Visualization and validation of (Q)SAR models

Analyzing and modeling relationships between the structure of chemical compounds, their physico-chemical properties, and biological or toxic effects in chemical datasets is a challenging task for scientific researchers in the field of cheminformatics. Therefore, (Q)SAR model validation is essential to ensure future model predictivity on unseen compounds. Proper validation is also one of the requirements of regulatory authorities in order to approve its use in real-world scenarios as an alternative testing method. However, at the same time, the question of how to validate a (Q)SAR model is still under discussion. In this work, we empirically compare a k-fold cross-validation with external test set validation. The introduced workflow allows to apply the built and validated models to large amounts of unseen data, and to compare the performance of the different validation approaches. Our experimental results indicate that cross-validation produces (Q)SAR models with higher predictivity than external test set validation and reduces the variance of the results. Statistical validation is important to evaluate the performance of (Q)SAR models, but does not support the user in better understanding the properties of the model or the underlying correlations. We present the 3D molecular viewer CheS-Mapper (Chemical Space Mapper) that arranges compounds in 3D space, such that their spatial proximity reflects their similarity. The user can indirectly determine similarity, by selecting which features to employ in the process. The tool can use and calculate different kinds of features, like structural fragments as well as quantitative chemical descriptors. Comprehensive functionalities including clustering, alignment of compounds according to their 3D structure, and feature highlighting aid the chemist to better understand patterns and regularities and relate the observations to established scientific knowledge. Even though visualization tools for analyzing (Q)SAR information in small molecule datasets exist, integrated visualization methods that allows for the investigation of model validation results are still lacking. We propose visual validation, as an approach for the graphical inspection of (Q)SAR model validation results. New functionalities in CheS-Mapper 2.0 facilitate the analysis of (Q)SAR information and allow the visual validation of (Q)SAR models. The tool enables the comparison of model predictions to the actual activity in feature space. Our approach reveals if the endpoint is modeled too specific or too generic and highlights common properties of misclassified compounds. Moreover, the researcher can use CheS-Mapper to inspect how the (Q)SAR model predicts activity cliffs. The CheS-Mapper software is freely available at http://ches-mapper.org.

Phage therapy: A software system for phage quantification and kinetic model inference.

One of the most serious problems of the modern medicine is the growing emergence of antibiotic resistance among pathogenic bacteria. In this circumstance, different and innovative approaches for treating infections caused by multidrug-resistant bacteria are imperatively required. Bacteriophage Therapy is one among the fascinating approaches to be taken into account. This consists of the use of bacteriophages, viruses that infect bacteria, in order to defeat specific bacterial pathogens. Phage therapy is not an innovative idea, indeed, it was widely used around the world in the 1930s and 1940s, in order to treat various infection diseases, and it is still used in Eastern Europe and the former Soviet Union. Nevertheless, Western scientists mostly lost interest in further use and study of phage therapy and abandoned it after the discovery and the spread of antibiotics. The advancement of scientific knowledge of the last years, together with the encouraging results from recent animal studies using phages to treat bacterial infections, and above all the urgent need for novel and effective antimicrobials, have given a prompt for additional rigorous researches in this field. In particular, in the laboratory of synthetic biology of the department of Life Sciences at the University of Warwick, a novel approach was adopted, starting from the original concept of phage therapy, in order to study a concrete alternative to antibiotics. The innovative idea of the project consists in the development of experimental methodologies, which allow to engineer a programmable synthetic phage system using a combination of directed evolution, automation and microfluidics. The main aim is to make “the therapeutics of tomorrow individualized, specific, and self-regulated” (Jaramillo, 2015). In this context, one of the most important key points is the Bacteriophage Quantification. Therefore, in this research work, a mathematical model describing complex dynamics occurring in biological systems involving continuous growth of bacteriophages, modulated by the performance of the host organisms, was implemented as algorithms into a working software using MATLAB. The developed program is able to predict different unknown concentrations of phages much faster than the classical overnight Plaque Assay. What is more, it gives a meaning and an explanation to the obtained data, making inference about the parameter set of the model, that are representative of the bacteriophage-host interaction.

