Taxonomies and Toolkits: uses for the Mathematics of program construction

In this extended abstract, we present a brief description of the tutorial. The primary reference material, a book and some software (1] , is available for ftp from the Eindhoven University of Technology. In this tutorial, we will consider a mathematical approach to the derivation of families of algorithms solving a particular problem. These families of algorithms are easily translated into practical toolkits of algorithms (C++ class libraries in our case). In the following paragraphs, we briefly describe why we need such toolkits, algorithm derivations, and a slightly non-standard algorithm derivation method. Generic programming (or template programming in C++) forms one of the cornerstones (along with object-oriented programming) of component programming. Generic algorithm libraries fill the need for standard algorithms such as sorting and string searching algorithms, freeing the programmer from re-implementing such error prone components. The algorithms in a generic library do not make unnecessary assumptions about the nature of the data being operated upon. For example, a string searching library would work well with strings of characters or strings of floating point numbers. The very nature of generic programs make them extremely difficult to debug and test. Exhaustive testing is generally not possible since the number of types (for the template parameter) is usually infinite. These practical difficulties can be alleviated by using the mathematics of program construction to design the program correctly in the first place. In the next paragraph, we will consider the mathematical appeal of taxonomies of algorithms. There are a number of mature areas of computer science (such as finite automata construction and string pattern matching) for which there are literally dozens of known algorithms. Many of these algorithms remain without rigorous proof, despite the fact that they were developed over twenty years ago. The differing presentation styles, and half-derivations of some of the algorithms makes them particularly difficult to compare to one another, and even more difficult to implement correctly. Dijkstra's approach to correct program construction is rarely, if ever, used by software engineers working on "real-life" projects. A great deal of time, patience, and practice are required to learn and apply the method. Unfortunately, the strict use of Dijkstra's calculus is still best suited to programming-in-the-small (the development of elegant algorithms solving small problems, such as greatest-common-divisor). We will present a method of constructing taxonomies of algorithms. The method starts with a naive first algorithm, which is easy to prove correct but is impractical to implement. The taxonomy will be grown as a ''family tree" , with the naive algorithm at the root. At each step, a variant of Dijkstra's discipline of programming is used to add either an algorithm detail (some algorithm transformation) or a problem detail (a problem restriction which allows an algorithmic improvement). The details are always added in a correctness-preserving manner, meaning that the correctness proof of any derived algorithm is in the composition of the details. The aim is to arrive at all of the known algorithms and hopefully derive some new ones. Once such a taxonomy has been developed, it is finally possible to provide implementations (in the form of class libraries) of all of the known algorithms solving a particular problem. The presence of the correctness proofs in the taxonomy has yielded impressive code quality in the class libraries (fewer than five bugs per 10,000 of code in the first release). In the tutorial, we will also discuss the implementation of one such class library

Trends in compiler construction

Compiler writing techniques have undergone a number of major revisions over the past forty years. The introduction of object-oriented design and implementation techniques promises to improve the quality of compilers, while malting large-scale compiler development more manageable. In this paper, we will show that a new way of thinking of a compiler's structure is required to achieve complete object-orientation. This new view on compiling can lead to alternative formulations of parsing and code generation. In practice, the object-oriented formulations have not only proven to be highly efficient, but they have also been particularly easy to teach to students

Faster subsequence recognition in compressed strings

Computation on compressed strings is one of the key approaches to processing massive data sets. We consider local subsequence recognition problems on strings compressed by straight-line programs (SLP), which is closely related to Lempel--Ziv compression. For an SLP-compressed text of length $\bar m$, and an uncompressed pattern of length $n$, C{\'e}gielski et al. gave an algorithm for local subsequence recognition running in time $O(\bar mn^2 \log n)$. We improve the running time to $O(\bar mn^{1.5})$. Our algorithm can also be used to compute the longest common subsequence between a compressed text and an uncompressed pattern in time $O(\bar mn^{1.5})$; the same problem with a compressed pattern is known to be NP-hard

