OpenStructure: a flexible software framework for computational structural biology

Motivation: Developers of new methods in computational structural biology are often hampered in their research by incompatible software tools and non-standardized data formats. To address this problem, we have developed OpenStructure as a modular open source platform to provide a powerful, yet flexible general working environment for structural bioinformatics. OpenStructure consists primarily of a set of libraries written in C++ with a cleanly designed application programmer interface. All functionality can be accessed directly in C++ or in a Python layer, meeting both the requirements for high efficiency and ease of use. Powerful selection queries and the notion of entity views to represent these selections greatly facilitate the development and implementation of algorithms on structural data. The modular integration of computational core methods with powerful visualization tools makes OpenStructure an ideal working and development environment. Several applications, such as the latest versions of IPLT and QMean, have been implemented based on OpenStructure—demonstrating its value for the development of next-generation structural biology algorithms. Availability: Source code licensed under the GNU lesser general public license and binaries for MacOS X, Linux and Windows are available for download at http://www.openstructure.org. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

Loss of AP-3 function affects spontaneous and evoked release at hippocampal mossy fiber synapses

Synaptic vesicle (SV) exocytosis mediating neurotransmitter release occurs spontaneously at low intraterminal calcium concentrations and is stimulated by a rise in intracellular calcium. Exocytosis is compensated for by the reformation of vesicles at plasma membrane and endosomes. Although the adaptor complex AP-3 was proposed to be involved in the formation of SVs from endosomes, whether its function has an indirect effect on exocytosis remains unknown. Using mocha mice, which are deficient in functional AP-3, we identify an AP-3-dependent tetanus neurotoxin-resistant asynchronous release that can be evoked at hippocampal mossy fiber (MF) synapses. Presynaptic targeting of the tetanus neurotoxin-resistant vesicle soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) tetanus neurotoxin-insensitive vesicle-associated membrane protein (TI-VAMP) is lost in mocha hippocampal MF terminals, whereas the localization of synaptobrevin 2 is unaffected. In addition, quantal release in mocha cultures is more frequent and more sensitive to sucrose. We conclude that lack of AP-3 results in more constitutive secretion and loss of an asynchronous evoked release component, suggesting an important function of AP-3 in regulating SV exocytosis at MF terminals

Reconstructing domestic violence as "terrorism against women" : disrupting dominant discourse

This thesis examines the different ways in which violence is constructed within legal discourse. Two specific types of violence are compared - domestic violence and terrorism. While on the face of it, these appear to be very different types of violence, in the second section of my thesis, I argue that there are significant parallels between the two. In particular, in Chapter 2.2 I argue that serious domestic violence is often committed with a particular ideological motive, that of masculinist ideology. Ideological motive is the first element of the legal definition of terrorism. In making this argument, I draw upon definitions of domestic violence that point to the elements of power and control inherent in some domestic violence, which is committed predominantly by men against women. I also argue that this type of violence is a manifestation of masculinist ideology in a broader sense, which permeates Australian society. In Chapter 2.3, I also argue for the reconceptualisation of domestic violence as a crime committed against women as a 'section of the public'. This accords with the second aspect of the legal definition of terrorism, as a crime committed with the intention of coercing a government, or intimidating the public, or a section of the public. This reconceptualisation contrasts with the usual conceptualisation of domestic violence as a crime committed in the private sphere, a feature of domestic violence which has been the subject of significant feminist critique. Having reconstructed domestic violence as fitting within the two key parameters of the legal definition of terrorism, in Section 3 I go on to consider some of the various ways in which the law differentially treats terrorism and domestic violence. In Chapters 3.1 and 3.2, I consider the treatment of preparatory forms of violence, and prevention of violence. In Chapter 3.1, I examine the regulation of incitement to violence, through the national system for classification of publications and films, and also through the regulation of hate speech in Australian and various overseas jurisdictions. Chapter 3.2 contains an examination of the civil regimes for the control and prevention of violence, specifically terrorism control orders and domestic violence protection orders. Chapters 3.3 and 3.4 consist of an examination of the treatment of more serious forms of violence. In Chapter 3.3 I compare sentencing decisions in Australian terrorism cases with sentences for male-perpetrated homicides against intimate partners, exploring the ways in which the concepts of 'ideology' and 'public' interact with the various considerations to be taken account of upon sentence. In Chapter 3.4, I examine cases in which female victims of domestic violence respond with lethal violence against their abusers, and how they are constructed in legal discourse, in comparison with law enforcement agents who respond to terrorism and other types of violence that threaten the safety of police or the community. I argue that the construction of domestic violence as a 'private' crime devoid of ideological aspects affects the ways in which female perpetrators of defensive homicide are treated in the legal system. Throughout each of these chapters, I consider how the differential constructions of domestic violence and terrorism serve to reflect and reinforce existing power relationships within society. In particular, the continued trivialisation of domestic violence serves masculinist interests in ways that I explore in each chapter. Finally, in Chapter 4, I draw upon some of the themes from these various chapters and discuss possibilities for legal reform and further ways in which reconceptualising domestic violence as an ideological/public crime may influence the way it is dealt with in the legal system

‘Does Anybody Have A Map?’ The Impact of ‘Virtual Broadway’ on Musical Theatre Composition.

