Diapiro de Salinas de AÑana: ¿Un diapiro con un overhang? Modelo 3D gravimetrico

Se presenta el mapa gravimétrico de la Cubeta Alavesa, donde se pueden localizar de forma clara los diapiros salinos aflorantes en la misma, y también otras estructuras también diapíricas situadas a mayor profundidad. Se ha modelizado en 3D, mediante dos técnicas gravimétricas diferentes, el diapiro de Salinas de Añana. El cual presenta una gran extensión en superficie pero que en cambio no se proyecta de la misma manera en profundidad, habiéndose detectado la presencia de una extensión lateral u overghang hacia el SW.

3D-tuoteyhdistelmämallien ja mittakuvien tuottaminen PDM-järjestelmästä

Tämä diplomityö on selvitystyö mittakuvien ja kolmiulotteisten CAD-mallien tuottamisesta. Mittakuvat ja 3D-CAD-mallit halutaan Neles-tuotemerkin omaaville tuotteille. Olennaisena osana työssä on tuotetiedonhallintajärjestelmä AtonPDM, koska mittakuvia ja malleja toivottaisiin hallittavan AtonPDM-järjestelmällä. Työ tehdään Metso Automationin (MA) Flow Control (FC) –liiketoimintalinjalle. Nykyiset mittakuvat aiheuttavat ongelmia sekä MA:ssa että asiakkaille. MA:ssa mittakuvien tekeminen kestää kauemmin kuin asiakas toivoisi. Nykyisen mittakuvaohjelmiston riittämättömät ominaisuudet aiheuttavat lisätyötä mittakuvien valmistuksessa. Asiakkaille mittakuvien viivästyminen on suunnittelua hidastava tekijä. Mittakuvissa olevat virheet ja puutteet vaikeuttavat asiakkaan suunnittelutyötä ja saattavat päästä läpi tarkatuksien myös loppusuunnitelmiin, jolloin seurauksena voi olla rahallisia menetyksiä. Tämän päivän putkistosuunnittelu hoidetaan suurimmaksi osaksi 3D-CADohjelmistoilla. Suunnittelua helpotetaan ja nopeutetaan valmiilla komponenttien 3Dmalleilla, joihin on liitetty tuotetietoa. Työssä on haastateltu MA:n henkilökuntaa, CAD-järjestelmien toimittajia ja asiakkaita. Haastattelut ovat työn tärkein tiedonlähde. Teoriatietoa on selvitetty kirjoista, lehdistä ja internetistä. Teoriaosiossa käydään läpi tuotetiedonhallinta (Product Data Management, PDM), tietokanta ja parametrinen mallintaminen. Työn lopputuloksena on pyritty saamaan kuvaus siitä miten tuotetaan 3D-CAD-mallit ja mittakuvat Neles-tuotteista käyttäen tiedonlähteenä AtonPDM:ää ja millaisia 3Dmallien ja mittakuvien tulee olla. Malleja ja mittakuvia tuottavaan järjestelmään on etsitty ratkaisuja CAD-ohjelmistoista. Ratkaisuja on verrattu keskenään ominaisuuksien, joustavuuden ja AtonPDM yhteensopivuuden perusteella.

Helping medical students to acquire a deeper understanding of truth-telling.

PROBLEM: Truth-telling is an important component of respect for patients' self-determination, but in the context of breaking bad news, it is also a distressing and difficult task. INTERVENTION: We investigated the long-term influence of a simulated patient-based teaching intervention, integrating learning objectives in communication skills and ethics into students' attitudes and concerns regarding truth-telling. We followed two cohorts of medical students from the preclinical third year to their clinical rotations (fifth year). Open-ended responses were analysed to explore medical students' reported difficulties in breaking bad news. CONTEXT: This intervention was implemented during the last preclinical year of a problem-based medical curriculum, in collaboration between the doctor-patient communication and ethics programs. OUTCOME: Over time, concerns such as empathy and truthfulness shifted from a personal to a relational focus. Whereas 'truthfulness' was a concern for the content of the message, 'truth-telling' included concerns on how information was communicated and how realistically it was received. Truth-telling required empathy, adaptation to the patient, and appropriate management of emotions, both for the patient's welfare and for a realistic understanding of the situation. LESSONS LEARNED: Our study confirms that an intervention confronting students with a realistic situation succeeds in making them more aware of the real issues of truth-telling. Medical students deepened their reflection over time, acquiring a deeper understanding of the relational dimension of values such as truth-telling, and honing their view of empathy.

