Out-of-plane action unit recognition using recurrent neural networks

A dissertation submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfilment of requirements for the degree of Master of Science. Johannesburg, 2015.The face is a fundamental tool to assist in interpersonal communication and interaction between people. Humans use facial expressions to consciously or subconsciously express their emotional states, such as anger or surprise. As humans, we are able to easily identify changes in facial expressions even in complicated scenarios, but the task of facial expression recognition and analysis is complex and challenging to a computer. The automatic analysis of facial expressions by computers has applications in several scientific subjects such as psychology, neurology, pain assessment, lie detection, intelligent environments, psychiatry, and emotion and paralinguistic communication. We look at methods of facial expression recognition, and in particular, the recognition of Facial Action Coding System’s (FACS) Action Units (AUs). Movements of individual muscles on the face are encoded by FACS from slightly different, instant changes in facial appearance. Contractions of specific facial muscles are related to a set of units called AUs. We make use of Speeded Up Robust Features (SURF) to extract keypoints from the face and use the SURF descriptors to create feature vectors. SURF provides smaller sized feature vectors than other commonly used feature extraction techniques. SURF is comparable to or outperforms other methods with respect to distinctiveness, robustness, and repeatability. It is also much faster than other feature detectors and descriptors. The SURF descriptor is scale and rotation invariant and is unaffected by small viewpoint changes or illumination changes. We use the SURF feature vectors to train a recurrent neural network (RNN) to recognize AUs from the Cohn-Kanade database. An RNN is able to handle temporal data received from image sequences in which an AU or combination of AUs are shown to develop from a neutral face. We are recognizing AUs as they provide a more fine-grained means of measurement that is independent of age, ethnicity, gender and different expression appearance. In addition to recognizing FACS AUs from the Cohn-Kanade database, we use our trained RNNs to recognize the development of pain in human subjects. We make use of the UNBC-McMaster pain database which contains image sequences of people experiencing pain. In some cases, the pain results in their face moving out-of-plane or some degree of in-plane movement. The temporal processing ability of RNNs can assist in classifying AUs where the face is occluded and not facing frontally for some part of the sequence. Results are promising when tested on the Cohn-Kanade database. We see higher overall recognition rates for upper face AUs than lower face AUs. Since keypoints are globally extracted from the face in our system, local feature extraction could provide improved recognition results in future work. We also see satisfactory recognition results when tested on samples with out-of-plane head movement, showing the temporal processing ability of RNNs

A new species of large Hemiandrus ground wētā (Orthoptera: Anostostomatidae) from North Island, New Zealand

A new species of Hemiandrus ground wētā is described from North Island, New Zealand. Hemiandrus jacindasp. nov.is larger and more brightly coloured than other species in the region, but appears to be scarce and restricted to remnant native forest habitat.fals

The Waipounamu Erosion Surface: questioning the antiquity of the New Zealand land surface and terrestrial fauna and flora

The Waipounamu Erosion Surface is a time-transgressive, nearly planar, wave-cut surface. It is not a peneplain. Formation of the Waipounamu Erosion Surface began in Late Cretaceous time following break-up of Gondwanaland, and continued until earliest Miocene time, during a 60 million year period of widespread tectonic quiescence, thermal subsidence and marine transgression. Sedimentary facies and geomorphological evidence suggest that the erosion surface may have eventually covered the New Zealand subcontinent (Zealandia). We can find no geological evidence to indicate that land areas were continuously present throughout the middle Cenozoic. Important implications of this conclusion are: (1) the New Zealand subcontinent was largely, or entirely, submerged and (2) New Zealand's present terrestrial fauna and flora evolved largely from fortuitous arrivals during the past 22 million years. Thus the modern terrestrial biota may not be descended from archaic ancestors residing on Zealandia when it broke away from Gondwanaland in the Cretaceous, since the terrestrial biota would have been extinguished if this landmass was submerged in Oligocene–Early Miocene time. We conclude that there is insufficient geological basis for assuming that land was continuously present in the New Zealand region through Oligocene to Early Miocene time, and we therefore contemplate the alternative possibility, complete submergence of Zealandia

