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.

Australian higher education evaluation through assurance of learning

A collaborative research project conducted by five Australian universities inquired into the philosophy and motivation for Assurance of Learning (AoL) as a process of education evaluation. Associate Deans Teaching and Learning representing Business schools from twenty-five universities across Australia participated in telephone interviews. Data was analysed using NVIVO9. Results indicated that articulated rationale for AoL was both ensuring that students had acquired the attributes and skills the universities claimed they had, and the philosophy of continuous improvement. AoL was motivated both by ritualistic objectives to satisfy accreditation requirements and virtuous agendas for quality improvement. Closing-the-loop was emphasised, but was mostly wishful thinking for next steps beyond data collection and reporting. AoL was conceptualised as one element within the larger context of quality review, but there was no evidence of comprehensive frameworks or strategic plans.

Hydrogen-bonding in cyclic imides and amide carboxylic acid derivatives from the facile reaction of cis-cyclohexane-1,2-carboxylic anhydride with o- and p-anisidine and m- and p-aminobenzoic acids

The structures of the open chain amide carboxylic acid rac-cis-[2-(2-methoxyphenyl)carbamoyl]cyclohexane-1-carboxylic acid, C15H19NO4, (I) and the cyclic imides rac-cis-2-(4-methoxyphenyl)-3a,4,5,6,7,7-hexahydroisoindole-1,3-dione,C15H17NO3, (II), chiral cis-2-(3-carboxyphenyl)-3a,4,5,6,7,7a-hexahydroisoindole-1,3-dione, C15H15NO4,(III) and rac-cis-2-(4-carboxyphenyl)- 3a,4,5,6,7,7a-hexahydroisoindole-1,3-dione monohydrate, C15H15NO4. H2O) (IV), are reported. In the amide acid (I), the phenylcarbamoyl group is essentially planar [maximum deviation from the least-squares plane = 0.060(1)Ang. for the amide O atom], the molecules form discrete centrosymmetric dimers through intermolecular cyclic carboxy-carboxy O-H...O hydrogen-bonding interactions [graph set notation R2/2(8)]. The cyclic imides (II)--(IV) are conformationally similar, with comparable phenyl ring rotations about the imide N-C(aromatic) bond [dihedral angles between the benzene and isoindole rings = 51.55(7)deg. in (II), 59.22(12)deg. in (III) and 51.99(14)deg. in (IV). Unlike (II) in which only weak intermolecular C-H...O(imide) hydrogen bonding is present, the crystal packing of imides (III) and (IV) shows strong intermolecular carboxylic acid O-H...O hydrogen-bonding associations. With (III), these involve imide O-atom acceptors, giving one-dimensional zigzag chains [graph set C(9)], while with the monohydrate (IV), the hydrogen bond involves the partially disordered water molecule which also bridges molecules through both imide and carboxyl O-atom acceptors in a cyclic R4/4(12) association, giving a two-dimensional sheet structure. The structures reported here expand the structural data base for compounds of this series formed from the facile reaction of cis-cyclohexane-1,2-dicarboxylic anhydride with substituted anilines, in which there is a much larger incidence of cyclic imides compared to amide carboxylic acids.

Fusing loop detector and probe vehicle data to estimate travel time statistics on signalized urban networks

This article presents a methodology that integrates cumulative plots with probe vehicle data for estimation of travel time statistics (average, quartile) on urban networks. The integration reduces relative deviation among the cumulative plots so that the classical analytical procedure of defining the area between the plots as the total travel time can be applied. For quartile estimation, a slicing technique is proposed. The methodology is validated with real data from Lucerne, Switzerland and it is concluded that the travel time estimates from the proposed methodology are statistically equivalent to the observed values.

From the editor

In this issue of the Project Management Journal, the reader will explore understanding better the contribution of project management to organizational performance, discovering the necessity to move beyond the old reigning paradigm of single-loop project control, raising the question whether PMP® certification leads to better performance, learning how to develop project management competence through a course based on service learning and an experiential learning approach, supporting new product development with the use of “dormant knowledge,” and increasing performance of virtual new product development projects...