In contemporary popular music, ‘There are no longer subjective gatekeepers controlling who gets let “in”, promoted and exposed. The choice is ours. Now, anyone can be famous.’ (Price, 2011). This is a transformation also evident in musical theatre, where an upsurge in ‘YouTube musical theatre composers’ (Pasek & Paul, 2015) and social media engagement challenges the dominance of the book musical. Opportunities for self-promotion on the internet are vast, and allow composers to reach a more diverse audience, but in what ways do these emerging opportunities also influence the form of works produced. For instance, online audiences often lack time to invest emotionally in a long theatrical piece, and prefer songs that deliver similar emotional arcs in condensed form. If humans on-line have an average attention span of 8 seconds (Riecke-Gonzales, 2015), for example, this paper considers how musical theatre might evolve to meet the requirements of millennials. The growing popularity of Dear Evan Hansen, arguably the first truly ‘digital age’ musical (Takiff, 2016), provides a present instance of the impact of ‘virtual Broadway’ (Pasek & Paul, 2015) on the musical theatre model. It is both possible and timely to debate the extent to which this hybrid has ‘democratized access to creation and distribution tools’ (Bhargava and Klat, 2017), allowing new voices and models to break through, or has actually limited the genre’s scope

Consent to Treatment for Transgender and Intersex Children

More than a decade has passed since the landmark High Court decision in Marion’s Case,1 where the Court authorised the sterilisation of a young woman who suffered from a disability. Recently, the principles established in that case were applied by the Family Court in a different context – for the provision of hormonal treatment for a 13 year old child,2 some aspects of which are irreversible. Previously, the Family Court had authorised gender reassignment surgery for a child suffering from a physical, congenital condition,3 but notably in Re Alex, the subject child suffered no identified physical condition indicating treatment, but from an identified psychological condition, gender identity dysphoria. This article considers the issues raised by recent applications of the principles relating to the capacity of children to consent to medical treatment, including the decision in Re Alex and the application of those principles to transgender and intersex children. While not all children or adults who identify as transgender or intersex choose the long and difficult path of gender reassignment, some will choose surgical gender reassignment or hormonal treatment at some stage of their lives. In cases where it is proposed that a minor undergo such treatment, the application of the principles of child consent poses particular difficulties

Seismic structure of the north-central Chilean convergent margin: Subduction erosion of a paleomagmatic arc

We study the erosive convergent margin of north-central Chile (at similar to 31 degrees S) by using high-resolution bathymetric, wide-angle refraction, and multichannel seismic reflection data to derive a detailed tomographic 2-D velocity-depth model. In the overriding plate, our velocity model shows that the lowermost crustal velocities beneath the upper continental slope are 6.0-6.5km/s, which are interpreted as the continental basement composed by characteristic metamorphic and igneous rocks of the Coastal Cordillera. Beneath the lower and middle continental slope, however, the presence of a zone of reduced velocities (3.5-5.0km/s) is interpreted as the outermost fore arc composed of volcanic rocks hydrofractured as a result of frontal and basal erosion. At the landward edge of the outermost fore arc, the bathymetric and seismic data provide evidence for the presence of a prominent trenchward dipping normal scarp (similar to 1km offset), which overlies a strong lateral velocity contrast from similar to 5.0 to similar to 6.0km/s. This pronounced velocity contrast propagates deep into the continental crust, and it resembles a major normal listric fault. We interpret this seismic discontinuity as the volcanic-continental basement contact of the submerged Coastal Cordillera characterized by a gravitational collapse of the outermost fore arc. Subduction erosion has, most likely, caused large-scale crustal thinning and long-term subsidence of the outermost fore arc

Laser induced surface modification for inkjet printing and coating

Lasers are nowadays widely applied in additive manufacturing and several laser based techniques related to inkjet printing are emerging. In this paper, surface treatment of nanoparticle coatings using a commercial laser engraving machine are presented. Experiments were performed on (i) thin thermally cured silver nanoparticle coatings on glass and (ii) iron oxide (Fe 2 O 3 ) nanoparticle dispersion coatings on glass. The laser treatment on Ag films illustrates local melting or dewetting behavior dependent on laser power and on the density of engraving patterns. For Fe 2 O 3 coatings, direct laser writing on dried layers and laser treatment on fluid nanoparticle ink layers are investigated. We demonstrate and discuss in particular the generation of large area laser induced microstructures in vertically confined nanoparticle ink films. Controlled ink accumulation is generated by the laser pulses. Furthermore, 2D porous network structures, as well as laser induced large area filament structures are generated by heat driven capillary flow. Tailored adjustments of nanoparticle inks, film thickness and laser treatment patterns open perspectives for the generation of laser induced self-assemblies, e.g. for novel fabrication processes for 2D metamaterials, for sensor developments or advanced anti-counterfeit applications

Some remarks on black quarter vaccines

The articles have been scanned in colour with a HP Scanjet 5590; 300dpi. Adobe Acrobat XI Pro was used to OCR the text and also for the merging and conversion to the final presentation PDF-format.The experiments detailed here tend to the following conclusions:- (1) Slight persistent local reactions may sometimes be expected to follow inoculation with blackquarter vaccines precipitated by alum or aluminium hydroxide. (2) Blackquarter vaccines containing alum afford a very strong protection against the disease. (3) The immunity from the best vaccines at present in use becomes gradually reduced after six to twelve months. (4) There is probably some diminution in the efficiency of all types of blackquarter vaccine after 6-12 months, but a fairly good protection was still afforded by one-year-old vaccine