Mastering the canonical loop of serine protease inhibitors : enhancing potency by optimising the internal hydrogen bond network

Background Canonical serine protease inhibitors commonly bind to their targets through a rigid loop stabilised by an internal hydrogen bond network and disulfide bond(s). The smallest of these is sunflower trypsin inhibitor (SFTI-1), a potent and broad-range protease inhibitor. Recently, we re-engineered the contact β-sheet of SFTI-1 to produce a selective inhibitor of kallikrein-related peptidase 4 (KLK4), a protease associated with prostate cancer progression. However, modifications in the binding loop to achieve specificity may compromise structural rigidity and prevent re-engineered inhibitors from reaching optimal binding affinity. Methodology/Principal Findings In this study, the effect of amino acid substitutions on the internal hydrogen bonding network of SFTI were investigated using an in silico screen of inhibitor variants in complex with KLK4 or trypsin. Substitutions favouring internal hydrogen bond formation directly correlated with increased potency of inhibition in vitro. This produced a second generation inhibitor (SFTI-FCQR Asn14) which displayed both a 125-fold increased capacity to inhibit KLK4 (Ki = 0.0386±0.0060 nM) and enhanced selectivity over off-target serine proteases. Further, SFTI-FCQR Asn14 was stable in cell culture and bioavailable in mice when administered by intraperitoneal perfusion. Conclusion/Significance These findings highlight the importance of conserving structural rigidity of the binding loop in addition to optimising protease/inhibitor contacts when re-engineering canonical serine protease inhibitors.

CO2 emissions from the combustion of native Australian trees

Carbon dioxide (CO2), as a primary product of combustion, is a known factor affecting climate change and global warming. In Australia, CO2 emissions from biomass burning are a significant contributor to total carbon in the atmosphere and therefore, it is important to quantify the CO2 emission factors from biomass burning in order to estimate their magnitude and impact on the Australian atmosphere. This paper presents the quantification of CO2 emission factors for five common tree species found in South East Queensland forests, as well as several grasses taken from savannah lands in the Northern Territory of Australia, under controlled ‘fast burning’ and ‘slow burning’ laboratory conditions. The results showed that CO2 emission factors varied according to the type of vegetation and burning conditions, with emission factors for fast burning being 2574 ± 254 g/kg for wood, 394 ± 40 g/kg for branches and leaves, and 2181 ± 120 g/kg for grass. Under slow burning conditions, the CO2 emission factors were 218 ± 20 g/kg for wood, 392± 80 g/kg for branches and leaves, and 2027 ± 809 g/kg for grass.

Predicting the effects of bagasse depithing operations on boiler combustion performance

The sugar industry is pursuing diversification options using bagasse as a feedstock. Depithing, the removal of the smaller bagasse particles, is an integral part of the manufacturing processes for bagasse by-products such as pulp and paper. There are possible environmental and economic benefits associated with incorporating depithing operations into a sugar factory. However there have only been limited investigations into the effects of depithing operations on a sugar factory boiler station. This paper describes a modelling investigation, using the lumped parameter boiler design tool BOILER and the CFD code FURNACE, to predict the effects of pith, depithed bagasse and mixed bagasse/pith firing on the efficiency, fuel consumption and combustion performance of a typical sugar factory boiler.

Finding additional semantic entity information for search engines

Entity-oriented search has become an essential component of modern search engines. It focuses on retrieving a list of entities or information about the specific entities instead of documents. In this paper, we study the problem of finding entity related information, referred to as attribute-value pairs, that play a significant role in searching target entities. We propose a novel decomposition framework combining reduced relations and the discriminative model, Conditional Random Field (CRF), for automatically finding entity-related attribute-value pairs from free text documents. This decomposition framework allows us to locate potential text fragments and identify the hidden semantics, in the form of attribute-value pairs for user queries. Empirical analysis shows that the decomposition framework outperforms pattern-based approaches due to its capability of effective integration of syntactic and semantic features.