Frequent burning promotes invasions of alien plants into a mesic African savanna

Fire is both inevitable and necessary for maintaining the structure and functioning of mesic savannas. Without disturbances such as fire and herbivory, tree cover can increase at the expense of grass cover and over time dominate mesic savannas. Consequently, repeated burning is widely used to suppress tree recruitment and control bush encroachment. However, the effect of regular burning on invasion by alien plant species is little understood. Here, vegetation data from a long-term fire experiment, which began in 1953 in a mesic Zimbabwean savanna, were used to test whether the frequency of burning promoted alien plant invasion. The fire treatments consisted of late season fires, lit at 1-, 2-, 3-, and 4-year intervals, and these regularly burnt plots were compared with unburnt plots. Results show that over half a century of frequent burning promoted the invasion by alien plants relative to areas where fire was excluded. More alien plant species became established in plots that had a higher frequency of burning. The proportion of alien species in the species assemblage was highest in the annually burnt plots followed by plots burnt biennially. Alien plant invasion was lowest in plots protected from fire but did not differ significantly between plots burnt triennially and quadrennially. Further, the abundance of five alien forbs increased significantly as the interval (in years) between fires became shorter. On average, the density of these alien forbs in annually burnt plots was at least ten times as high as the density of unburnt plots. Plant diversity was also altered by long-term burning. Total plant species richness was significantly lower in the unburnt plots compared to regularly burnt plots. These findings suggest that frequent burning of mesic savannas enhances invasion by alien plants, with short intervals between fires favouring alien forbs. Therefore, reducing the frequency of burning may be a key to minimising the risk of alien plant spread into mesic savannas, which is important because invasive plants pose a threat to native biodiversity and may alter savanna functioning

Time-to-birth prediction models and the influence of expert opinions

Preterm birth is the leading cause of death among children under five years old. The pathophysiology and etiology of preterm labor are not yet fully understood. This causes a large number of unnecessary hospitalizations due to high--sensitivity clinical policies, which has a significant psychological and economic impact. In this study, we present a predictive model, based on a new dataset containing information of 1,243 admissions, that predicts whether a patient will give birth within a given time after admission. Such a model could provide support in the clinical decision-making process. Predictions for birth within 48 h or 7 days after admission yield an Area Under the Curve of the Receiver Operating Characteristic (AUC) of 0.72 for both tasks. Furthermore, we show that by incorporating predictions made by experts at admission, which introduces a potential bias, the prediction effectiveness increases to an AUC score of 0.83 and 0.81 for these respective tasks

Efficient Online Timed Pattern Matching by Automata-Based Skipping

The timed pattern matching problem is an actively studied topic because of its relevance in monitoring of real-time systems. There one is given a log $w$ and a specification $\mathcal{A}$ (given by a timed word and a timed automaton in this paper), and one wishes to return the set of intervals for which the log $w$, when restricted to the interval, satisfies the specification $\mathcal{A}$. In our previous work we presented an efficient timed pattern matching algorithm: it adopts a skipping mechanism inspired by the classic Boyer--Moore (BM) string matching algorithm. In this work we tackle the problem of online timed pattern matching, towards embedded applications where it is vital to process a vast amount of incoming data in a timely manner. Specifically, we start with the Franek-Jennings-Smyth (FJS) string matching algorithm---a recent variant of the BM algorithm---and extend it to timed pattern matching. Our experiments indicate the efficiency of our FJS-type algorithm in online and offline timed pattern matching

Parasitic chytrids could promote copepod survival by mediating material transfer from inedible diatoms

Diatoms form large spring blooms in lakes and oceans, providing fuel for higher trophic levels at the start of the growing season. Some of the diatom blooms, however, are not grazed by filter-feeding zooplankton like Daphnia due to their large size. Several of these large diatoms are susceptible to chytrid infections. Zoospores of chytrids appeared to be excellent food for Daphnia, both in terms of size, shape, and quality (PUFAs and cholesterol). Thus, zoospores of chytrids can bridge the gap between inedible diatoms and Daphnia. In order to examine the effects of diatoms and chytrids on the survival of copepods, we performed one grazing and one survival experiment. The grazing experiment revealed that the diatom, Asterionella formosa, was not grazed by the copepod, Eudiaptomus gracilis, even after being infected by the chytrid Zygorhizidium planktonicum. However, carbon and nitrogen concentrations were significantly reduced by E. gracilis only when A. formosa was infected by Z. planktonicum, indicating that the chytrids might facilitate material transfer from inedible diatoms to the copepods. The survival experiment revealed that E. gracilis lived shorter with A. formosa than with the cryptophyta Cryptomonas pyrenoidifera. However, the survival of E. gracilis increased significantly in the treatment where A. formosa cells were infected by Z. planktonicum. Since E. gracilis could not graze A. formosa cells due to their large colonial forms, E. gracilis may acquire nutrients by grazing on the zoospores, and were so able to survive in the presence of the A. formosa. This provides new insights into the role of parasitic fungi in aquatic food webs, where chytrids may improve copepod survival during diatom blooms.

