Monitoring inland waters with the APEX sensor, a wavelet approach

In this study a new curve fitting approach is presented to derive TSM, CHL and CDOM concentrations in inland and coastal waters from water leaving-reflectance spectra. The approach is based on the wavelet transform and is tested on simulated water-leaving reflectance spectra. For simulations SIOPS and water concentrations, representative for the Scheldt river, were used. The results shown that the approach is less sensitive to errors in the atmospheric correction or specific sensor noise. The idea is based on the development of a new minimization criteria for curve fitting. Instead of minimizing the difference between modeled and measured spectra using a simple RMSE, the RMSE is now combined with specific wavelet features. Several types of errors and noise are added to the simulated spectra to find robust features. Two minimization criteria were found which are almost insensitive to a white error and less sensitive to adjacency effects

The perspectives of clinical staff and bereaved informal care-givers on the use of continuous sedation until death for cancer patients: The study protocol of the UNBIASED study

Background: A significant minority of dying people experience refractory symptoms or extreme distress unresponsive to conventional therapies. In such circumstances, sedation may be used to decrease or remove consciousness until death occurs. This practice is described in a variety of ways, including: ‘palliative sedation’, ‘terminal sedation’, ‘continuous deep sedation until death’, ‘proportionate sedation’ or ‘palliative sedation to unconsciousness’. Surveys show large unexplained variation in incidence of sedation at the end of life across countries and care settings and there are ethical concerns about the use, intentions, risks and significance of the practice in palliative care. There are also questions about how to explain international variation in the use of the practice. This protocol relates to the UNBIASED study (UK Netherlands Belgium International Sedation Study), which comprises three linked studies with separate funding sources in the UK, Belgium and the Netherlands. The aims of the study are to explore decision-making surrounding the application of continuous sedation until death in contemporary clinical practice, and to understand the experiences of clinical staff and decedents’ informal caregivers of the use of continuous sedation until death and their perceptions of its contribution to the dying process. The UNBIASED study is part of the European Association for Palliative Care Research Network. Methods/Design: To realize the study aims, a two-phase study has been designed. The study settings include: the domestic home, hospital and expert palliative care sites. Phase 1 consists of: a) focus groups with health care staff and bereaved informal care-givers; and b) a preliminary case notes review to study the range of sedation therapy provided at the end of life to cancer patients who died within a 12 week period. Phase 2 employs qualitative methods to develop 30 patient-centred case studies in each country. These involve interviews with staff and informal care-givers closely involved in the care of cancer patients who received continuous sedation until death. Discussion: To our knowledge, this is one of the few studies which seek to take a qualitative perspective on clinical decision making surrounding the use of continuous sedation until death and the only one which includes the perspectives of nurses, physicians, as well as bereaved informal care-givers. It has several potential strengths, weaknesses, opportunities and threats associated with the specific design of the study, as well as with the sensitive nature of the topic and the different frameworks for ethical review in the participating countries

Break it Down for Me: A Study in Automated Lyric Annotation

Comprehending lyrics, as found in songs and poems, can pose a challenge to human and machine readers alike. This motivates the need for systems that can under- stand the ambiguity and jargon found in such creative texts, and provide commentary to aid readers in reaching the correct interpretation. We introduce the task of automated lyric annotation (ALA). Like text simplification, a goal of ALA is to rephrase the original text in a more easily understand- able manner. However, in ALA the system must often include additional infor- mation to clarify niche terminology and abstract concepts. To stimulate research on this task, we release a large collection of crowdsourced annotations for song lyrics. We analyze the performance of translation and retrieval models on this task, measuring performance with both automated and human evaluation. We find that each model captures a unique type of information important to the task.Research Foundation - Flanders (FWO) and U.K. Engineering and Physical Sciences Research Council (EPSRC grant EP/L027623/1

Thermodynamic Stability of the Transcription Regulator PaaR2 from Escherichia coli O157:H7