Oxidative demethylation of DNA damage by Escherichia coli AlkB and its human homologs ABH2 and ABH3

The E. coli AlkB protein was implicated in the repair or tolerance of DNA methylation damage. However, despite the early isolation of an E. coli alkB mutant, the function of the AlkB protein had not been resolved (Kataoka et al., 1983). The E. coli alkB mutant is defective in processing methylated single stranded DNA, therefore, it was suggested that the AlkB protein either repairs or tolerates lesions generated in single stranded DNA, such as 1-methyladenine (1-meA) or 3-methylcytosine (3-meC), or that AlkB only acts on single stranded DNA (Dinglay et al, 2000). However, despite extensive testing, no enzymatic activity could be assigned to the AlkB protein. Recently, theoretical protein fold recognition suggested that the AlkB protein resembles members of the α-ketoglutarate-Fe(II) dependent dioxygenase superfamily (Aravind and Koonin, 2001). Here, the biochemical function of the enigmatic E. coli AlkB protein and its two human homologs ABH2 and ABH3 are elucidated. An in vitro assay was developed for the AlkB, ABH2 and ABH3 proteins and it was demonstrated that the activities of these proteins are dependent on α-ketoglutarate and Fe(II) and are stimulated by ascorbic acid. The requirement of AlkB, ABH2 and ABH3 for these distinctive co-factors strongly supports the proposal that these proteins are members of the α-ketoglutarate-Fe(II) dependent dioxygenase superfamily, which employ iron-oxo intermediates to oxidise chemically inert compounds. The AlkB, ABH2 and ABH3 proteins are shown to act specifically on 1-meA and 3-meC in both double and single stranded DNA. It was demonstrated that these proteins convert 1-meA and 3-meC to their unsubstituted parent residues in DNA and therefore act by a direct reversal mechanism. It is proposed that the E. coli AlkB protein and its human homologs directly revert DNA damage by oxidative demethylation, an unprecedented mechanism of DNA repair. This discovery may have implications for the treatment of cancer because antagonists of the human ABH2 and ABH3 proteins could be useful adjuncts to cancer chemotherapy that uses simple alkylating agents

Genome-Wide Studies of Histone Demethylation Catalysed by the Fission Yeast Homologues of Mammalian LSD1

In order to gain a more global view of the activity of histone demethylases, we report here genome-wide studies of the fission yeast SWIRM and polyamine oxidase (PAO) domain homologues of mammalian LSD1. Consistent with previous work we find that the two S. pombe proteins, which we name Swm1 and Swm2 (after SWIRM1 and SWIRM2), associate together in a complex. However, we find that this complex specifically demethylates lysine 9 in histone H3 (H3K9) and both up- and down-regulates expression of different groups of genes. Using chromatin-immunoprecipitation, to isolate fragments of chromatin containing either H3K4me2 or H3K9me2, and DNA microarray analysis (ChIP-chip), we have studied genome-wide changes in patterns of histone methylation, and their correlation with gene expression, upon deletion of the swm1+ gene. Using hyper-geometric probability comparisons we uncover genetic links between lysine-specific demethylases, the histone deacetylase Clr6, and the chromatin remodeller Hrp1. The data presented here demonstrate that in fission yeast the SWIRM/PAO domain proteins Swm1 and Swm2 are associated in complexes that can remove methyl groups from lysine 9 methylated histone H3. In vitro, we show that bacterially expressed Swm1 also possesses lysine 9 demethylase activity. In vivo, loss of Swm1 increases the global levels of both H3K9me2 and H3K4me2. A significant accumulation of H3K4me2 is observed at genes that are up-regulated in a swm1 deletion strain. In addition, H3K9me2 accumulates at some genes known to be direct Swm1/2 targets that are down-regulated in the swm1¿ strain. The in vivo data indicate that Swm1 acts in concert with the HDAC Clr6 and the chromatin remodeller Hrp1 to repress gene expression. In addition, our in vitro analyses suggest that the H3K9 demethylase activity requires an unidentified post-translational modification to allow it to act. Thus, our results highlight complex interactions between histone demethylase, deacetylase and chromatin remodelling activities in the regulation of gene expression

