The iridescent enigma: genome evolution and species boundaries of the blue-ringed octopus species complex (Octopodidae: Hapalochlaena)

Brooke Whitelaw examined the evolution of the blue-ringed octopus genus (Octopodidae: Hapalochlaena) species complex. The current state of Hapalochlaena systematics was revealed to be insufficient for the species diversity observed. Furthermore, evolution of the Hapalochlaena genome revealed distinct differences to non-tetrodotoxin (TTX) bearing octopod genomes. This work provides a genetic basis for systematic re-evaluation of the genus, in conjunction with an annotated genome and linkage map for H. maculosa

ACE: A Cliché-based Program Structure Editor

ACE extends the syntax-directed paradigm of program editing by adding support for programming clichés. A programming cliché is a standard algorithmic fragment. ACE supports the rapid construction of programs through the combination of clichés selected from a cliché library. ACE is also innovative in the way it support the basic structure editor operations. Instead of being based directly on the grammar for a programming language, ACE is based on a modified grammar which is designed to facilitate editing. Uniformity of the user interface is achieved by encoding the modified grammar as a set of clichés.MIT Artificial Intelligence Laborator

Trauma Immediately Preceding REM-Behavior Disorder:A Valuable Prognostic Marker?

Background: The definition of rapid eye movement (REM) sleep behavior disorder (RBD) has varied over the years. Rapid eye movement sleep behavior disorder can be considered isolated or idiopathic or can occur in the context of other disorders, including trauma-associated sleep disorder (TSD) and overlap parasomnia. However, whether trauma in RBD carries any prognostic specificity is currently unknown. Study Objectives: To test the hypothesis that RBD secondary to trauma is less likely to result in the development of neurodegeneration compared to idiopathic RBD (iRBD) without trauma in the general population. Methods: A retrospective cohort study of 122 consecutive RBD patients (103 males) at two tertiary sleep clinics in Europe between 2005 and 2020 was studied. Patients were diagnosed as having iRBD by video polysomnography (vPSG) and had a semi-structured interview at presentation, including specifically eliciting any history of trauma. Patients with secondary RBD to recognized causes were excluded from the study. Patients with iRBD were categorized into three groups according to reported trauma history: (1) No history of trauma, (2) traumatic experience at least 12 months prior to RBD symptom onset, and (3) traumatic experience within 12 months of RBD symptom onset. Idiopathic RBD duration was defined as the interval between estimated onset of RBD symptoms and last hospital visit or death. Follow-up duration was defined as the interval between iRBD diagnosis and last hospital visit or death. Results: In a follow-up period of up to 18 years, no patient who experienced trauma within 12 months preceding their iRBD diagnosis received a diagnosis of a neurodegenerative disorder (n = 35), whereas 38% of patients without trauma within the 12 months of symptom onset developed a neurodegenerative illness. These patients were also significantly more likely to have a family history of α-synucleinopathy or tauopathy. Conclusions: The development of RBD within 12 months of experiencing a traumatic life event, indistinguishable clinically from iRBD, did not lead to phenoconversion to a neurodegenerative disorder even after 18 years (mean follow up 6 years). We suggest that a sub-type of RBD be established and classified as secondary RBD due to trauma. Additionally, we advocate that a thorough psychological and trauma history be undertaken in all patients presenting with dream enactment behaviors (DEB)

Cognitive Reserve in Isolated Rapid Eye-Movement Sleep Behavior Disorder

Isolated rapid-eye-movement sleep behaviour disorder (RBD) is considered the prodromal stage of α-synucleinopathies (e.g., Parkinson’s disease and dementia with Lewy bodies); however, iRBD patients show a wide variety in the progression timing (5–15 years). The model of cognitive reserve (CR) might contribute to explaining this phenomenon. Our exploratory study aimed to evaluate, for the first time, the impact of CR level on cognitive performance in polysomnography-confirmed iRBD patients. Fifty-five iRBD patients (mean age ± SD: 66.38 ± 7.51; M/F 44/11) underwent clinical and neuropsychological evaluations at the time of diagnosis. The CR Index questionnaire was part of the clinical assessment. We found that iRBD patients with high levels of CR showed: (i) the lowest percentage of mild cognitive impairment (10%), and (ii) the best performance in visuo-constructive and verbal memory functions (i.e., the recall of the Rey–Osterrieth complex figure test). Our results suggest that CR might help iRBD patients better cope with the cognitive decline related to the neurodegenerative process, providing the first preliminary findings supporting CR as a possible protective factor in this condition. This might pave the way for future longitudinal studies to evaluate the role of CR as a modulating factor in the timing of iRBD conversion and cognitive deterioration development.</p

The development and assessment of novel non-invasive methods of measuring sleep in dairy cows : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Animal Science at Massey University, Manawatū, New Zealand