Prevention, diagnosis, therapy and follow-up care of sepsis: 1st revision of S-2k guidelines of the German Sepsis Society (Deutsche Sepsis-Gesellschaft e.V. (DSG)) and the German Interdisciplinary Association of Intensive Care and Emergency Medicine (Deutsche Interdisziplinäre Vereinigung für Intensiv- und Notfallmedizin (DIVI))

Practice guidelines are systematically developed statements and recommendations that assist the physicians and patients in making decisions about appropriate health care measures for specific clinical circumstances taking into account specific national health care structures. The 1(st) revision of the S-2k guideline of the German Sepsis Society in collaboration with 17 German medical scientific societies and one self-help group provides state-of-the-art information (results of controlled clinical trials and expert knowledge) on the effective and appropriate medical care (prevention, diagnosis, therapy and follow-up care) of critically ill patients with severe sepsis or septic shock. The guideline had been developed according to the "German Instrument for Methodological Guideline Appraisal" of the Association of the Scientific Medical Societies (AWMF). In view of the inevitable advancements in scientific knowledge and technical expertise, revisions, updates and amendments must be periodically initiated. The guideline recommendations may not be applied under all circumstances. It rests with the clinician to decide whether a certain recommendation should be adopted or not, taking into consideration the unique set of clinical facts presented in connection with each individual patient as well as the available resources.

Bringing results to fruition through publication: An analysis of a peer-reviewed, open access and context-focused journal's editorial practice

When it comes to helping to shape sustainable development, research is most useful when it bridges the science–implementation/management gap and when it brings development specialists and researchers into a dialogue (Hurni et al. 2004); can a peer-reviewed journal contribute to this aim? In the classical system for validation and dissemination of scientific knowledge, journals focus on knowledge exchange within the academic community and do not specifically address a ‘life-world audience’. Within a North-South context, another knowledge divide is added: the peer review process excludes a large proportion of scientists from the South from participating in the production of scientific knowledge (Karlsson et al. 2007). Mountain Research and Development (MRD) is a journal whose mission is based on an editorial strategy to build the bridge between research and development and ensure that authors from the global South have access to knowledge production, ultimately with a view to supporting sustainable development in mountains. In doing so, MRD faces a number of challenges that we would like to discuss with the td-net community, after having presented our experience and strategy as editors of this journal. MRD was launched in 1981 by mountain researchers who wanted mountains to be included in the 1992 Rio process. In the late 1990s, MRD realized that the journal needed to go beyond addressing only the scientific community. It therefore launched a new section addressing a broader audience in 2000, with the aim of disseminating insights into, and recommendations for, the implementation of sustainable development in mountains. In 2006, we conducted a survey among MRD’s authors, reviewers, and readers (Wymann et al. 2007): respondents confirmed that MRD had succeeded in bridging the gap between research and development. But we realized that MRD could become an even more efficient tool for sustainability if development knowledge were validated: in 2009, we began submitting ‘development’ papers (‘transformation knowledge’) to external peer review of a kind different from the scientific-only peer review (for ‘systems knowledge’). At the same time, the journal became open access in order to increase the permeability between science and society, and ensure greater access for readers and authors in the South. We are currently rethinking our review process for development papers, with a view to creating more space for communication between science and society, and enhancing the co-production of knowledge (Roux 2008). Hopefully, these efforts will also contribute to the urgent debate on the ‘publication culture’ needed in transdisciplinary research (Kueffer et al. 2007).

Definitions and outcome measures for bullous pemphigoid: recommendations by an international panel of experts

Our scientific knowledge of bullous pemphigoid (BP) has dramatically progressed in recent years. However, despite the availability of various therapeutic options for the treatment of inflammatory diseases, only a few multicenter controlled trials have helped to define effective therapies in BP. A major obstacle in sharing multicenter-based evidences for therapeutic efforts is the lack of generally accepted definitions for the clinical evaluation of patients with BP. Common terms and end points of BP are needed so that experts in the field can accurately measure and assess disease extent, activity, severity, and therapeutic response, and thus facilitate and advance clinical trials. These recommendations from the International Pemphigoid Committee represent 2 years of collaborative efforts to attain mutually acceptable common definitions for BP and proposes a disease extent score, the BP Disease Area Index. These items should assist in the development of consistent reporting of outcomes in future BP reports and studies.