Impact of the internal business environment on knowledge management within construction organisations

Purpose: Recent knowledge management (KM) literature suggests that KM activities are influenced by the elements of the internal business environment (BE) of organisations. This paper attempts to provide some unique insights into the contextual input of the KM process through empirically identifying the major factors (i.e. “forces”) within the internal BE of construction organisations operating in Hong Kong, and investigating their impact on the intensity of KM activities. Design/methodology/approach: A questionnaire survey was administered to a sample of construction contractors operating in Hong Kong to elicit opinions on the internal BE and intensity of KM activities as executed by targeted organisations. A total of 149 usable responses were received from 99 organisations representing about 38 percent of the research population. In parallel, to the survey, a total of 15 semi-structured interviews were undertaken to provide more insights into the phenomenon under investigation. Findings: Supported by the empirical and qualitative evidence, this study established that firstly, both organisational and technical environments have the capacity to either positively or negatively impact the intensity of KM activities, and both environments serve as stimuli in increasing each other's dynamism; secondly, certain types of KM activities are stronger “energy receivers” and easily to be “powered up” by manipulating factors representing these two environments. Then, through interactions between KM activities, the intensity of the whole strategic KM cycle will be increased thus helping to strengthen organisational competitive advantage.

Combustion products of bulk aluminum rods burning in high pressure oxygen

Characterization of the combustion products released during the burning of commonly used engineering metallic materials may aid in material selection and risk assessment for the design of oxygen systems. The characterization of combustion products in regards to size distribution and morphology gives useful information for systems addressing fire detection. Aluminum rods (3.2-mm diameter cylinders) were vertically mounted inside a combustion chamber and ignited in pressurized oxygen by resistively heating an aluminum/palladium igniter wire attached to the bottom of the test sample. This paper describes the experimental work conducted to establish the particle size distribution and morphology of the resultant combustion products collected after the burning was completed and subsequently analyzed. In general, the combustion products consisted of a re-solidified oxidized slag and many small hollow spheres of size ranging from about 500 nm to 1000 µm in diameter, surfaced with quenched dendritic and grain-like structures. The combustion products were characterized using optical and scanning electron microscopy.

Investigation of the airborne submicrometer particles emitted by dredging vessels using a plume capture method

This paper presents a method for investigating ship emissions, the plume capture and analysis system (PCAS), and its application in measuring airborne pollutant emission factors (EFs) and particle size distributions. The current investigation was conducted in situ, aboard two dredgers (Amity: a cutter suction dredger and Brisbane: a hopper suction dredger) but the PCAS is also capable of performing such measurements remotely at a distant point within the plume. EFs were measured relative to the fuel consumption using the fuel combustion derived plume CO2. All plume measurements were corrected by subtracting background concentrations sampled regularly from upwind of the stacks. Each measurement typically took 6 minutes to complete and during one day, 40 to 50 measurements were possible. The relationship between the EFs and plume sample dilution was examined to determine the plume dilution range over which the technique could deliver consistent results when measuring EFs for particle number (PN), NOx, SO2, and PM2.5 within a targeted dilution factor range of 50-1000 suitable for remote sampling. The EFs for NOx, SO2, and PM2.5 were found to be independent of dilution, for dilution factors within that range. The EF measurement for PN was corrected for coagulation losses by applying a time dependant particle loss correction to the particle number concentration data. For the Amity, the EF ranges were PN: 2.2 - 9.6 × 1015 (kg-fuel)-1; NOx: 35-72 g(NO2).(kg-fuel)-1, SO2 0.6 - 1.1 g(SO2).(kg-fuel)-1and PM2.5: 0.7 – 6.1 g(PM2.5).(kg-fuel)-1. For the Brisbane they were PN: 1.0 – 1.5 x 1016 (kg-fuel)-1, NOx: 3.4 – 8.0 g(NO2).(kg-fuel)-1, SO2: 1.3 – 1.7 g(SO2).(kg-fuel)-1 and PM2.5: 1.2 – 5.6 g(PM2.5).(kg-fuel)-1. The results are discussed in terms of the operating conditions of the vessels’ engines. Particle number emission factors as a function of size as well as the count median diameter (CMD), and geometric standard deviation of the size distributions are provided. The size distributions were found to be consistently uni-modal in the range below 500 nm, and this mode was within the accumulation mode range for both vessels. The representative CMDs for the various activities performed by the dredgers ranged from 94-131 nm in the case of the Amity, and 58-80 nm for the Brisbane. A strong inverse relationship between CMD and EF(PN) was observed.

