Activating a zymogen without proteolytic processing: mutation of Lys15 and Asn194 activates trypsinogen

The zymogen and mature enzyme forms of trypsin-like serine proteases exhibit a wide range of activities. The prototypical trypsinogen-trypsin system is an example of a minimally active zymogen and a maximally active mature protease. The present work identifies several features of trypsinogen which govern its activity. Our results indicate that rat trypsin is 10(8)-fold more active than rat trypsinogen. Rat trypsinogen appears to be less active than bovine trypsinogen. His40 is believed to be an important determinant of zymogen activity. We are unable to verify this role for His40 in trypsinogen since the mutation of His40 to Phe appears to change the trypsin-substrate interface. Deletion of the N-terminal Ile16 from trypsin is expected to produce a trypsinogen-like protein since the Ile16-Asp194 salt bridge cannot form. Such mutants have higher activity and BPTI affinity than trypsinogen, which indicates that the activation peptide stabilizes the inactive trypsinogen conformation. The mutation of Lys15 to Ala increases the BPTI affinity and activity of trypsinogen to an even greater extent; thus, removal of Lys15 can account for the effect of the loss of the activation peptide. These results suggest that Lys15 is an important determinant of zymogen activity. The mutation of Asp194 to Asn also increases the BPTI affinity and activity of trypsinogen. This result suggests that in addition to stabilizing the active conformation of trypsin via the Ile16-Asp194 salt bridge, Asp194 also maintains the inactive conformation of trypsinogen. A correlation exists between the values of kcat/Km and BPTI affinity of mutant trypsinogens and trypsins. However, the slope of this correlation is 0.64, which indicates that different "active" conformations are involved in BPTI binding and substrate hydrolysis. DeltaI16V17 trypsinogen is the lone outlier; its BPTI affinity is higher than would be expected based on the value of kcat/Km. We show that the rate of BPTI association is slower for DeltaI16V17 trypsinogen than for a mutant trypsinogen with a similar BPTI affinity. This observation suggests that BPTI binds to an "active" trypsinogen conformation that is not kinetically accessible to substrates.     

Nonlinear buckling optimization of composite structures

The paper presents an approach to nonlinear buckling fiber angle optimization of laminated composite shell structures. The approach accounts for the geometrically nonlinear behaviour of the structure by utilizing response analysis up until the critical point. Sensitivity information is obtained efficiently by an estimated critical load factor at a precritical state. In the optimization formulation, which is formulated as a mathematical programming problem and solved using gradient-based techniques, a number of the lowest buckling factors are included such that the risk of “mode switching” during optimization is avoided. The presented optimization formulation is compared to the traditional linear buckling formulation and two numerical examples, including a large laminated composite wind turbine main spar, to clearly illustrate the pitfalls of the traditional formulation and the advantage and potential of the presented approach.     

Explanation and reliability of prediction models: the case of breast cancer recurrence

In this paper, we describe the first practical application of two methods, which bridge the gap between the non-expert user and machine learning models. The first is a method for explaining classifiers’ predictions, which provides the user with additional information about the decision-making process of a classifier. The second is a reliability estimation methodology for regression predictions, which helps the users to decide to what extent to trust a particular prediction. Both methods are successfully applied to a novel breast cancer recurrence prediction data set and the results are evaluated by expert oncologists.     

Improved PLSOM algorithm

The original Parameter-Less Self-Organising Map (PLSOM) algorithm was introduced as a solution to the problems the Self-Organising Map (SOM) encounters when dealing with certain types of mapping tasks. Unfortunately the PLSOM suffers from over-sensitivity to outliers and over-reliance on the initial weight distribution. The PLSOM2 algorithm is introduced to address these problems with the PLSOM. PLSOM2 is able to cope well with outliers without exhibiting the problems associated with the standard PLSOM algorithm. The PLSOM2 requires very little computational overhead compared to the standard PLSOM, thanks to an efficient method of approximating the diameter of the inputs, and does not rely on a priori knowledge of the training input space. This paper provides a discussion of the reasoning behind the PLSOM2 and experimental results showing its effectiveness for mapping tasks.     

Understanding cost drivers of software evolution: a quantitative and qualitative investigation of change effort in two evolving software systems

Making changes to software systems can prove costly and it remains a challenge to understand the factors that affect the costs of software evolution. This study sought to identify such factors by investigating the effort expended by developers to perform 336 change tasks in two different software organizations. We quantitatively analyzed data from version control systems and change trackers to identify factors that correlated with change effort. In-depth interviews with the developers about a subset of the change tasks further refined the analysis. Two central quantitative results found that dispersion of changed code and volatility of the requirements for the change task correlated with change effort. The analysis of the qualitative interviews pointed to two important, underlying cost drivers: Difficulties in comprehending dispersed code and difficulties in anticipating side effects of changes. This study demonstrates a novel method for combining qualitative and quantitative analysis to assess cost drivers of software evolution. Given our findings, we propose improvements to practices and development tools to manage and reduce the costs.     