De-novo assembly of four rail (Aves: Rallidae) genomes: A resource for comparative genomics.

Rails are a phenotypically diverse family of birds that includes 130 species and displays a wide distribution around the world. Here we present annotated genome assemblies for four rails from Aotearoa New Zealand: two native volant species, pūkeko Porphyrio melanotus and mioweka Gallirallus philippensis, and two endemic flightless species takahē Porphyrio hochstetteri and weka Gallirallus australis. Using the sequence read data, heterozygosity was found to be lowest in the endemic flightless species and this probably reflects their relatively small populations. The quality checks and comparison with other rallid genomes showed that the new assemblies were of good quality. This study significantly increases the number of available rallid genomes and will enable future genomic studies on the evolution of this family.fals

Genotypic detection of barriers to rat dispersal: Rattus rattus behind a peninsula predator-proof fence.

Clear delimitation of management units is essential for effective management of invasive species. Analysis of population genetic structure of target species can improve identification and interpretation of natural and artificial barriers to dispersal. In Aotearoa New Zealand where the introduced ship rat (Rattus rattus) is a major threat to native biodiversity, effective suppression of pest numbers requires removal and limitation of reinvasion from outside the managed population. We contrasted population genetic structure in rat populations over a wide scale without known barriers, with structure over a fine scale with potential barriers to dispersal. MtDNA D-loop sequences and microsatellite genotypes resolved little genetic structure in southern North Island population samples of ship rat 100 km apart. In contrast, samples from major islands differed significantly for both mtDNA and nuclear markers. We also compared ship rats collected within a small peninsula reserve bounded by sea, suburbs and, more recently, a predator fence with rats in the surrounding forest. Here, mtDNA did not differ but genotypes from 14 nuclear loci were sufficient to distinguish the fenced population. This suggests that natural (sea) and artificial barriers (town, fence) are effectively limiting gene flow among ship rat populations over the short distance (~ 500 m) between the peninsula reserve and surrounding forest. The effectiveness of the fence alone is not clear given it is a recent feature and no historical samples exist; resampling population genetic diversity over time will improve understanding. Nonetheless, the current genetic isolation of the fenced rat population suggests that rat eradication is a sensible management option given that reinvasion appears to be limited and could probably be managed with a biosecurity programme.fals

Lack of assortative mating might explain reduced phenotypic differentiation where two grasshopper species meet

Hybridization is an evolutionary process with wide-ranging potential outcomes, from providing populations with important genetic variation for adaptation to being a substantial fitness cost leading to extinction. Here, we focussed on putative hybridization between two morphologically distinct species of New Zealand grasshopper. We collected Phaulacridium marginale and Phaulacridium otagoense specimens from a region where mitochondrial introgression had been detected and where their habitat has been modified by introduced mammals eating the natural vegetation and by the colonization of many non-native plant species. In contrast to observations in the 1970s, our sampling of wild pairs of grasshoppers in copula provided no evidence of assortative mating with respect to species. Geometric morphometrics on pronotum shape of individuals from areas of sympatry detected phenotypically intermediate specimens (putative hybrids), and the distribution of phenotypes in most areas of sympatry was found to be unimodal. These results suggest that hybridization associated with anthropogenic habitat changes has led to these closely related species forming a hybrid swarm, with random mating. Without evidence of hybrid disadvantage, we suggest a novel hybrid lineage might eventually result from the merging of these two species.fals