Application of multi-criteria decision making methods to compression ignition engine efficiency and gaseous, particulate and greenhouse gas emissions

Compression ignition (CI) engine design is subject to many constraints which presents a multi-criteria optimisation problem that the engine researcher must solve. In particular, the modern CI engine must not only be efficient, but must also deliver low gaseous, particulate and life cycle greenhouse gas emissions so that its impact on urban air quality, human health, and global warming are minimised. Consequently, this study undertakes a multi-criteria analysis which seeks to identify alternative fuels, injection technologies and combustion strategies that could potentially satisfy these CI engine design constraints. Three datasets are analysed with the Preference Ranking Organization Method for Enrichment Evaluations and Geometrical Analysis for Interactive Aid (PROMETHEE-GAIA) algorithm to explore the impact of 1): an ethanol fumigation system, 2): alternative fuels (20 % biodiesel and synthetic diesel) and alternative injection technologies (mechanical direct injection and common rail injection), and 3): various biodiesel fuels made from 3 feedstocks (i.e. soy, tallow, and canola) tested at several blend percentages (20-100 %) on the resulting emissions and efficiency profile of the various test engines. The results show that moderate ethanol substitutions (~20 % by energy) at moderate load, high percentage soy blends (60-100 %), and alternative fuels (biodiesel and synthetic diesel) provide an efficiency and emissions profile that yields the most “preferred” solutions to this multi-criteria engine design problem. Further research is, however, required to reduce Reactive Oxygen Species (ROS) emissions with alternative fuels, and to deliver technologies that do not significantly reduce the median diameter of particle emissions.

Application of profluorescent nitroxides for measurements of oxidative capacity of combustion generated particles

Oxidative stress caused by generation of free radicals and related reactive oxygen species (ROS) at the sites of deposition has been proposed as a mechanism for many of the adverse health outcomes associated with exposure to particulate matter (PM). Recently, a new profluorescent nitroxide molecular probe (BPEAnit) developed at QUT was applied in an entirely novel, rapid and non-cell based assay for assessing the oxidative potential of particles (i.e. potential of particles to induce oxidative stress). The technique was applied on particles produced by several combustion sources, namely cigarette smoke, diesel exhaust and wood smoke. One of the main findings from the initial studies undertaken at QUT was that the oxidative potential per PM mass significantly varies for different combustion sources as well as the type of fuel used and combustion conditions. However, possibly the most important finding from our studies was that there was a strong correlation between the organic fraction of particles and the oxidative potential measured by the PFN assay, which clearly highlights the importance of organic species in particle-induced toxicity.

Permeability of high-performance concrete incorporating presoaked lightweight aggregates for internal curing

This paper presents an experimental study on the effect of presoaked lightweight aggregates (LWAs) for internal curing on water permeability, water absorption and resistance of concrete to chloride-ion penetration in comparison with those of a control concrete and a concrete with shrinkage reducing admixture (SRA) of similar water/cement ratios (w/c). In general, the concretes with LWA particles had initial water absorption, sorptivity and water permeability similar to or lower than those of the control concrete and the concrete with SRA. The charges passed, chloride migration coefficient and chloride diffusion coefficient of such concretes were in the same order as those of the control concrete and the concrete with SRA. However, the incorporation of the LWAs for internal curing reduced unit weight, compressive strength and elastic modulus of the concrete. Comparing the LWAs of different sizes for internal curing, finer particles were more efficient in reducing the shrinkage and generally resulted in less reduction in the unit weight, compressive strength, and elastic modulus. However, the increase in the more porous crushed LW particles in concrete seems to increase the penetration of chloride ions in the concrete. The concrete with SRA had initial water absorption, sorptivity, water permeability and resistance to chloride ion penetration comparable with those of the control concrete. The use of SRA in concrete does not affect the elastic modulus of the concrete, except for a minor influence on the compressive strength of the concrete.