Tolerance and Critical Thinking

Post-soviet countries are in the process of transformation from a totalitarian order to a democratic one, a transformation which is impossible without a profound shift in people's way of thinking. The group set themselves the task of determining the essence of this shift. Using a multidisciplinary approach, they looked at concrete ways of overcoming the totalitarian mentality and forming that necessary for an open democratic society. They studied the contemporary conceptions of tolerance and critical thinking and looked for new foundations of criticism, especially in hermeneutics. They then sought to substantiate the complementary relation between tolerance and criticism in the democratic way of thinking and to prepare a a syllabus for teaching on the subject in Ukrainian higher education. In a philosophical exploration of tolerance they began with relgious tolerance as its first and most important form. Political and social interests often lay at the foundations of religious intolerance and this implicitly comprised the transition to religious tolerance when conditions changed. Early polytheism was more or less indifferent to dogmatic deviations but monotheism is intolerant of heresies. The damage wrought by the religious wars of the Reformations transformed tolerance into a value. They did not create religious tolerance but forced its recognition as a positive phenomenon. With the weakening of religious institutions in the modern era, the purely political nature of many conflicts became evident and this stimulated the extrapolation of tolerance into secular life. Each historical era has certain acts and operations which may be interpreted as tolerant and these can be classified as to whether or not they are based on the conscious following of the principle of tolerance. This criterion requires the separation of the phenomenon of tolerance from its concept and from tolerance as a value. Only the conjunction of a concept of tolerance with a recognition of its value can transform it into a principle dictating a norm of conscious behaviour. The analysis of the contemporary conception of tolerance focused on the diversity of the concept and concluded that the notions used cannot be combined in the framework of a single more or less simple classification, as the distinctions between them are stimulated by the complexity of the realty considered and the variety of its manifestations. Notions considered in relation to tolerance included pluralism, respect and particular-universal. The rationale of tolerance was also investigated and the group felt that any substantiation of the principle of tolerance must take into account human beings' desire for knowledge. Before respecting or being tolerant of another person different from myself, I should first know where the difference lies, so knowledge is a necessary condition of tolerance.The traditional division of truth into scientific (objective and unique) and religious, moral, political (subjective and so multiple) intensifies the problem of the relationship between truth and tolerance. Science was long seen as a field of "natural" intolerance whereas the validity of tolerance was accepted in other intellectual fields. As tolerance eemrges when there is difference and opposition, it is essentially linked with rivaly and there is a a growing recognition today that unlimited rivalry is neither able to direct the process of development nor to act as creative matter. Social and economic reality has led to rivalry being regulated by the state and a natural requirement of this is to associate tolerance with a special "purified" form of rivalry, an acceptance of the actiivity of different subjects and a specification of the norms of their competition. Tolerance and rivalry should therefore be subordinate to a degree of discipline and the group point out that discipline, including self-discipline, is a regulator of the balance between them. Two problematic aspects of tolerance were identified: why something traditionally supposed to have no positive content has become a human activity today, and whether tolerance has full-scale cultural significance. The resolution of these questions requires a revision of the phenomenon and conception of tolerance to clarify its immanent positive content. This involved an investigation of the contemporary concept of tolerance and of the epistemological foundations of a negative solution of tolerance in Greek thought. An original soution to the problem of the extrapolation of tolerance to scientific knowledge was proposed based on the Duhem-Quine theses and conceptiion of background knowledge. In this way tolerance as a principle of mutual relations between different scientific positions gains an essential epistemological rationale and so an important argument for its own universal status. The group then went on to consider the ontological foundations for a positive solution of this problem, beginning with the work of Poincare and Reichenbach. The next aspect considered was the conceptual foundations of critical thinking, looking at the ideas of Karl Popper and St. Augustine and at the problem of the demarcation line between reasonable criticism and apologetic reasoning. Dogmatic and critical thinking in a political context were also considered, before an investigation of critical thinking's foundations. As logic is essential to critical thinking, the state of this discipline in Ukrainian and Russian higher education was assessed, together with the limits of formal-logical grounds for criticism, the role of informal logical as a basis for critical thinking today, dialectical logic as a foundation for critical thinking and the universality of the contemporary demand for criticism. The search for new foundations of critical thinking covered deconstructivism and critical hermeneutics, including the problem of the author. The relationship between tolerance and criticism was traced from the ancient world, both eastern and Greek, through the transitional community of the Renaissance to the industrial community (Locke and Mill) and the evolution of this relationship today when these are viewed not as moral virtues but as ordinary norms. Tolerance and criticism were discussed as complementary manifestations of human freedom. If the completeness of freedom were accepted it would be impossible to avoid recognition of the natural and legal nature of these manifestations and the group argue that critical tolerance is able to avoid dismissing such negative phenomena as the degradation of taste and manner, pornography, etc. On the basis of their work, the group drew up the syllabus of a course in "Logic with Elements of Critical Thinking, and of a special course on the "Problem of Tolerance".