Architectural characterization of a delta-front reservoir analogue combining ground penetrating radar and electrical resistivity tomography: Roda Sandstone (Lower Eocene, Graus-Tremp basin, Spain)

Three-dimensional reconstruction of reservoir analogues can be improved combining data from different geophysical methods. Ground Penetrating Radar (GPR) and Electrical Resistivity Tomography (ERT) data are valuable tools, since they provide subsurface information from internal architecture and facies distribution of sedimentary rock bodies, enabling the upgrading of depositional models and heterogeneity reconstruction. The Lower Eocene Roda Sandstone is a well-known deltaic complex widely studied as a reservoir analogue that displays a series of sandstone wedges with a general NE to SW progradational trend. To provide a better understanding of internal heterogeneity of a 10m-thick progradational delta-front sandstone unit, 3D GPR data were acquired. In addition, common midpoints (CMP) to measure the sandstone subsoil velocity, test profiles with different frequency antennas (25, 50 and 100MHz) and topographic data for subsequent correction in the geophysical data were also obtained. Three ERT profiles were also acquired to further constrain GPR analysis. These geophysical results illustrate the geometry of reservoir analogue heterogeneities both depositional and diagenetic in nature, improving and complementing previous outcrop-derived data. GPR interpretation using radar stratigraphy principles and attributes analysis provided: 1)tridimensional geometry of major stratigraphic surfaces that define four units in the GPR Prism, 2) image the internal architecture of the units and their statistical study of azimuth and dips, useful for a quick determination of paleocurrent directions. These results were used to define the depositional architecture of the progradational sandbody that shows an arrangement in very-high-frequency sequences characterized by clockwise paleocurrent variations and decrease of the sedimentary flow, similar to those observed at a greater scale in the same system. This high-frequency sequential arrangement has been attributed to the autocyclic dynamics of a supply-dominated delta- front where fluvial and tidal currents are in competition. The resistivity models enhanced the viewing of reservoir quality associated with cement distribution caused by depositional and early diagenetic processes related to the development of transgressive and regressive systems tracts in igh-frequency sequences.

Study of criteria influencing the success rate of DNA swabs in operational conditions: a contribution to an evidence-based approach to crime scene investigation and triage

DNA is nowadays swabbed routinely to investigate serious and volume crimes, but research remains scarce when it comes to determining the criteria that may impact the success rate of DNA swabs taken on different surfaces and situations. To investigate these criteria in fully operational conditions, DNA analysis results of 4772 swabs taken by the forensic unit of a police department in Western Switzerland over a 2.5-year period (2012-2014) in volume crime cases were considered. A representative and random sample of 1236 swab analyses was extensively examined and codified, describing several criteria such as whether the swabbing was performed at the scene or in the lab, the zone of the scene where it was performed, the kind of object or surface that was swabbed, whether the target specimen was a touch surface or a biological fluid, and whether the swab targeted a single surface or combined different surfaces. The impact of each criterion and of their combination was assessed in regard to the success rate of DNA analysis, measured through the quality of the resulting profile, and whether the profile resulted in a hit in the national database or not. Results show that some situations - such as swabs taken on door and window handles for instance - have a higher success rate than average swabs. Conversely, other situations lead to a marked decrease in the success rate, which should discourage further analyses of such swabs. Results also confirm that targeting a DNA swab on a single surface is preferable to swabbing different surfaces with the intent to aggregate cells deposited by the offender. Such results assist in predicting the chance that the analysis of a swab taken in a given situation will lead to a positive result. The study could therefore inform an evidence-based approach to decision-making at the crime scene (what to swab or not) and at the triage step (what to analyse or not), contributing thus to save resource and increase the efficiency of forensic science efforts.

