be identified as a criterion to indicate the beginning and the interval of fungicide applications to control both diseases.

Comparative analysis of different meat traceability systems using multiple criteria and a social network approach

The adoption of a proper traceability system is being incorporated into meat production practices as a method of gaining consumer confidence. The various partners operating in the chain of meat production can be considered a social network, and they have the common goal of generating a communication process that can ensure each characteristic of the product, including safety. This study aimed to select the most appropriate meat traceability system “from farm to fork” that could be applied to Brazilian beef and pork production for international trade. The research was done in three steps. The first used the analytical hierarchy process (AHP) for selecting the best on-farm livestock traceability. In the second step, the actors in the meat production chain were identified to build a framework and defined each role in the network. In the third step, the selection of the traceability system was done. Results indicated that with an electronic traceability system, it is possible to acquire better connections between the links in the chain and to provide the means for managing uncertainties by creating structures that facilitate information flow more efficiently.

E-PORT. Improving efficiency of Finnish port community by intelligent systems Final report of the Mobile Port project

The management of port-related supply chains is challenging due to the complex and heterogeneous operations of the ports with several actors and processes. That is why the importance of information sharing is emphasised in the ports. However, the information exchange between different port-related actors is often cumbersome and it still involves a lot of manual work and paper. Major ports and port-related actors usually have advanced information systems in daily use but these systems are seldom interoperable with each other, which prevents economies of scale to be reached. Smaller ports and companies might not be equipped with electronic data transmission at all. This is the final report of the Mobile port (MOPO) project, which has sought ways to improve the management and control of port-related sea and inland traffic with the aid of ICT technologies. The project has studied port community systems (PCS) used worldwide, evaluated the suitability of a PCS for the Finnish port operating environment and created a pilot solution of a Finnish PCS in the port of HaminaKotka. Further, the dry port concept and its influences on the transportation system have been explored. The Mobile Port project comprised of several literature reviews, interviews of over 50 port-related logistics and/or ICT professionals, two different kinds of simulation models as well as designing and implementing of the pilot solution of the Finnish PCS. The results of these multiple studies are summarised in this report. Furthermore, recommendations for future actions and the topics for further studies are addressed in the report. The study revealed that the information sharing in a typical Finnish port-related supply chain contains several bottlenecks that cause delays in shipments and waste resources. The study showed that many of these bottlenecks could be solved by building a port community system for the Finnish port community. Almost 30 different kinds of potential services or service entities of a Finnish PCS were found out during the study. The basic requirements, structure, interfaces and operation model of the Finnish PCS were also defined in the study. On the basis of the results of the study, a pilot solution of the Finnish PCS was implemented in the port of HaminaKotka. The pilot solution includes a Portconnect portal for the Finnish port community system (available at https://www.portconnect.fi) and two pilot applications, which are a service for handling the information flows concerning the movements of railway wagons and a service for handling the information flows between Finnish ports and Finland-Russian border. The study also showed that port community systems can be used to improve the environmental aspects of logistics in two different ways: 1) PCSs can bring direct environmental benefits and 2) PCSs can be used as an environmental tool in a port community. On the basis of the study, the development of the Finnish port community system should be continued by surveying other potential applications for the Finnish PCS. It is also important to study if there is need and resources to extend the Finnish PCS to operate in several ports or even on a national level. In the long run, it could be reasonable to clarify whether there would be possibilities to connect the Finnish PCS as a part of Baltic Sea wide, European-wide or even worldwide maritime and port-related network in order to get the best benefit from the system

From electronic spare part catalog to eBusiness: Finding the best practices

Companies and organizations business activities rely on information. IT systems that manage master data must provide the highest level of service, world-class scalability and reliable information. This study discusses product information and how it can support the creation of a spare part catalog and the launching of eBusiness. The study consists of a theoretical and empirical part. The theoretical part contains a literature review and a framework for the analysis. For the empirical study two companies were selected and their information management processes were studied and analyzed based on the framework. The empirical results indicate that the challenges the companies face reflect the ones that can be found in the literature study. The results of the empirical study also show that the companies had recognized the issues which need to be developed and had recognized trends in eBusiness and product information management.

Linear-quadratic optimal control of descriptor systems

In recent years the analysis and synthesis of (mechanical) control systems in descriptor form has been established. This general description of dynamical systems is important for many applications in mechanics and mechatronics, in electrical and electronic engineering, and in chemical engineering as well. This contribution deals with linear mechanical descriptor systems and its control design with respect to a quadratic performance criterion. Here, the notion of properness plays an important role whether the standard Riccati approach can be applied as usual or not. Properness and non-properness distinguish between the cases if the descriptor system is exclusively governed by the control input or by its higher-order time-derivatives additionally. In the unusual case of non-proper systems a quite different problem of optimal control design has to be considered. Both cases will be solved completely.