Identification of long intergenic region sequences involved in maize streak virus replication

The main cis-acting control regions for replication of the single-stranded DNA genome of maize streak virus (MSV) are believed to reside within an approximately 310 nt long intergenic region (LIR). However, neither the minimum LIR sequence required nor the sequence determinants of replication specificity have been determined experimentally. There are iterated sequences, or iterons, both within the conserved inverted-repeat sequences with the potential to form a stem-loop structure at the origin of virion-strand replication, and upstream of the rep gene TATA box (the rep-proximal iteron or RPI). Based on experimental analyses of similar iterons in viruses from other geminivirus genera and their proximity to known Rep-binding sites in the distantly related mastrevirus wheat dwarf virus, it has been hypothesized that the iterons may be Rep-binding and/or -recognition sequences. Here, a series of LIR deletion mutants was used to define the upper bounds of the LIR sequence required for replication. After identifying MSV strains and distinct mastreviruses with incompatible replication-specificity determinants (RSDs), LIR chimaeras were used to map the primary MSV RSD to a 67 nt sequence containing the RPI. Although the results generally support the prevailing hypothesis that MSV iterons are functional analogues of those found in other geminivirus genera, it is demonstrated that neither the inverted-repeat nor RPI sequences are absolute determinants of replication specificity. Moreover, widely divergent mastreviruses can trans-replicate one another. These results also suggest that sequences in the 67 nt region surrounding the RPI interact in a sequence-specific manner with those of the inverted repeat.

Drugs, labels and (p)ill-fitting boxes : ADHD and children who are hard to teach

In offering a critical review of the problem we call “ADHD” this paper progresses in three stages. The first two parts juxtapose the dominant voices emanating from the literature in medicine and psychology, highlighting some interdependency between these otherwise competing interest groups. In part three, the nature of the relationship between these groups and the institution of the school is considered, as is the role that the school may play in the psycho-pathologisation of fidgety, distractible, active children who prove hard to teach. In so doing, the author provides an insight as to why the problem we call “ADHD” has achieved celebrity status in Australia and what the effects of that may be for children who come to be described in these ways.

Adsorption of p-nitrophenol on organoclays

In this study, organoclays were prepared through ion exchange of a single cationic surfactant, hexadecyltrimethylammonium bromide and characterised by a range of methods including X-ray diffraction (XRD) and thermogravimetric analysis. Changes in the surface properties of montmorillonite and the organoclays were observed and the basal spacings of organoclays with and without p-nitrophenol were determined using XRD. The thermal stability of both organoclays were measured using thermogravimetry. As the surfactant loading increased, the expanded basal spacings were observed, and different molecular configurations of surfactant were identified. When the surfactant loading exceeded 1.0 CEC, surfactant molecules tend to adsorb strongly on the clay surface and this resulted in increased affinity to organic compounds. The adsorbed p-nitrophenol and the surfactant decomposed simultaneously. Hence, the surfactant molecules and adsorbed p-nitrophenol are important in determining the thermal stabilities of organoclays. This study enhances the understanding of the structure and adsorption properties of organoclays and has further implications for the application of organoclays as filter materials for the removal of organic pollutants in aqueous solutions.

Algorithm for queue estimation with loop detector of time occupancy in off-ramps on signalized motorways

Long traffic queues on off-ramps significantly compromise the safety and throughput of motorways. Obtaining accurate queue information is crucial for countermeasure strategies. However, it is challenging to estimate traffic queues with locally installed inductive loop detectors. This paper deals with the problem of queue estimation with the interpretation of queuing dynamics and the corresponding time-occupancy distribution over motorway off-ramps. A novel algorithm for real-time queue estimation with two detectors is presented and discussed. Results derived from microscopic traffic simulation validated the effectiveness of the algorithm and revealed some of its useful features: (a) long and intermediate traffic queues could be accurately measured, (b) relatively simple detector input (i.e., time occupancy) was required, and (c) the estimation philosophy was independent with signal timing changes and provided the potential to cooperate with advanced strategies for signal control. Some issues concerning field implementation are also discussed.

Traffic queue estimation for metered motorway on-ramps through use of loop detector time occupancies

The primary objective of this study is to develop a robust queue estimation algorithm for motorway on-ramps. Real-time queue information is a vital input for dynamic queue management on metered on-ramps. Accurate and reliable queue information enables the management of on-ramp queue in an adaptive manner to the actual traffic queue size and thus minimises the adverse impacts of queue flush while increasing the benefit of ramp metering. The proposed algorithm is developed based on the Kalman filter framework. The fundamental conservation model is used to estimate the system state (queue size) with the flow-in and flow-out measurements. This projection results are updated with the measurement equation using the time occupancies from mid-link and link-entrance loop detectors. This study also proposes a novel single point correction method. This method resets the estimated system state to eliminate the counting errors that accumulate over time. In the performance evaluation, the proposed algorithm demonstrated accurate and reliable performances and consistently outperformed the benchmarked Single Occupancy Kalman filter (SOKF) method. The improvements over SOKF are 62% and 63% in average in terms of the estimation accuracy (MAE) and reliability (RMSE), respectively. The benefit of the innovative concepts of the algorithm is well justified by the improved estimation performance in congested ramp traffic conditions where long queues may significantly compromise the benchmark algorithm’s performance.