Rockfall susceptibility assessment and remote geological mapping with LiDAR point clouds

Characterizing the geological features and structures in three dimensions over inaccessible rock cliffs is needed to assess natural hazards such as rockfalls and rockslides and also to perform investigations aimed at mapping geological contacts and building stratigraphy and fold models. Indeed, the detailed 3D data, such as LiDAR point clouds, allow to study accurately the hazard processes and the structure of geologic features, in particular in vertical and overhanging rock slopes. Thus, 3D geological models have a great potential of being applied to a wide range of geological investigations both in research and applied geology projects, such as mines, tunnels and reservoirs. Recent development of ground-based remote sensing techniques (LiDAR, photogrammetry and multispectral / hyperspectral images) are revolutionizing the acquisition of morphological and geological information. As a consequence, there is a great potential for improving the modeling of geological bodies as well as failure mechanisms and stability conditions by integrating detailed remote data. During the past ten years several large rockfall events occurred along important transportation corridors where millions of people travel every year (Switzerland: Gotthard motorway and railway; Canada: Sea to sky highway between Vancouver and Whistler). These events show that there is still a lack of knowledge concerning the detection of potential rockfalls, making mountain residential settlements and roads highly risky. It is necessary to understand the main factors that destabilize rocky outcrops even if inventories are lacking and if no clear morphological evidences of rockfall activity are observed. In order to increase the possibilities of forecasting potential future landslides, it is crucial to understand the evolution of rock slope stability. Defining the areas theoretically most prone to rockfalls can be particularly useful to simulate trajectory profiles and to generate hazard maps, which are the basis for land use planning in mountainous regions. The most important questions to address in order to assess rockfall hazard are: Where are the most probable sources for future rockfalls located? What are the frequencies of occurrence of these rockfalls? I characterized the fracturing patterns in the field and with LiDAR point clouds. Afterwards, I developed a model to compute the failure mechanisms on terrestrial point clouds in order to assess the susceptibility to rockfalls at the cliff scale. Similar procedures were already available to evaluate the susceptibility to rockfalls based on aerial digital elevation models. This new model gives the possibility to detect the most susceptible rockfall sources with unprecented detail in the vertical and overhanging areas. The results of the computation of the most probable rockfall source areas in granitic cliffs of Yosemite Valley and Mont-Blanc massif were then compared to the inventoried rockfall events to validate the calculation methods. Yosemite Valley was chosen as a test area because it has a particularly strong rockfall activity (about one rockfall every week) which leads to a high rockfall hazard. The west face of the Dru was also chosen for the relevant rockfall activity and especially because it was affected by some of the largest rockfalls that occurred in the Alps during the last 10 years. Moreover, both areas were suitable because of their huge vertical and overhanging cliffs that are difficult to study with classical methods. Limit equilibrium models have been applied to several case studies to evaluate the effects of different parameters on the stability of rockslope areas. The impact of the degradation of rockbridges on the stability of large compartments in the west face of the Dru was assessed using finite element modeling. In particular I conducted a back-analysis of the large rockfall event of 2005 (265'000 m3) by integrating field observations of joint conditions, characteristics of fracturing pattern and results of geomechanical tests on the intact rock. These analyses improved our understanding of the factors that influence the stability of rock compartments and were used to define the most probable future rockfall volumes at the Dru. Terrestrial laser scanning point clouds were also successfully employed to perform geological mapping in 3D, using the intensity of the backscattered signal. Another technique to obtain vertical geological maps is combining triangulated TLS mesh with 2D geological maps. At El Capitan (Yosemite Valley) we built a georeferenced vertical map of the main plutonio rocks that was used to investigate the reasons for preferential rockwall retreat rate. Additional efforts to characterize the erosion rate were made at Monte Generoso (Ticino, southern Switzerland) where I attempted to improve the estimation of long term erosion by