Reactive scheduling in the multi-mode RCPSP

The multi-mode resource-constrained project scheduling problem (MRCPSP) involves the determination of a baseline schedule of the project activities, which can be executed in multiple modes, satisfying the precedence relations and resource constraints while minimizing the project duration. During the execution of the project, the baseline schedule may become infeasible due to activity duration and resource disruptions. We propose and evaluate a number of dedicated exact reactive scheduling procedures as well as a tabu search heuristic for repairing a disrupted schedule, under the assumption that no activity can be started before its baseline starting time. We report on promising computational results obtained on a set of benchmark problems.     

The Covering Law Model Applied to Dynamical Cognitive Science: A Comment on Joel Walmsley

In a 2008 paper, Walmsley argued that the explanations employed in the dynamical approach to cognitive science, as exemplified by the Haken, Kelso and Bunz model of rhythmic finger movement, and the model of infant preservative reaching developed by Esther Thelen and her colleagues, conform to Carl Hempel and Paul Oppenheim’s deductive-nomological model of explanation (also known as the covering law model). Although we think Walmsley’s approach is methodologically sound in that it starts with an analysis of scientific practice rather than a general philosophical framework, we nevertheless feel that there are two problems with his paper. First, he focuses only on the deductivenomological model and so neglects the important fact that explanations are causal. Second, the explanations offered by the dynamical approach do not take the deductive-nomological format, because they do not deduce the explananda from exceptionless laws. Because of these two points, Walmsley makes the dynamical explanations in cognitive science appear problematic, while in fact they are not.     

Classifying species of individual trees by intensity and structure features derived from airborne laser scanner data

The objective of this study was to identify candidate features derived from airborne laser scanner (ALS) data suitable to discriminate between coniferous and deciduous tree species. Both features related to structure and intensity were considered. The study was conducted on 197 Norway spruce and 180 birch trees (leaves on conditions) in a boreal forest reserve in Norway. The ALS sensor used was capable of recording multiple echoes. The point density was 6.6 m^− 2. Laser echoes located within the vertical projection of the tree crowns, which were assumed to be circular and defined according to field measurements, were attributed to three categories: “first echoes of many”, “single echoes”, or “last echoes of many echoes”. They were denoted FIRST, SINGLE, and LAST, respectively. In tree species classification using ALS data features should be independent of tree heights. We found that many features were dependent on tree height and that this dependency influenced selection of candidate features. When we accounted for this dependency, it was revealed that FIRST and SINGLE echoes were located higher and LAST echoes lower in the birch crowns than in spruce crowns. The intensity features of the FIRST echoes differed more between species than corresponding features of the other echo categories. For the FIRST echoes the intensity values tended to be higher for birch than spruce. When using the various features for species classification, maximum overall classification accuracies of 77% and 73% were obtained for structural and intensity features, respectively. Combining candidate features related to structure and intensity resulted in an overall classification accuracy of 88%.     

Effects of different sensors, flying altitudes, and pulse repetition frequencies on forest canopy metrics and biophysical stand properties derived from small-footprint airborne laser data

Canopy height distributions were created from small-footprint airborne laser scanner (ALS) data collected over 40 field sample plots with size 1000 m² located in mature conifer forest. ALS data were collected with two different instruments, i.e., the ALTM 1233 and ALTM 3100 laser scanners (Optech Inc.). The ALTM 1233 data were acquired at a flying altitude of 1200 m and a pulse repetition frequency (PRF) of 33 kHz. Three different acquisitions were carried out with ALTM 3100, i.e., (1) a flying altitude of 1100 m and a PRF of 50 kHz, (2) a flying altitude of 1100 m and a PRF of 100 kHz, and (3) a flying altitude of 2000 m and a PRF of 50 kHz. Height percentiles, mean and maximum height values, coefficients of variation of the heights, and canopy density at different height intervals above the ground were derived from the four different ALS datasets and for single + first and last echoes of the ALS data separately. The ALS-derived height- and density variables were assessed in pair-wise comparisons to evaluate the effects of (a) instrument, (b) flying altitude, and (c) PRF. A systematic shift in height values of up to 0.3 m between sensors when the first echoes were compared was demonstrated. Also the density-related variables differed significantly between the two instruments. Comparisons of flying altitudes and PRFs revealed upwards shifted canopy height distributions for the highest flying altitude (2000 m) and the lowest PRF (50 kHz). The distribution of echoes on different echo categories, i.e., single and multiple (first and last) echoes, differed significantly between acquisitions. The proportion of multiple echoes decreased with increasing flying altitude and PRF. Different echo categories have different properties since it is likely that single echoes tend to occur in the densest parts of the tree crowns, i.e., near the apex where the concentration of biological matter is highest and distance to the ground is largest. To assess the influence of instrument, flying altitude, and PRF on biophysical properties derived from ALS data, regression analysis was carried out to relate ALS-derived metrics to mean tree height (h_L) and timber volume (V). Cross validation revealed only minor differences in precision for the different ALS acquisitions, but systematic differences between acquisitions of up to 2.5% for h_L and 10.7% for V were found when comparing data from different acquisitions.