Detection of the protein dimers, multiple monomeric states and hydrated forms of Plasmodium falciparum triosephosphate isomerase in the gas phase

Dimeric and monomeric forms of the enzyme triosephosphate isomerase (TIM) from Plasmodium falciparum (Pf) have been detected under conditions of nanoflow by electrospray mass spectrometry. The dimer (M = 55 663 Da) exhibits a narrow charge state distribution with intense peaks limited to values of 18(+) to 21(+), maximal intensity being observed for charge states 19(+) and 20(+). A monomeric species with a charge state distribution ranging from 11(+) to 16(+) is also observed, which may be assigned to folded dissociated subunits. Complete dimer dissociation results under normal electrospray condition. The effects of solution pH and source temperature have been investigated. The observation of four distinct charge state distributions which may be assigned to a dimer, folded monomer, partially folded monomer and unfolded monomer is reported. Circular dichromism and fluorescence studies of Pf TIM at low pH support the retention of substantial secondary and tertiary structures. Satellite peaks in mass spectra corresponding to hydrated species are also observed and isotope shift upon deuteration is demonstrated. The analysis of all available independent crystal structures of Pf TIM and TIMs from other organisms permits identification of structurally conserved water molecules. Hydration observed in the dimer and folded monomeric forms in the gas phase may correspond to these conserved sites.

VisArchive: a time and relevance based visual interface for searching, browsing, and exploring project archives

Background Project archives are becoming increasingly large and complex. On construction projects in particular, the increasing amount of information and the increasing complexity of its structure make searching and exploring information in the project archive challenging and time-consuming. Methods This research investigates a query-driven approach that represents new forms of contextual information to help users understand the set of documents resulting from queries of construction project archives. Specifically, this research extends query-driven interface research by representing three types of contextual information: (1) the temporal context is represented in the form of a timeline to show when each document was created; (2) the search-relevance context shows exactly which of the entered keywords matched each document; and (3) the usage context shows which project participants have accessed or modified a file. Results We implemented and tested these ideas within a prototype query-driven interface we call VisArchive. VisArchive employs a combination of multi-scale and multi-dimensional timelines, color-coded stacked bar charts, additional supporting visual cues and filters to support searching and exploring historical project archives. The timeline-based interface integrates three interactive timelines as focus + context visualizations. Conclusions The feasibility of using these visual design principles is tested in two types of project archives: searching construction project archives of an educational building project and tracking of software defects in the Mozilla Thunderbird project. These case studies demonstrate the applicability, usefulness and generality of the design principles implemented.

Evaluation of mud filtrate clarification to improve factory performance

Clarification performance and flocculant dosage is strongly linked to the mud solids loading in the feed entering the clarifier. The recycle of filtrate can represent an extra ~10-15% mud solids loading on the clarifier, thereby reducing its effective capacity. Filtrate recycling may cause significant increase in turbidity, complexed calcium ion formation, phosphate, proteins and polysaccharides in mixed juice that impact on evaporator scale formation and molasses exhaustion. The paper details the results obtained from laboratory, pilot scale and factory trials of filtrate clarification using both sedimentation and flotation methods. Clarified filtrate could be produced of similar quality to ESJ. Filtrate clarification was able to significantly remove insoluble solids, turbidity, phosphate, and polysaccharides content with slight reductions in minerals content of the filtrate. On the basis of improved filtrate quality, the clarified filtrate could be directed to ESJ, instead of the normal practice of directing the mud filtrate to mixed juice. The potential impacts of implementing filtrate clarification are discussed in respect to improved performance and throughput of the clarification station.

Pivotal principles for digital earth development in the 21st century

Reductionist thinking will no longer suffice to address contemporary, complex challenges that defy sectoral, national, or disciplinary boundaries. Furthermore, lessons learned from the past cannot be confidently used to predict outcomes or help guide future actions. The authors propose that the confluence of a number of technology and social disruptors presents a pivotal moment in history to enable real-time, accelerated and integrated action that can adequately support a ‘future earth’ through transformational solutions. Building on more than a decade of dialogues hosted by the International Society for Digital Earth (ISDE), and evolving a briefing note presented to delegates of Pivotal2015, the paper presents an emergent context for collectively addressing spatial information, sustainable development and good governance through three guiding principles for enabling prosperous living in the 21st Century. These are: (1) open data, (2) real world context and (3) informed visualization for decision support. The paper synthesizes an interdisciplinary dialogue to create a credible and positive future vision of collaborative and transparent action for the betterment of humanity and planet. It is intended that the three Pivotal Principles can be used as an elegant framework for action towards the Digital Earth vision, across local, regional, and international communities and organizations.

Guest editorial: Urban nature for resilient and liveable cities

It is a transforming experience to imagine that in 50 years, our current built environment might look as foreign to our grandchildren as the computers of the 1960s look to us today. We can already see emerging attempts to create cities that are resilient and liveable in the face of physical stresses including population growth, increasing climate variability, resource shortages and pollution. The capacity for transforming every aspect of development towards resilience and liveability goals is profoundly exciting, from heating and cooling through to energy generation, water reticulation, food production, transportation, communication and recreational spaces...

A model based factorization approach for dense 3D recovery from monocular video

Feature track matrix factorization based methods have been attractive solutions to the Structure-front-motion (Sfnl) problem. Group motion of the feature points is analyzed to get the 3D information. It is well known that the factorization formulations give rise to rank deficient system of equations. Even when enough constraints exist, the extracted models are sparse due the unavailability of pixel level tracks. Pixel level tracking of 3D surfaces is a difficult problem, particularly when the surface has very little texture as in a human face. Only sparsely located feature points can be tracked and tracking error arc inevitable along rotating lose texture surfaces. However, the 3D models of an object class lie in a subspace of the set of all possible 3D models. We propose a novel solution to the Structure-from-motion problem which utilizes the high-resolution 3D obtained from range scanner to compute a basis for this desired subspace. Adding subspace constraints during factorization also facilitates removal of tracking noise which causes distortions outside the subspace. We demonstrate the effectiveness of our formulation by extracting dense 3D structure of a human face and comparing it with a well known Structure-front-motion algorithm due to Brand.