taking into account also the volumes of the unstable rock compartments. Eventually, the following points summarize the main out puts of my research: The new model to compute the failure mechanisms and the rockfall susceptibility with 3D point clouds allows to define accurately the most probable rockfall source areas at the cliff scale. The analysis of the rockbridges at the Dru shows the potential of integrating detailed measurements of the fractures in geomechanical models of rockmass stability. The correction of the LiDAR intensity signal gives the possibility to classify a point cloud according to the rock type and then use this information to model complex geologic structures. The integration of these results, on rockmass fracturing and composition, with existing methods can improve rockfall hazard assessments and enhance the interpretation of the evolution of steep rockslopes. -- La caractérisation de la géologie en 3D pour des parois rocheuses inaccessibles est une étape nécessaire pour évaluer les dangers naturels tels que chutes de blocs et glissements rocheux, mais aussi pour réaliser des modèles stratigraphiques ou de structures plissées. Les modèles géologiques 3D ont un grand potentiel pour être appliqués dans une vaste gamme de travaux géologiques dans le domaine de la recherche, mais aussi dans des projets appliqués comme les mines, les tunnels ou les réservoirs. Les développements récents des outils de télédétection terrestre (LiDAR, photogrammétrie et imagerie multispectrale / hyperspectrale) sont en train de révolutionner l'acquisition d'informations géomorphologiques et géologiques. Par conséquence, il y a un grand potentiel d'amélioration pour la modélisation d'objets géologiques, ainsi que des mécanismes de rupture et des conditions de stabilité, en intégrant des données détaillées acquises à distance. Pour augmenter les possibilités de prévoir les éboulements futurs, il est fondamental de comprendre l'évolution actuelle de la stabilité des parois rocheuses. Définir les zones qui sont théoriquement plus propices aux chutes de blocs peut être très utile pour simuler les trajectoires de propagation des blocs et pour réaliser des cartes de danger, qui constituent la base de l'aménagement du territoire dans les régions de montagne. Les questions plus importantes à résoudre pour estimer le danger de chutes de blocs sont : Où se situent les sources plus probables pour les chutes de blocs et éboulement futurs ? Avec quelle fréquence vont se produire ces événements ? Donc, j'ai caractérisé les réseaux de fractures sur le terrain et avec des nuages de points LiDAR. Ensuite, j'ai développé un modèle pour calculer les mécanismes de rupture directement sur les nuages de points pour pouvoir évaluer la susceptibilité au déclenchement de chutes de blocs à l'échelle de la paroi. Les zones sources de chutes de blocs les plus probables dans les parois granitiques de la vallée de Yosemite et du massif du Mont-Blanc ont été calculées et ensuite comparés aux inventaires des événements pour vérifier les méthodes. Des modèles d'équilibre limite ont été appliqués à plusieurs cas d'études pour évaluer les effets de différents paramètres sur la stabilité des parois. L'impact de la dégradation des ponts rocheux sur la stabilité de grands compartiments de roche dans la paroi ouest du Petit Dru a été évalué en utilisant la modélisation par éléments finis. En particulier j'ai analysé le grand éboulement de 2005 (265'000 m3), qui a emporté l'entier du pilier sud-ouest. Dans le modèle j'ai intégré des observations des conditions des joints, les caractéristiques du réseau de fractures et les résultats de tests géoméchaniques sur la roche intacte. Ces analyses ont amélioré l'estimation des paramètres qui influencent la stabilité des compartiments rocheux et ont servi pour définir des volumes probables pour des éboulements futurs. Les nuages de points obtenus avec le scanner laser terrestre ont été utilisés avec succès aussi pour produire des cartes géologiques en 3D, en utilisant l'intensité du signal réfléchi. Une autre technique pour obtenir des cartes géologiques des zones verticales consiste à combiner un maillage LiDAR avec une carte géologique en 2D. A El Capitan (Yosemite Valley) nous avons pu géoréferencer une carte verticale des principales roches plutoniques que j'ai utilisé ensuite pour étudier les raisons d'une érosion préférentielle de certaines zones de la paroi. D'autres efforts pour quantifier le taux d'érosion ont été effectués au Monte Generoso (Ticino, Suisse) où j'ai essayé d'améliorer l'estimation de l'érosion au long terme en prenant en compte les volumes des compartiments rocheux instables. L'intégration de ces résultats, sur la fracturation et la composition de l'amas rocheux, avec les méthodes existantes permet d'améliorer la prise en compte de l'aléa chute de pierres et éboulements et augmente les possibilités d'interprétation de l'évolution des parois rocheuses.