Studies in power hardware in the loop (PHIL) simulation using real-time digital simulator (RTDS)

In power hardware in the loop (PHIL) simulations, a real-time simulated power system is interfaced to a piece of hardware, usually called hardware under test (HuT). A PHIL test can be realized using several simulation tools. Among them Real Time Digital Simulator (RTDS) is an ideal tool to perform complex power system simulations in near real-time. Stable operation of the entire system, along with the accuracy of simulation results are the main concerns regarding a PHIL simulation. In this paper, a simulated power network on RTDS will be interfaced to HuT through a voltage source converter (VSC). Issues around stability and other interface problems are studied and a new method to stabilize some unstable PHIL cases is proposed. PHIL simulation results in PSCAD and RSCAD are presented.

Who drives E&P innovation?

Few would argue that the upstream oil and gas industry has become more technology- intensive over the years. At the same time, the increasing costs and complexity of today’s exploration and production (E&P) technologies are making it increasingly difficult for any one company to support an aggressive research and development (R&D) agenda single handedly. The coming together of these two evolutionary forces gives rise to important questions. How does innovation happen in the E&P industry? Specifically, what ideas and inputs flow from which parts of the industry’s value network, and where do these inputs go? And how do firms and organizations from different countries contribute differently to this process? This survey was designed to shed light on these issues.

P.I.C.U., H.D.U., A.O.A. What treatment do we provide?: Current descriptions of the function of intensive care for inpatient Psychiatric Health Care.

Purpose – This paper adds to growing research of psychiatric intensive care units (PICU) by recounting descriptions of psychiatric intensive care settings and discusses the perceptions held by nurses of the organisational interfaces, arrangements and provisions of care in these settings. Design/methodology/approach – Data gathered from focus groups held with nurses from two PICUs was used to establish terminology, defining attributes, related concepts, antecedents, values, processes and concepts related to current practices. A literature search was conducted to permit a review of the conceptual arrangements and contemporary understanding of intensive care for people experiencing acute psychiatric illness based on the perspectives held by the nurses from the focus groups. Findings – Dissonance between service needs and the needs and management of individual patients overshadow strategies to implement comprehensive recovery-oriented approaches. Three factors are reported in this paper that influence standards and procedural practice in PICU; organisational structures; physical structures; and subtype nomenclature. Practical implications – Acute inpatient care is an important part of a comprehensive approach to mental health services. Commonly intensive acute care is delivered in specialised wards or units co-located with acute mental health inpatient units mostly known as PICU. Evidence of the most effective treatment and approaches in intensive care settings that support comprehensive recovery for improved outcomes is nascent. Originality/value – Current descriptions from nurses substantiate wide variations in the provisions, design and classifications of psychiatric intensive care. Idiosyncratic and localised conceptions of psychiatric intensive care are not adequately entailing effective treatment and methods in support of recovery principles for improved and comprehensive outcomes. The authors suggest that more concrete descriptions, guidelines, training and policies for provision of intensive psychiatric health care encompassing the perspective of nursing professionals, would reinforce conceptual construction and thus optimum treatments within a comprehensive, recovery-oriented approach to mental health services.

Insights into the mechanism of the reaction between ttrachloro-p-bnzoquinone and hydrogen peroxide and their implications in the catalytic role of water molecules in producing the hydroxyl radial

Detailed mechanisms for the formation of hydroxyl or alkoxyl radicals in the reactions between tetrachloro-p-benzoquinone (TCBQ) and organic hydroperoxides are crucial for better understanding the potential carcinogenicity of polyhalogenated quinones. Herein, the mechanism of the reaction between TCBQ and H2O2 has been systematically investigated at the B3LYP/6-311++G** level of theory in the presence of different numbers of water molecules. We report that the whole reaction can easily take place with the assistance of explicit water molecules. Namely, an initial intermediate is formed first. After that, a nucleophilic attack of H2O2 onto TCBQ occurs, which results in the formation of a second intermediate that contains an OOH group. Subsequently, this second intermediate decomposes homolytically through cleavage of the O-O bond to produce a hydroxyl radical. Energy analyses suggest that the nucleophilic attack is the rate-determining step in the whole reaction. The participation of explicit water molecules promotes the reaction significantly, which can be used to explain the experimental phenomena. In addition, the effects of F, Br, and CH3 substituents on this reaction have also been studied.