Gene and stem cell therapy in peripheral arterial occlusive disease

Peripheral arterial occlusive disease (PAOD) is a manifestation of systemic atherosclerosis strongly associated with a high risk of cardiovascular morbidity and mortality. In a considerable proportion of patients with PAOD, revascularization either by endovascular means or by open surgery combined with best possible risk factor modification does not achieve limb salvage or relief of ischaemic rest pain. As a consequence, novel therapeutic strategies have been developed over the last two decades aiming to promote neovascularization and remodelling of collaterals. Gene and stem cell therapy are the main directions for clinical investigation concepts. For both, preclinical studies have shown promising results using a wide variety of genes encoding for growth factors and populations of adult stem cells, respectively. As a consequence, clinical trials have been performed applying gene and stem cell-based concepts. However, it has become apparent that a straightforward translation into humans is not possible. While several trials reported relief of symptoms and functional improvement, other trials did not confirm this early promise of efficacy. Ongoing clinical trials with an improved study design are needed to confirm the potential that gene and cell therapy may have and to prevent the gaps in our scientific knowledge that will jeopardize the establishment of angiogenic therapy as an additional medical treatment of PAOD. This review summarizes the experimental background and presents the current status of clinical applications and future perspectives of the therapeutic use of gene and cell therapy strategies for PAOD.

[Neither Descartes nor Freud? current pain models in psychosomatic medicine]

Models explaining chronic pain based on the mere presence or absence of peripheral somatic findings or which view pain of psychological origin when there is no somatic explanation, have their shortcomings. Current scientific knowledge calls for distinct pain concepts, which integrate neurobiological and neuropsychological aspects of pain processing.

Handbook of Swiss Politics

Approaching Switzerland as a “laboratory” for democracy, this Handbook contributes to a refined understanding of the res publica. Over the years, the Handbook of Swiss Politics has established itself as a classic work. This new and extended second edition of the Handbook comprises 32 chapters, all by leading Swiss political scientists. The contributors write about fundamentals, institutions, interest groups, political parties, new social movements, the cantons and municipalities, elections, popular votes, policy processes and public policies. They address several important issues in the current international debates, such as the internationalization of domestic politics, multi-level governance, and the role of metropolitan agglomerations. Nine new chapters enrich this second, completely updated version. The section on public policies has been significantly extended, and covers a dozen of policy domains. Grounded on the latest scientific knowledge, this volume also serves as an indispensable reference for a non-academic audience of decision-makers, diplomats, senior officials and journalists.

Hardness and Electrical Resistivity of Copper-Iron Powder Metal Compacts

Although powder metallurgical methods have been used for years to fabricate tungsten and platinum, very little scientific data have been recorded until the beginning of this century. A large percentage of all commercial production at present is based upon past practice rather than upon scientific knowledge.

Appraising and selecting conservation measures to mitigate desertification and land degradation based on stakeholder participation and global best practices

Most desertification research focuses on degradation assessments without putting sufficient emphasis on prevention and mitigation strategies, although the concept of Sustainable Land Management (SLM) is increasingly being acknowledged. A variety of already applied conservation measures exist at the local level, but they are not adequately recognised, evaluated and shared, either by land users, technicians, researchers, or policy makers. Likewise, collaboration between research and implementation is often insufficient. The aim of this paper is to present a new methodology for a participatory process of appraising and selecting desertification mitigation strategies, and to present first experiences from its application in the EU-funded DESIRE project. The methodology combines a collective learning and decision approach with the use of evaluated global best practices. In three parts, it moves through a concise process, starting with identifying land degradation and locally applied solutions in a stakeholder workshop, leading to assessing local solutions with a standardised evaluation tool, and ending with jointly selecting promising strategies for implementation with the help of a decision support tool. The methodology is currently being applied in 16 study sites. Preliminary analysis from the application of the first part of the methodology shows that the initial stakeholder workshop results in a good basis for stakeholder cooperation, and in promising land conservation practices for further assessment. Study site research teams appreciated the valuable results, as burning issues and promising options emerged from joint reflection. The methodology is suitable to initiate mutual learning among different stakeholder groups and to integrate local and scientific knowledge.