The importance of distinguishing information from evidence/observations when formulating propositions

The value of forensic results crucially depends on the propositions and the information under which they are evaluated. For example, if a full single DNA profile for a contemporary marker system matching the profile of Mr A is assessed, given the propositions that the DNA came from Mr A and given it came from an unknown person, the strength of evidence can be overwhelming (e.g., in the order of a billion). In contrast, if we assess the same result given that the DNA came from Mr A and given it came from his twin brother (i.e., a person with the same DNA profile), the strength of evidence will be 1, and therefore neutral, unhelpful and irrelevant 1 to the case at hand. While this understanding is probably uncontroversial and obvious to most, if not all practitioners dealing with DNA evidence, the practical precept of not specifying an alternative source with the same characteristics as the one considered under the first proposition may be much less clear in other circumstances. During discussions with colleagues and trainees, cases have come to our attention where forensic scientists have difficulty with the formulation of propositions. It is particularly common to observe that results (e.g., observations) are included in the propositions, whereas-as argued throughout this note-they should not be. A typical example could be a case where a shoe-mark with a logo and the general pattern characteristics of a Nike Air Jordan shoe is found at the scene of a crime. A Nike Air Jordan shoe is then seized at Mr A's house and control prints of this shoe compared to the mark. The results (e.g., a trace with this general pattern and acquired characteristics corresponding to the sole of Mr A's shoe) are then evaluated given the propositions 'The mark was left by Mr A's Nike Air Jordan shoe-sole' and 'The mark was left by an unknown Nike Air Jordan shoe'. As a consequence, the footwear examiner will not evaluate part of the observations (i.e., the mark presents the general pattern of a Nike Air Jordan) whereas they can be highly informative. Such examples can be found in all forensic disciplines. In this article, we present a few such examples and discuss aspects that will help forensic scientists with the formulation of propositions. In particular, we emphasise on the usefulness of notation to distinguish results that forensic scientists should evaluate from case information that the Court will evaluate.

Understanding academics' popular science publishing : institution culture and management style effects

Most universities and higher education systems have formally taken up a third mission, which involves various public outreach and engagement activities. Little is known regarding how higher education institutions' organisations interact with academic's level of public outreach. This article examines to which extent the perceptions academics have of their institutions' culture and management style, as well as some of their own individual and statutory characteristics interact with their level of public outreach. Using the Academic Profession in Europe comparative and quantitative research database, this article focuses on two countries on the extremities of the spectrum - Switzerland and the United Kingdom.

The polymorhism of crime scene investigation: an exploratory analysis of the influence of crime and forensic intelligence on decisions made by crime scene examiners

A growing body of scientific literature recurrently indicates that crime and forensic intelligence influence how crime scene investigators make decisions in their practices. This study scrutinises further this intelligence-led crime scene examination view. It analyses results obtained from two questionnaires. Data have been collected from nine chiefs of Intelligence Units (IUs) and 73 Crime Scene Examiners (CSEs) working in forensic science units (FSUs) in the French speaking part of Switzerland (six cantonal police agencies). Four salient elements emerged: (1) the actual existence of communication channels between IUs and FSUs across the police agencies under consideration; (2) most CSEs take into account crime intelligence disseminated; (3) a differentiated, but significant use by CSEs in their daily practice of this kind of intelligence; (4) a probable deep influence of this kind of intelligence on the most concerned CSEs, specially in the selection of the type of material/trace to detect, collect, analyse and exploit. These results contribute to decipher the subtle dialectic articulating crime intelligence and crime scene investigation, and to express further the polymorph role of CSEs, beyond their most recognised input to the justice system. Indeed, they appear to be central, but implicit, stakeholders in intelligence-led style of policing.

Creatine deficiency syndomes : a new model of partial GAMT deficiency affecting brain cell development

