Deforestation in the Miombo woodlands: a pixel-based semi-automated change detection method

Most methods of change detection require a considerable amount of effort and expertise. The procedures of change detection are visual-, classification-, object- or vector-based. The target of this research was to develop an automated and generally unsupervised combination of methods to quantify deforestation on a per pixel basis. The study area was the Gutu district in Zimbabwe. In the first step, Landsat Thematic Mapper (TM) scenes were spectrally unmixed by the Spectral Mixture Analysis (SMA). The calculation of the necessary endmembers was performed by means of the N-FINDR algorithm. After the unmixing process, the data were analysed with change vector analysis (CVA) utilizing spherical statistics. Thereafter, a combination of constraints, including a Bayesian threshold and spherical angles, was applied to identify deforestation. The combination of these methods provided an accurate idea of the state of deforestation and enabled attribution to ‘fire-induced’ and ‘non fire-induced’ classes.     

MI-Pack: Increased confidence of metabolite identification in mass spectra by integrating accurate masses and metabolic pathways

Metabolite identification is of central importance to metabolomics as it provides the route to new knowledge. Automated identification of the thousands of peaks detected by high resolution mass spectrometry is currently not possible, largely due to the finite mass accuracy of the spectrometer and the complexity that one peak can be assigned to one or more empirical formula(e) and each formula maps to one or more metabolites. Biological samples are not, however, composed of random metabolite mixtures, but instead comprise of thousands of compounds related through specific chemical transformations. Here we evaluate if prior biological knowledge of these transformations can improve metabolite identification accuracy.Our identification algorithm - which uses metabolite interconnectivity from the KEGG database to putatively identify metabolites by name - is based on mapping an experimentally-derived empirical formula difference for a pair of peaks to a known empirical formula difference between substrate-product pairs derived from KEGG, termed transformation mapping (TM). To maximize identification accuracy, we also developed a novel semi-automated method to calculate a mass error surface associated with experimental peak-pair differences. The TM algorithm with mass error surface has been extensively validated using simulated and experimental datasets by calculating false positive and false negative rates of metabolite identification. Compared to the traditional identification method of database searching accurate masses on a single-peak-by-peak basis, the TM algorithm reduces the false positive rate of identification by > 4-fold, while maintaining a minimal false negative rate. The mass error surface, putative identification of metabolite names, and calculation of false positive and false negative rates collectively advance and improve upon related previous research on this topic [1, 2]. We conclude that inclusion of prior biological knowledge in the form of metabolic pathways provides one route to more accurate metabolite identification.     

Clinorotation Increases the Growth of Utricular Otoliths of Developing Cichlid Fish

It has been shown earlier that hypergravity slows down inner ear otolith growth in developing fish as an adaptation towards increased environmental gravity. Suggesting that otolith growth is regulated by the central nervous system, thus adjusting otolithic weight to produce a test mass, applying functional weightlessness should yield an opposite effect, i.e. larger than normal otoliths. Therefore, larval siblings of cichlid fish (Oreochromis mossambicus) were housed for 7 days in a submersed, two-dimensional clinostat, which provided a residual gravity of approximately 0.007g. After the experiment, otoliths were dissected and their size (area grown during the experiment) was determined. Maintenance in the clinostat resulted in significantly larger utricular otoliths (lapilli, involved in graviperception). There were no statistical significant differences regarding saccular otoliths obtained (sagittae, involved in transmitting linear acceleration and, especially, in the hearing process). These results indicated, that the animals had in fact received functional weightlessness. In line and contrasting results on the otoliths of other teleost species kept at actual microgravity (spaceflight) or within rotating wall vessels are discussed.     

Augmentation

A semantic and pragmatic interpreter that combines automatic and interactive disambiguation is described. This augmentor has an interactive disambiguation component that is called upon to aid automatic disambiguation when automated strategies prove inadequate. In addition to interactive disambiguation, the augmentor also provides the user interface for the KBMT-89 project.     

Internal and external algorithms for the points-in-regions problem—the inside join of geo-relational algebra

We consider the problem of collectively locating a set of points within a set of disjoint polygonal regions when neither for points nor for regions preprocessing is allowed. This problem arises in geometric database systems. More specifically it is equivalent to computing theinside join of geo-relational algebra, a conceptual model for geo-data management. We describe efficient algorithms for solving this problem based on plane-sweep and divide-and-conquer, requiringO(n(logn) +t) andO(n(log² n) +t) time, respectively, andO(n) space, wheren is the total number of points and edges, and (is the number of reported (point, region) pairs. Since the algorithms are meant to be practically useful we consider as well as the internal versions-running completely in main memory-versions that run internally but use much less than linear space and versions that run externally, that is, require only a constant amount of internal memory regardless of the amount of data to be processed. Comparing plane-sweep and divide-and-conquer, it turns out that divide-and-conquer can be expected to perform much better in the external case even though it has a higher internal asymptotic worst-case complexity. An interesting theoretical by-product is a new general technique for handling arbitrarily large sets of objects clustered on a singlex-coordinate within a planar divide-and-conquer algorithm and a proof that the resulting “unbalanced” dividing does not lead to a more than logarithmic height of the tree of recursive calls.