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

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

Reproductive strategies of Diaeretiella rapae (Hymenoptera: Aphidiinae) during fluctuating temperatures of spring season in New Zealand

Reproductive activities of naturally occurring population of Diaeretiella rapae (M’Intosh) (Hymenoptera: Aphidiinae) on Myzus persicae were studied during spring season in New Zealand. The cabbage seedlings were highly infested with the aphids (272+-25 individuals/plant) with about 30% on average parasitised by D. rapae. Rate of parasitism was positively correlated with the aphid density(R2-�0.64). Adult emergence from aphid mummies was 90%, with a higher frequency of females than males. Increase in female/male sex ratio was found between early and late spring (1.1 vs. 1.8). Mating in D. rapae occurred throughout the day. Nearly half of the mating pairs collected were male�-male pairs, which were especially prevalent during morning and evening while more male-�female mating pairs were found during midday. Male�-male mounting was probably because of low number of virgin females in morning and evening populations. About 80% females were mounted by smaller size males. Male�-male mounting is discussed in correlation with operational sex ratio of D. rapae population

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

Bird evolution: testing the Metaves clade with six new mitochondrial genomes

Background Evolutionary biologists are often misled by convergence of morphology and this has been common in the study of bird evolution. However, the use of molecular data sets have their own problems and phylogenies based on short DNA sequences have the potential to mislead us too. The relationships among clades and timing of the evolution of modern birds (Neoaves) has not yet been well resolved. Evidence of convergence of morphology remain controversial. With six new bird mitochondrial genomes (hummingbird, swift, kagu, rail, flamingo and grebe) we test the proposed Metaves/Coronaves division within Neoaves and the parallel radiations in this primary avian clade. Results Our mitochondrial trees did not return the Metaves clade that had been proposed based on one nuclear intron sequence. We suggest that the high number of indels within the seventh intron of the β-fibrinogen gene at this phylogenetic level, which left a dataset with not a single site across the alignment shared by all taxa, resulted in artifacts during analysis. With respect to the overall avian tree, we find the flamingo and grebe are sister taxa and basal to the shorebirds (Charadriiformes). Using a novel site-stripping technique for noise-reduction we found this relationship to be stable. The hummingbird/swift clade is outside the large and very diverse group of raptors, shore and sea birds. Unexpectedly the kagu is not closely related to the rail in our analysis, but because neither the kagu nor the rail have close affinity to any taxa within this dataset of 41 birds, their placement is not yet resolved. Conclusion Our phylogenetic hypothesis based on 41 avian mitochondrial genomes (13,229 bp) rejects monophyly of seven Metaves species and we therefore conclude that the members of Metaves do not share a common evolutionary history within the Neoaves

Comparative cytogenetics of North Island tree wētā in sympatry

In North Island New Zealand three species of tree wētā (Hemideina) [XX]); the karyotypes of H. trewicki and H. crassidens are more similar to each other than either is to H. thoracica. Elements within each karyotype were identified that are species specific and will aid identification of putative hybrids. Quantitative cytogenetics was used to identify the sex chromosome for H. crassidens and H. trewicki, which in contrast to previous inferences, is most likely the fifthlongest metacentric chromosome in H. crassidens, and the third-longest metacentric chromosome in H. trewicki

Is severe hypocalcemia immediately life threatening?

Objective: Severe hypocalcemia (Ca <1.9 mmol/L) is often considered an emergency because of a potential risk of cardiac arrest or seizures. However, there is little evidence to support this. The aim of our study was to assess whether severe hypocalcemia was associated with immediately life-threatening cardiac arrhythmias or neurological complications. Methods: A retrospective observational study was carried out over a 2-year period in the Adult Emergency Department (ED) of Nantes University Hospital. All patients who had a protein-corrected calcium concentration measure were eligible for inclusion. Patients with multiple myeloma were excluded. The primary outcome was the number of life-threatening cardiac arrhythmias and/or neurological complications during the stay in the ED. Results: A total of 41,823 patients had protein-corrected calcium (pcCa) concentrations measured, 155 had severe hypocalcemia, 22 were excluded because of myeloma leaving 133 for analysis. Median pcCa concentration was 1.73 mmol/L (1.57–1.84). Seventeen (12.8%) patients presented a life-threatening condition, 14 (10.5%) neurological and 3 (2.2%) cardiac during ED stay. However, these complications could be explained by the presence of underlying co-morbidities and or electrolyte disturbances other than hypocalcemia. Overall, 24 (18%) patients died in hospital. Vitamin D deficiency, chronic kidney disease and hypoparathyroidism were the most frequently found causes of hypocalcemia. Conclusion: Thirteen percent of patients with severe hypocalcemia presented a life-threatening cardiac or neurological complication on the ED. However, a perfectly valid alternative cause could account for these complications. Further research is warranted to define the precise role of hypocalcemia

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

Cryptic Speciation in Brazilian Epiperipatus (Onychophora: Peripatidae) Reveals an Underestimated Diversity among the Peripatid Velvet Worms

Taxonomical studies of the neotropical Peripatidae (Onychophora, velvet worms) have proven difficult, due to intraspecific variation and uniformity of morphological characters across this onychophoran subgroup. We therefore used molecular approaches, in addition to morphological methods, to explore the diversity of Epiperipatus from the Minas Gerais State of Brazil.Our analyses revealed three new species. While Epiperipatus diadenoproctussp. nov. can be distinguished from E. adenocryptussp. nov. and E. paurognostussp. nov. based on morphology and specific nucleotide positions in the mitochondrial cytochrome c oxidase subunit I (COI) and small ribosomal subunit RNA gene sequences (12S rRNA), anatomical differences between the two latter species are not evident. However, our phylogenetic analyses of molecular data suggest that they are cryptic species, with high Bayesian posterior probabilities and bootstrap and Bremer support values for each species clade. The sister group relationship of E. adenocryptussp. nov. and E. paurognostussp. nov. in our analyses correlates with the remarkable morphological similarity of these two species. To assess the species status of the new species, we performed a statistical parsimony network analysis based on 582 base pairs of the COI gene in our specimens, with the connection probability set to 95%. Our findings revealed no connections between groups of haplotypes, which have been recognized as allopatric lineages in our phylogenetic analyses, thus supporting our suggestion that they are separate species.Our findings suggest high cryptic species diversity and endemism among the neotropical Peripatidae and demonstrate that the combination of morphological and molecular approaches is helpful for clarifying the taxonomy and species diversity of this apparently large and diverse onychophoran group