Les syndromes de déficiences cérébrales en créatine (CCDS) sont dus à des mutations dans les gènes GATM et G AMT (codant pour les enzymes AGAT et G AMT de la voie de synthèse de créatine) ainsi que SLC6A8 (transporteur de créatine), et génèrent une absence ou une très forte baisse de créatine (Cr) dans le cerveau, mesurée par spectroscopic de résonance magnétique. Les patients CCDS développent des handicaps neurologiques sévères. Les patients AGAT et GAMT peuvent être traités avec des doses importantes de Cr, mais gardent dans la plupart des cas des séquelles neurologiques irréversibles. Aucun traitement efficace n'existe à ce jour pour la déficience en SLC6A8. Bien que de nombreux modèles aient été développés pour comprendre la Cr cérébrale en conditions physiologiques, les pathomécanismes des CCDS ne sont pas encore compris. Des souris transgéniques pour les gènes Gatm, Gamt et Slc6a8 ont été générées, mais elles ne miment que partiellement la pathologie humaine. Parmi les CCDS, la déficience en GAMT est la plus sévère, en raison de l'accumulation cérébrale de l'intermédiaire guanidinoacétate (GAA). Alors que la toxicité cérébrale du GAA a été étudiée par exposition directe au GAA d'animaux adultes sains, les mécanismes de la toxicité du GAA en condition de déficience en GAMT dans le cerveau en développement sont encore inconnus. Le but de ce projet était donc de développer un modèle de déficience en GAMT dans des cultures 3D primaires de cellules nerveuses de rat en agrégats par knock-down du gène GAMT, en utilisant un virus adéno-associé (AAV) induisant le mécanisme d'interférence à l'ARN (RNAi). Le virus scAAV2, à la multiplicité d'infection de 1000, s'est révélé le plus efficace pour transduire tous les types de cellules nerveuses des cultures (neurones, astrocytes, oligodendrocytes), et générer un knock-down maximal de la protéine GAMT de 85% (jour in vitro 18). Cette déficience partielle en GAMT s'est révélée insuffisante pour générer une déficience en Cr, mais a causé l'accumulation attendue de GAA, à des doses comparables aux niveaux observés dans le LCR des patients GAMT. Le GAA a induit une croissance axonale anarchique accompagnée d'une baisse de l'apoptose naturelle, suivis par une induction tardive de mort cellulaire non-apoptotique. Le co-traitement par la Cr a prévenu tous les effets toxiques du GAA. Ce travail montre que l'accumulation de GAA en absence de déficience en Cr est suffisante pour affecter le développement du tissu nerveux, et suggère que des formes de déficiences en GAMT supplémentaires, ne présentant pas de déficiences en Cr, pourraient être découvertes par mesure du GAA, en particulier à travers les programmes récemment proposés de dépistage néonatal de la déficience en GAMT. -- Cerebral creatine deficiency syndromes (CCDS) are caused by mutations in the genes GATM and GAMT (respectively coding for the two enzymes of the creatine synthetic pathway, AGAT and GAMT) as well as SLC6A8 (creatine transporter), and lead to the absence or very strong decrease of creatine (Cr) in the brain when measured by magnetic resonance spectroscopy. Affected patients show severe neurological impairments. While AGAT and GAMT deficient patients can be treated with high dosages of Cr, most remain with irreversible brain sequelae. No treatment has been successful so far for SLC6A8 deficiency. While many models have helped understanding the cerebral Cr pathways in physiological conditions, the pathomechanisms underlying CCDS are yet to be elucidated. Transgenic mice carrying mutations in the Gatm, Gamt and Slc6a8 genes have been developed, but only partially mimic the human pathology. Among CCDS, GAMT deficiency is the most severe, due to the CNS accumulation of the guanidinoacetate (GAA) intermediate. While brain toxicity of GAA has been explored through direct GAA exposure of adult healthy animals, the mechanisms underlying GAA toxicity in GAMT deficiency conditions on the developing CNS are yet unknown. The aim of this project was thus to develop and characterize a GAMT deficiency model in developing brain cells by gene knockdown, by adeno-associated virus (AAV)-driven RNA interference (RNAi) in rat 3D organotypic primary brain cell cultures in aggregates. scAAV2 with a multiplicity of infection of 1000 was shown as the most efficient serotype, was able to transduce all brain cell types (neurons, astrocytes, oligodendrocytes) and to induce a maximal GAMT protein knockdown of 85% (day in vitro 18). Metabolite analysis showed that partial GAMT knockdown was insufficient to induce Cr deficiency but generated the awaited GAA accumulation at concentrations comparable to the levels observed in cerebrospinal fluid of GAMT-deficient patients. Accumulated GAA induced axonal hypersprouting paralleled with inhibition of natural apoptosis, followed by a later induction in non-apoptotic cell death. Cr supplementation led to the prevention of all GAA-induced toxic effects. This work shows that GAA accumulation without Cr deficiency is sufficient to affect CNS development, and suggests that additional partial GAMT deficiencies, which may not show the classical brain Cr deficiency, may be discovered through GAA measurement including by recently proposed neonatal screening programs for GAMT deficiency.