The use of artificial neural networks for identifying sustainable biodiesel feedstocks

Over the past few decades, biodiesel produced from oilseed crops and animal fat is receiving much attention as a renewable and sustainable alternative for automobile engine fuels, and particularly petroleum diesel. However, current biodiesel production is heavily dependent on edible oil feedstocks which are unlikely to be sustainable in the longer term due to the rising food prices and the concerns about automobile engine durability. Therefore, there is an urgent need for researchers to identify and develop sustainable biodiesel feedstocks which overcome the disadvantages of current ones. On the other hand, artificial neural network (ANN) modeling has been successfully used in recent years to gain new knowledge in various disciplines. The main goal of this article is to review recent literatures and assess the state of the art on the use of ANN as a modeling tool for future generation biodiesel feedstocks. Biodiesel feedstocks, production processes, chemical compositions, standards, physio-chemical properties and in-use performance are discussed. Limitations of current biodiesel feedstocks over future generation biodiesel feedstock have been identified. The application of ANN in modeling key biodiesel quality parameters and combustion performance in automobile engines is also discussed. This review has determined that ANN modeling has a high potential to contribute to the development of renewable energy systems by accelerating biodiesel research.

Methyl ester preparation from peanut oil and its effect on DI diesel engine combustion

This study investigated the preparation of methyl ester (Biodiesel) from peanut oil by transesterification method and its effect on DI diesel engine. Two parameters were measured during the engine operation: one is engine performance (brake thermal efficiency and brake specific fuel consumption), and the other is the exhaust emissions (NOx and CO). The result showed that, when compared with neat diesel fuel, the brake thermal efficiency of biodiesel blend was almost similar or a slight lower. However, brake specific fuel consumption (bsfc) was a little higher than neat diesel. CO was lower and NOx was little higher with biodiesel blend than that of diesel. The engine performance for B10 and B20 was very similar. At medium and high load conditions the engine emissions for B10 and B20 has no significant variation. Hence, B20 can safely be used in diesel engine without any significant penalty in engine performance and emissions.

A retrospective cohort investigation of active range of motion within one week of open reduction and internal fixation of distal radius fractures

Distal radius fractures stabilized by open reduction internal fixation (ORIF) have become increasingly common. There is currently no consensus on the optimal time to commence range of motion (ROM) exercises post-ORIF. A retrospective cohort review was conducted over a five-year period to compare wrist and forearm range of motion outcomes and number of therapy sessions between patients who commenced active ROM exercises within the first seven days and from day eight onward following ORIF of distal radius fractures. One hundred and twenty-one patient cases were identified. Clinical data, active ROM at initial and discharge therapy assessments, fracture type, surgical approaches, and number of therapy sessions attended were recorded. One hundred and seven (88.4%) cases had complete datasets. The early active ROM group (n = 37) commenced ROM a mean (SD) of 4.27 (1.8) days post-ORIF. The comparator group (n = 70) commenced ROM exercises 24.3 (13.6) days post-ORIF. No significant differences were identified between groups in ROM at initial or discharge assessments, or therapy sessions attended. The results from this study indicate that patients who commenced active ROM exercises an average of 24 days after surgery achieved comparable ROM outcomes with similar number of therapy sessions to those who commenced ROM exercises within the first week.

β-Actin—an unsuitable internal control for RT-PCR

Despite reports confirming cell-cycle dependent gene expression and a number of studies describing specific circumstances in which β-actin is also regulated, the mRNA for β-actin remains a widely used housekeeping gene internal control. Utilizing differential reverse transcriptase-polymerase chain reaction (RT-PCR), we report here the dose-dependent inhibition of β-actin by matrigel. This was detected by comparison to the very moderate inhibition of the target gene, membrane type-1 matrix metalloproteinase (MT1-MMP), with results independently confirmed by similar findings on MT1-MMP expression using competitive RT-PCR. Furthermore, RT-PCR of the housekeeping gene 18 Svedberg Units (S) rRNA demonstrated excellent consistency, reproducibility and non-regulation by a matrigel treatment. We conclude that β-actin is highly regulated by matrigel and therefore unsuitable as an internal control in this treatment. Hence, these findings suggest that researchers have a responsibility to ensure that the housekeeping gene of choice is not regulated in their specific application, as such regulation may dramatically affect the accuracy of their results. This study reinforces the necessity for minimally regulated housekeeping genes such as 18S rRNA, and the superiority of competitive templates as internal controls for quantitative applications of RT-PCR.