Onet published article in Appendix C was removed for copyright reasons, but may be accessed via its source: Hunter, L.B., O’Connor, C., Haskell, M.J., Langford, F.M., Webster, J.R., & Stafford, K.J. 2021, September. Lying posture does not accurately indicate sleep stage in dairy cows. Applied Animal Behaviour Science, 242, 105427. https://doi.org/10.1016/j.applanim.2021.105427Sleep is important for animal health and welfare and there are many factors, for example, the environment, illness, or stress, that are likely to have an impact on cow sleep and consequently affect their welfare. Polysomnography (PSG) is considered the gold standard for precise identification of sleep stages. It consists of electrophysiological recordings of the brain activity, eye movements and muscle activity but is costly and difficult to use with cows on farm. Accordingly, the study of sleep in cows may be limited due to the impracticability of PSG. Alternative methods of assessing sleep have been developed for humans. Some such work has been conducted for cows, but this has yet to be validated with PSG. The main aim of this thesis was to investigate alternative methods to PSG to accurately detect sleep stages in dairy cows. Specifically, I aimed to develop a detailed 5-stage scoring system for assessing sleep stages from the cow PSG, to investigate the suitability of using lying postures and heart rate (HR) measures to assess sleep stages and to develop a model to accurately predict sleep stages using non-invasive measures in dairy cows compared with PSG. Two studies were conducted using 6 non-lactating dairy cows in an indoor housed environment in Scotland, and outdoors at pasture in New Zealand. PSG was recorded with each cow over a period of seven days. From these data a 5-stage sleep-scoring criteria with good reliability was developed which identified two stages of light sleep, two stages of deep sleep as well as awake and rumination stages. Video was recorded during sleep recordings and the cow’s behaviour was analysed and compared with the scored sleep stages from the PSG. Some sleep stages were found to occur mainly in specific lying postures; however, overall, postures were not useful indicators of sleep stages. Heart rate (HR) and heart rate variability (HRV) were measured using a Polar HR monitor ii and data logging device. Differences in the HR and HRV measures were found between the sleep stages, and the patterns of these changes were similar between both Scottish and NZ cows. Finally, machine learning models were developed using supervised learning methods to predict sleep stage from the HR and HRV measures as well as the surface EMG data recorded during PSG. The models were able to learn to recognize and accurately predict sleep stages compared with the PSG scoring. This research demonstrates that non-invasive alternatives can be used to identify sleep stages accurately in dairy cows compared with PSG. Further research is necessary with larger sample sizes and cows of various breeds and life stages; however, the success of the methods developed during this thesis demonstrates their suitability for the future measurement of sleep in cows and in the assessment of cow welfare

Incremental Dynamic Semantics for Language-Based Programming Environments

Attribute grammars are a formal notation for expressing the static semantics of programming languages — those properties that can be derived from inspection of the program text. Attribute grammars have become popular as a mechanism for generating language-based programming environments that incrementally perform symbol resolution, type checking, code generation and derivation of other static semantic properties as the program is modified. However, attribute grammars are not suitable for expressing dynamic semantics — those properties that reflect the history of program execution and/or user interactions with the programming environment. This article presents action equations, an extension of attribute grammars suitable for specifying the static and the dynamic semantics of programming languages. It describes how action equations can be used to generate language-based programming environments that incrementally derive static and dynamic properties as the user modifies and debugs the program

Sleep in the Arabian oryx, Oryx leucoryx

Original published work submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in fulfillment of the requirements for the degree of Doctor of Philosophy, Johannesburg, 2018The evolution and function of sleep remains an enigma in modern science. Significant variation can be observed within species and across taxa. Little is understood about how sleep exists, or presents itself in species surviving in extreme conditions. For example, harsh desert ecosystems with notably lower survival rates for resident species. It has been hypothesized that specialized sleep-related behaviours impact thermoregulation to promote survival advantage. The threatened Arabian oryx (Oryx leucoryx), a member of the Cetartiodactyl superorder, is a large desert dwelling ungulate species successfully residing in the arid zones of the Middle East. Arabian Oryx exhibit numerous morphophysiological adaptations and capabilities to cope with their harsh environment. The current thesis provides an examination of the neuroanatomy, physiology and behavioural patterns related to sleep in wild, freeroaming Arabian oryx under natural conditions. It was our objective to determine whether the extreme conditions and climate of the Arabian Desert has led to novelties within the organization of the oryx’s sleep related neuronal architecture, seasonal behaviour patterns and sleep physiology. Using immunohistochemistry and stereology our results indicate the sleep related nuclei in the brain of the oryx exhibit a typical mammalian organizational plan with additional order-specific and novel, species-specific features. Actigraphy revealed that oryx exhibit temporal niche switching patterns seasonally presenting with winter diurnal- and summer nocturnal activity and intermittent patterns during the transitional periods of spring and autumn. Polysomnography results indicate novel sleep patterns between seasons and physiologically confirm activity-based temporal niche switching at a seasonal level. Our work covers the first examination of the Arabian oryx brain sleep centers as well as its yearlong activity patterns. Importantly, it is the first examination of physiological sleep in wild mammals within a desert environment. Our results suggest that ambient temperature acts a dominant driving force for the adaptive behavioural and physiological features described. The Arabian oryx is a remarkable species, well adapted to such an extreme environment and its highly plastic survival mechanisms appear unique. Considering the continual desertification of our planet and the predicted consequences of climate change, knowledge of such species and their continued conservation is of vital importanceXL201