Living with invasive plants in the Anthropocene : the importance of understanding practice and experience

The role of humans in facilitating the rapid spread of plants at a scale that is considered invasive is one manifestation of the Anthropocene, now framed as a geological period in which humans are the dominant force in landscape transformation. Invasive plant management faces intensified challenges, and can no longer be viewed in terms of 'eradication' or 'restoration of original landscapes'. In this perspectives piece, we focus on the practice and experience of people engaged in invasive plant management, using examples from Australia and Canada. We show how managers 1) face several pragmatic trade-offs; 2) must reconcile diverse views, even within stakeholder groups; 3) must balance competing temporal scales; 4) encounter tensions with policy; and 5) face critical and under-acknowledged labour challenges. These themes show the variety of considerations based on which invasive plant managers make complex decisions about when, where, and how to intervene. Their widespread pragmatic acceptance of small, situated gains (as well as losses) combines with impressive long-term commitments to the task of invasives management. We suggest that the actual practice of weed management challenges those academic perspectives that still aspire to attain pristine nature.

Epigenetic regulatory elements: Recent advances in understanding their mode of action and use for recombinant protein production in mammalian cells.

Successful generation of high producing cell lines requires the generation of cell clones expressing the recombinant protein at high levels and the characterization of the clones' ability to maintain stable expression levels. The use of cis-acting epigenetic regulatory elements that improve this otherwise long and uncertain process has revolutionized recombinant protein production. Here we review and discuss new insights into the molecular mode of action of the matrix attachment regions (MARs) and ubiquitously-acting chromatin opening elements (UCOEs), i.e. cis-acting elements, and how these elements are being used to improve recombinant protein production. These elements can help maintain the chromatin environment of the transgene genomic integration locus in a transcriptionally favorable state, which increases the numbers of positive clones and the transgene expression levels. Moreover, the high producing clones tend to be more stable in long-term cultures even in the absence of selection pressure. Therefore, by increasing the probability of isolating a high producing clone, as well as by increasing transcription efficiency and stability, these elements can significantly reduce the time and cost required for producing large quantities of recombinant proteins.

Structure-Based, Rational Design of T Cell Receptors.

Adoptive cell transfer using engineered T cells is emerging as a promising treatment for metastatic melanoma. Such an approach allows one to introduce T cell receptor (TCR) modifications that, while maintaining the specificity for the targeted antigen, can enhance the binding and kinetic parameters for the interaction with peptides (p) bound to major histocompatibility complexes (MHC). Using the well-characterized 2C TCR/SIYR/H-2K(b) structure as a model system, we demonstrated that a binding free energy decomposition based on the MM-GBSA approach provides a detailed and reliable description of the TCR/pMHC interactions at the structural and thermodynamic levels. Starting from this result, we developed a new structure-based approach, to rationally design new TCR sequences, and applied it to the BC1 TCR targeting the HLA-A2 restricted NY-ESO-1157-165 cancer-testis epitope. Fifty-four percent of the designed sequence replacements exhibited improved pMHC binding as compared to the native TCR, with up to 150-fold increase in affinity, while preserving specificity. Genetically engineered CD8(+) T cells expressing these modified TCRs showed an improved functional activity compared to those expressing BC1 TCR. We measured maximum levels of activities for TCRs within the upper limit of natural affinity, K D = ∼1 - 5 μM. Beyond the affinity threshold at K D < 1 μM we observed an attenuation in cellular function, in line with the "half-life" model of T cell activation. Our computer-aided protein-engineering approach requires the 3D-structure of the TCR-pMHC complex of interest, which can be obtained from X-ray crystallography. We have also developed a homology modeling-based approach, TCRep 3D, to obtain accurate structural models of any TCR-pMHC complexes when experimental data is not available. Since the accuracy of the models depends on the prediction of the TCR orientation over pMHC, we have complemented the approach with a simplified rigid method to predict this orientation and successfully assessed it using all non-redundant TCR-pMHC crystal structures available. These methods potentially extend the use of our TCR engineering method to entire TCR repertoires for which no X-ray structure is available. We have also performed a steered molecular dynamics study of the unbinding of the TCR-pMHC complex to get a better understanding of how TCRs interact with pMHCs. This entire rational TCR design pipeline is now being used to produce rationally optimized TCRs for adoptive cell therapies of stage IV melanoma.