Application of Importance Sampling for Point Source Analysis with the IceCube Neutrino Observatory

The IceCube Neutrino Observatory observes astrophysical neutrinos produced by the most energetic processes in the Universe. To date, the exact sources of these neutrinos, particles with no electric charge and almost negligible mass, are still a mystery. In an attempt to identify the sources of the highest energy neutrinos, the IceCube Collaboration uses likelihood analysis to search for clustering of neutrino events in the sky. An important part of this analysis is knowing how often neutrinos randomly cluster on the sky to replicate what an astrophysical neutrino source would look like. However, numerous simulations are required to properly understand this, and hence so are excessive computational resources. In this thesis, importance sampling is used to force rare clusters of neutrinos to occur on simulated skies. Two methods of importance sampling have been created to force these clusters to occur, a Gaussian weighting method and a binomial weighting method. Once these events are clustered, an appropriate weight can be applied to the sky the cluster is created on, and a likelihood analysis can be performed. We demonstrate how these methods can be used to identify the frequency at which rare clusterings of neutrinos occur, without the requirement of exhaustive computational time. We find that these rare clusters can be forced to occur on a sky with importance sampling, as can appropriate weights indicating the frequency the cluster would appear at a fixed point in space. However, further investigation is required to understand how to correctly apply sampling weights to the results when we perform the likelihood analysis over a full sky. The result of using importance sampling to identify rare clusters of neutrinos is used to investigate the effectiveness of a new test statistic for hypothesis testing in point source analysis. The most powerful test statistic for this analysis is the maximum likelihood, ℒ.̂ This is obtained by maximising a likelihood function relative to the maximum number of signal events, ̂, from some position on the sky. We construct a new statistic using a combination of the ℒ̂ and ̂ values, which has been suggested to be a more powerful test statistic than ℒ̂on its own. Using distributions obtained with importance sampling, we find that there is no evidence to indicate that a test statistic constructed using ℒ̂and ̂ is more powerful than ℒ̂on its own. Furthermore, we find that it simply replicates the results of ℒ̂by itself, due to the strong correlation between the ℒ̂and ̂ combinations in the null and alternate hypotheses tested.Thesis (MPhil) -- University of Adelaide, School of Physical Sciences, 202

Higher physical fitness levels are associated with less language decline in healthy ageing

Healthy ageing is associated with decline in cognitive abilities such as language. Aerobic fitness has been shown to ameliorate decline in some cognitive domains, but the potential benefits for language have not been examined. In a cross-sectional sample, we investigated the relationship between aerobic fitness and tip-of-the-tongue states. These are among the most frequent cognitive failures in healthy older adults and occur when a speaker knows a word but is unable to produce it. We found that healthy older adults indeed experience more tip-of-the-tongue states than young adults. Importantly, higher aerobic fitness levels decrease the probability of experiencing tip-of-the-tongue states in healthy older adults. Fitness-related differences in word finding abilities are observed over and above effects of age. This is the first demonstration of a link between aerobic fitness and language functioning in healthy older adults

Acute Progressive Neurological Decline in an Elderly Man

The patient was an 88-year-old man referred to a physical therapist by his primary care physician for a 1-week history of severe neck pain of insidious onset. Based upon the history and physical examination, the physical therapist concluded that the patient’s neck pain was mechanical in nature. Initial physical therapist intervention included cervical taping, cervical collar use and instruction in home exercise. At his follow-up visit 4 days after his initial physical therapy visit, the patient reported no improvement. The patient’s son, who accompanied him to this visit, also reported that his father had a recent onset of fever and mild confusion. The case was discussed with the patient’s physician and it was recommended that the patient report to the emergency department. Evaluation in the emergency department revealed that the patient was febrile with diminished oxygen saturation and an elevated white blood cell count. Chest radiographs were consistent with pneumonia and blood cultures were positive for methicillin-resistant Staphylococcus aureus. The patient was hospitalized and over the next 6 days, his condition progressively declined and quadriplegia below the C4 myotomal level developed. Magnetic resonance imaging of the cervical spine revealed severe cervical central canal stenosis with extensive signal abnormality in the cervical cord, as well as diffuse oedema in the perivertebral soft tissues that was consistent with a retropharyngeal abscess. Despite medical management, the patient subsequently succumbed to the complications of pneumonia and quadriplegia

Higher physical fitness levels are associated with less language decline in healthy ageing

publishedVersio

Do female association preferences predict the likelihood of reproduction?

Sexual selection acting on male traits through female mate choice is commonly inferred from female association preferences in dichotomous mate choice experiments. However, there are surprisingly few empirical demonstrations that such association preferences predict the likelihood of females reproducing with a particular male. This information is essential to confirm association preferences as good predictors of mate choice. We used green swordtails (<i>Xiphophorus helleri</i>) to test whether association preferences predict the likelihood of a female reproducing with a male. Females were tested for a preference for long- or short-sworded males in a standard dichotomous choice experiment and then allowed free access to either their preferred or non-preferred male. If females subsequently failed to produce fry, they were provided a second unfamiliar male with similar sword length to the first male. Females were more likely to reproduce with preferred than non-preferred males, but for those that reproduced, neither the status (preferred/non-preferred) nor the sword length (long/short) of the male had an effect on brood size or relative investment in growth by the female. There was no overall preference based on sword length in this study, but male sword length did affect likelihood of reproduction, with females more likely to reproduce with long- than short-sworded males (independent of preference for such males in earlier choice tests). These results suggest that female association preferences are good indicators of female mate choice but that ornament characteristics of the male are also important