Atmospheric Evolution

Earth's atmosphere has evolved as volatile species cycle between the atmosphere, ocean, biomass and the solid Earth. The geochemical, biological and astrophysical processes that control atmospheric evolution are reviewed from an "Earth Systems" perspective, with a view not only to understanding the history of Earth, but also to generalizing to other solar system planets and exoplanets.Comment: 34 pages, 3 figures, 2 tables. Accepted as a chapter in "Encyclopaedia of Geochemistry", Editor Bill White, Springer-Nature, 201

Genomic breeding value estimation using nonparametric additive regression models

Genomic selection refers to the use of genomewide dense markers for breeding value estimation and subsequently for selection. The main challenge of genomic breeding value estimation is the estimation of many effects from a limited number of observations. Bayesian methods have been proposed to successfully cope with these challenges. As an alternative class of models, non- and semiparametric models were recently introduced. The present study investigated the ability of nonparametric additive regression models to predict genomic breeding values. The genotypes were modelled for each marker or pair of flanking markers (i.e. the predictors) separately. The nonparametric functions for the predictors were estimated simultaneously using additive model theory, applying a binomial kernel. The optimal degree of smoothing was determined by bootstrapping. A mutation-drift-balance simulation was carried out. The breeding values of the last generation (genotyped) was predicted using data from the next last generation (genotyped and phenotyped). The results show moderate to high accuracies of the predicted breeding values. A determination of predictor specific degree of smoothing increased the accuracy

The bile salt sodium taurocholate induces Campylobacter jejuni outer membrane vesicle production and increases OMV-associated proteolytic activity

Campylobacter jejuni, the leading cause of bacterial acute gastroenteritis worldwide, secretes an arsenal of virulence‐associated proteins within outer membrane vesicles (OMVs). C. jejuni OMVs contain three serine proteases (HtrA, Cj0511, and Cj1365c) that cleave the intestinal epithelial cell (IEC) tight and adherens junction proteins occludin and E‐cadherin, promoting enhanced C. jejuni adhesion to and invasion of IECs. C. jejuni OMVs also induce IECs innate immune responses. The bile salt sodium taurocholate (ST) is sensed as a host signal to coordinate the activation of virulence‐associated genes in the enteric pathogen Vibrio cholerae. In this study, the effect of ST on C. jejuni OMVs was investigated. Physiological concentrations of ST do not have an inhibitory effect on C. jejuni growth until the early stationary phase. Coculture of C. jejuni with 0.1% or 0.2% (w/v) ST stimulates OMV production, increasing both lipid and protein concentrations. C. jejuni ST‐OMVs possess increased proteolytic activity and exhibit a different protein profile compared to OMVs isolated in the absence of ST. ST‐OMVs exhibit enhanced cytotoxicity and immunogenicity to T84 IECs and enhanced killing of Galleria mellonella larvae. ST increases the level of mRNA transcripts of the OMVs‐associated serine protease genes and the cdtABC operon that encodes the cytolethal distending toxin. Coculture with ST significantly enhances the OMVs‐induced cleavage of E‐cadherin and occludin. C. jejuni OMVs also cleave the major endoplasmic reticulum chaperone protein BiP/GRP78 and this activity is associated with the Cj1365c protease. These data suggest that C. jejuni responds to the presence of physiological concentrations of the bile salt ST that increases OMV production and the synthesis of virulence‐associated factors that are secreted within the OMVs. We propose that these events contribute to pathogenesis