PaaR2 is a putative transcription regulator encoded by a three-component parDE-like toxin-antitoxin module from Escherichia coli O157:H7. Although this module’s toxin, antitoxin, and toxin-antitoxin complex have been more thoroughly investigated, little remains known about its transcription regulator PaaR2. Using a wide range of biophysical techniques (circular dichroism spectroscopy, size-exclusion chromatography-multiangle laser light scattering, dynamic light scattering, small-angle x-ray scattering, and native mass spectrometry), we demonstrate that PaaR2 mainly consists of α-helices and displays a concentration-dependent octameric build-up in solution and that this octamer contains a global shape that is significantly nonspherical. Thermal unfolding of PaaR2 is reversible and displays several transitions, suggesting a complex unfolding mechanism. The unfolding data obtained from spectroscopic and calorimetric methods were combined into a unifying thermodynamic model, which suggests a five-state unfolding trajectory. Furthermore, the model allows the calculation of a stability phase diagram, which shows that, under physiological conditions, PaaR2 mainly exists as a dimer that can swiftly oligomerize into an octamer depending on local protein concentrations. These findings, based on a thorough biophysical and thermodynamic analysis of PaaR2, may provide important insights into biological function such as DNA binding and transcriptional regulation

Patenting and licensing of university research: promoting innovation or undermining academic values?

Since the 1980s in the US and the 1990s in Europe, patenting and licensing activities by universities have massively increased. This is strongly encouraged by governments throughout the Western world. Many regard academic patenting as essential to achieve 'knowledge transfer' from academia to industry. This trend has far-reaching consequences for access to the fruits of academic research and so the question arises whether the current policies are indeed promoting innovation or whether they are instead a symptom of a pro-intellectual property (IP) culture which is blind to adverse effects. Addressing this question requires both empirical analysis (how real is the link between academic patenting and licensing and 'development' of academic research by industry?) and normative assessment (which justifications are given for the current policies and to what extent do they threaten important academic values?). After illustrating the major rise of academic patenting and licensing in the US and Europe and commenting on the increasing trend of 'upstream' patenting and the focus on exclusive as opposed to non-exclusive licences, this paper will discuss five negative effects of these trends. Subsequently, the question as to why policymakers seem to ignore these adverse effects will be addressed. Finally, a number of proposals for improving university policies will be made

The challenges of the expanded availability of genomic information: an agenda-setting paper

Rapid advances in microarray and sequencing technologies are making genotyping and genome sequencing more affordable and readily available. There is an expectation that genomic sequencing technologies improve personalized diagnosis and personalized drug therapy. Concurrently, provision of direct-to-consumer genetic testing by commercial providers has enabled individuals’ direct access to their genomic data. The expanded availability of genomic data is perceived as influencing the relationship between the various parties involved including healthcare professionals, researchers, patients, individuals, families, industry, and government. This results in a need to revisit their roles and responsibilities. In a 1-day agenda-setting meeting organized by the COST Action IS1303 “Citizen’s Health through public-private Initiatives: Public health, Market and Ethical perspectives,” participants discussed the main challenges associated with the expanded availability of genomic information, with a specific focus on public-private partnerships, and provided an outline from which to discuss in detail the identified challenges. This paper summarizes the points raised at this meeting in five main parts and highlights the key cross-cutting themes. In light of the increasing availability of genomic information, it is expected that this paper will provide timely direction for future research and policy making in this area.Funding Deborah Mascalzoni is supported under Grant Agreement number 305444. Álvaro Mendes is supported by the FCT—The Portuguese Foundation for Science and Technology under postdoctoral grant SFRH/BPD/88647/2012. Isabelle Budin-Ljøsne receives support from the National Research and Innovation Platform for Personalized Cancer Medicine funded by The Research Council of Norway (NFR BIOTEK2021/ES495029) and Biobank Norway funded by The Research Council of Norway—grant number 245464. Heidi Carmen Howard is partly supported by supported by the Swedish Foundation for Humanities and Social Science under grant M13-0260:1), the Biobanking and Molecular Resource Infrastructure of Sweden (BBMRI.se) and the BBMRI-ERIC. Brígida Riso is supported by the Portuguese Foundation for Science and Technology (FCT) under the PhD grant SFRH/BD/100779/2014. Heidi Beate Bentzen receives support from the project Legal Regulation of Information Processing relating to Personalized Cancer Medicine funded by The Research Council of Norway BIOTEK2021/238999