Searching the Rhone delta channel in Lake Geneva since François‐Alphonse Forel

In the late 19th century, F.A. FOREL led investigations of the Rhone River delta area of Lake Geneva that resulted in the dis- covery of a textbook example of a river-fed delta system containing impressive subaquatic channels. Well ahead of the marine counterparts, scientific observations and interpretations of water currents shaping the delta edifice for the first time documented how underflow currents carry cold, suspension-laden waters from the river mouth all the way to the deep basin. These early investigations of the Rhone delta laid the basis for follow-up studies in the 20th and 21th centuries. Sediment coring, water-column measurements, manned submersible diving, seismic reflection profiling and bathymetric sur- veying eventually provided a rich database to unravel the key erosional and depositional processes, further documenting the impact of human-induced changes in the catchment. With the merging of old and new scientific knowledge, today a comprehensive understanding prevails of how a delta changes through time, how its channels are formed, and what potential natural hazards may be related to its evolution. New and efficient bathymetric techniques, paired with novel coring operations, provided a time-series of morphologic evolution showing and quantifying the high dynamics of the delta/channel evolution in an unprecedented temporal and spatial reso- lution. Future investigations will continue to further quantify these dynamic processes and to link the evolution of the subaquatic domain with changes and processes in the catchment and with natural hazards. Its size, easy access, and large variety of states and processes will continue to make the Rhone delta area a perfect ‘laboratory’ in which general processes can be studied that could be upscaled or downscaled to other marine and lacustrine deltas.

Use of multi-media for spreading the experiences

The global World Overview of Conservation Approaches and Technologies (WOCAT) initiative has developed standardised tools and methods to compile and evaluate knowledge available about SLM. This knowledge is now combined and enriched with audiovisual information in order to give a voice to land users, reach a broad range of stakeholders, and assist in scaling up SLM to reverse trends of degradation, desertification, and drought. Five video products, adapted to the needs of different target groups, are created and embedded in already existing platforms for knowledge sharing of SLM such as the WOCAT database and Google Earth application. A pilot project was carried out in Kenya and Tajikistan to verify ideas and tools while at the same time assessing the usefulness of the suggested products on the ground. Video has the potential to bridge the gap between different actor groups and enable communication and sharing on different levels and scales: locally, regionally, and globally. Furthermore, it is an innovative tool to link local and scientific knowledge, raise awareness, and support advocacy for SLM.

Drivers of collaboration to mitigate climate change: An illustration of Swiss climate policy over 15 years

Climate change mitigation policy is driven by scientific knowledge and involves actors from the international, national and local decision-making levels. This multi-level and cross-sectoral context requires collaborative management when designing mitigation solutions over time and space. But collaboration in general policymaking settings, and particularly in the complex domain of climate mitigation, is not an easy task. This paper addresses the question of what drives collaboration among collective actors involved in climate mitigation policy. We wish to investigate whether common beliefs or power structures influence collaboration among actors. We adopt a longitudinal approach to grasp differences between the early and more advanced stages of mitigation policy design. We use survey data to investigate actors’ collaboration, beliefs and power, and apply a Stochastic Actor-oriented Model for network dynamics to three subsequent networks in Swiss climate policy between 1995 and 2012. Results show that common beliefs among actors, as well as formal power structures, have a higher impact on collaboration relations than perceived power structures. Furthermore, those effects hold true for decision-making about initial mitigation strategies, but less so for the implementation of those measures.

The canine neuronal ceroid-lipofuscinosis: a review.

The present article gives a survey over the current scientific knowledge of the canine neuronal ceroid-lipofuscinosis (NCL). NCL is a heterogenous group of lysosomal storage diseases in humans and animals. In consequence of a gene mutation, there is an accumulation of ceroid-lipofuscin in neurons, cells of the retina and the skin and other cells. The stored ceroid-lipofuscin in neurons leads to an impaired cell function and subsequently to cell death. Recently, the underlying genetic defect was discovered in several dog breeds. Genetic testing permits an ante mortem diagnosis of the disease, which up to now was only possible with a positive biopsy result. Another advantage is the identification of carrier animals to eliminate the deleterious alleles.