Contra-thermodynamic E → Z isomerization of cinnamamides via selective energy transfer catalysis

A bio-inspired, photocatalytic E → Z isomerization of cinnamides is reported using inexpensive (−)-riboflavin (vitamin B2) under irradiation at λ = 402 nm. This operationally simple transformation is compatible with a range of amide derivatives including –NR2, –NHSO2R and N(Boc)2 (up to 99:1 Z:E). Selective energy transfer from the excited state photocatalyst to the starting E-isomer ensures that directionality is achieved: The analogous process with the Z-isomer is inefficient due to developing allylic strain causing chromophore deconjugation. This is supported by X-ray analysis and Stern-Volmer photo-quenching studies. Preliminary validation of the method in manipulating the conformation of a simple model Leu-enkephalin penta-peptide is disclosed via the incorporation of a cinnamamide-based amino acid

Social Context–Induced Song Variation Affects Female Behavior and Gene Expression

Social cues modulate the performance of communicative behaviors in a range of species, including humans, and such changes can make the communication signal more salient. In songbirds, males use song to attract females, and song organization can differ depending on the audience to which a male sings. For example, male zebra finches (Taeniopygia guttata) change their songs in subtle ways when singing to a female (directed song) compared with when they sing in isolation (undirected song), and some of these changes depend on altered neural activity from a specialized forebrain-basal ganglia circuit, the anterior forebrain pathway (AFP). In particular, variable activity in the AFP during undirected song is thought to actively enable syllable variability, whereas the lower and less-variable AFP firing during directed singing is associated with more stereotyped song. Consequently, directed song has been suggested to reflect a “performance” state, and undirected song a form of vocal motor “exploration.” However, this hypothesis predicts that directed–undirected song differences, despite their subtlety, should matter to female zebra finches, which is a question that has not been investigated. We tested female preferences for this natural variation in song in a behavioral approach assay, and we found that both mated and socially naive females could discriminate between directed and undirected song—and strongly preferred directed song. These preferences, which appeared to reflect attention especially to aspects of song variability controlled by the AFP, were enhanced by experience, as they were strongest for mated females responding to their mate's directed songs. We then measured neural activity using expression of the immediate early gene product ZENK, and found that social context and song familiarity differentially modulated the number of ZENK-expressing cells in telencephalic auditory areas. Specifically, the number of ZENK-expressing cells in the caudomedial mesopallium (CMM) was most affected by whether a song was directed or undirected, whereas the caudomedial nidopallium (NCM) was most affected by whether a song was familiar or unfamiliar. Together these data demonstrate that females detect and prefer the features of directed song and suggest that high-level auditory areas including the CMM are involved in this social perception

Variability of Female Responses to Conspecific vs. Heterospecific Male Mating Calls in Polygynous Deer: An Open Door to Hybridization?

Males of all polygynous deer species (Cervinae) give conspicuous calls during the reproductive season. The extreme interspecific diversity that characterizes these vocalizations suggests that they play a strong role in species discrimination. However, interbreeding between several species of Cervinae indicates permeable interspecific reproductive barriers. This study examines the contribution of vocal behavior to female species discrimination and mating preferences in two closely related polygynous deer species known to hybridize in the wild after introductions. Specifically, we investigate the reaction of estrous female red deer (Cervus elaphus) to playbacks of red deer vs. sika deer (Cervus nippon) male mating calls, with the prediction that females will prefer conspecific calls. While on average female red deer preferred male red deer roars, two out of twenty females spent more time in close proximity to the speaker broadcasting male sika deer moans. We suggest that this absence of strict vocal preference for species-specific mating calls may contribute to the permeability of pre-zygotic reproductive barriers observed between these species. Our results also highlight the importance of examining inter-individual variation when studying the role of female preferences in species discrimination and intraspecific mate selection

A new approach to assess and predict the functional roles of proteins across all known structures

The three dimensional atomic structures of proteins provide information regarding their function; and codified relationships between structure and function enable the assessment of function from structure. In the current study, a new data mining tool was implemented that checks current gene ontology (GO) annotations and predicts new ones across all the protein structures available in the Protein Data Bank (PDB). The tool overcomes some of the challenges of utilizing large amounts of protein annotation and measurement information to form correspondences between protein structure and function. Protein attributes were extracted from the Structural Biology Knowledgebase and open source biological databases. Based on the presence or absence of a given set of attributes, a given protein’s functional annotations were inferred. The results show that attributes derived from the three dimensional structures of proteins enhanced predictions over that using attributes only derived from primary amino acid sequence. Some predictions reflected known but not completely documented GO annotations. For example, predictions for the GO term for copper ion binding reflected used information a copper ion was known to interact with the protein based on information in a ligand interaction database. Other predictions were novel and require further experimental validation. These include predictions for proteins labeled as unknown function in the PDB. Two examples are a role in the regulation of transcription for the protein AF1396 from Archaeoglobus fulgidus and a role in RNA metabolism for the protein psuG from Thermotoga maritima