Soliton dynamics in nonlinear planar systems

The work in this thesis is concerned with the study of stability and scattering of solitons in planar models ie where spacetime is (2+l)-dimensional. We consider both integrable models, where exact solutions can be written in closed form, and non-integrable models, where approximations and numerical methods must be employed. In chapter III we use a 'collective coordinate' approximation to study the scattering of solitons in a model motivated by elementary particle physics. In chapter IV we discuss a method to obtain approximate soliton configurations which can then be used to investigate soliton dynamics. In chapter V we perform a test of the 'collective coordinate' approximation by applying it to the study of classical and quantum soliton scattering in an integrable model, where exact results are known. Chapters VI and VII are concerned with an integrable chiral model. First we construct exact solutions using twistor methods and then we go on to study soliton stability using numerical techniques. Through computer simulations we find that there exist solitons which scatter in a way unlike any previously found in integrable models. Furthermore, this soliton scattering resembles very closely that found in certain non-integrable models, thereby providing a link between the two classes. Finally, chapter VIII is an outlook on current and future research

Genomic analyses confirm close relatedness between Rhodococcus defluvii and Rhodococcus equi (Rhodococcus hoagii)

Rhodococcus defluvii strain Ca11T was isolated from a bioreactor involved in extensive phosphorus removal. We have sequenced the whole genome of this strain and our comparative genomic and phylogenetic analyses confirm its close relatedness with Rhodococcus equi (Rhodococcus hoagii) strains, which share >80% of the gene content. The R. equi virulence plasmid is absent though most of the chromosomal R. equi virulence-associated genes are present in R. defluvii Ca11T. These data suggest that although R. defluvii is an environmental organism, it has the potential to colonise animal hosts

Inactivity/sleep in two wild free-roaming African elephant matriarchs - Does large body size make elephants the shortest mammalian sleepers?

The current study provides details of sleep (or inactivity) in two wild, free-roaming African elephant matriarchs studied in their natural habitat with remote monitoring using an actiwatch subcutaneously implanted in the trunk, a standard elephant collar equipped with a GPS system and gyroscope, and a portable weather station. We found that these two elephants were polyphasic sleepers, had an average daily total sleep time of 2 h, mostly between 02:00 and 06:00, and displayed the shortest daily sleep time of any mammal recorded to date. Moreover, these two elephants exhibited both standing and recumbent sleep, but only exhibited recumbent sleep every third or fourth day, potentially limiting their ability to enter REM sleep on a daily basis. In addition, we observed on five occasions that the elephants went without sleep for up to 46 h and traversed around 30 km in 10 h, possibly due to disturbances such as potential predation or poaching events, or a bull elephant in musth. They exhibited no form of sleep rebound following a night without sleep. Environmental conditions, especially ambient air temperature and relative humidity, analysed as wet-bulb globe temperature, reliably predict sleep onset and offset times. The elephants selected novel sleep sites each night and the amount of activity between sleep periods did not affect the amount of sleep. A number of similarities and differences to studies of elephant sleep in captivity are noted, and specific factors shaping sleep architecture in elephants, on various temporal scales, are discussed

Next-generation systematics: An innovative approach to resolve the structure of complex prokaryotic taxa

Prokaryotic systematics provides the fundamental framework for microbiological research but remains a discipline that relies on a labour- and time-intensive polyphasic taxonomic approach, including DNA-DNA hybridization, variation in 16S rRNA gene sequence and phenotypic characteristics. These techniques suffer from poor resolution in distinguishing between closely related species and often result in misclassification and misidentification of strains. Moreover, guidelines are unclear for the delineation of bacterial genera. Here, we have applied an innovative phylogenetic and taxogenomic approach to a heterogeneous actinobacterial taxon, Rhodococcus, to identify boundaries for intrageneric and supraspecific classification. Seven species-groups were identified within the genus Rhodococcus that are as distantly related to one another as they are to representatives of other mycolic acid containing actinobacteria and can thus be equated with the rank of genus. It was also evident that strains assigned to rhodococcal species-groups are underspeciated with many misclassified using conventional taxonomic criteria. The phylogenetic and taxogenomic methods used in this study provide data of theoretical value for the circumscription of generic and species boundaries and are also of practical significance as they provide a robust basis for the classification and identification of rhodococci of agricultural, industrial and medical/veterinary significance

Symmetric Instantons and Skyrme Fields

By explicit construction of the ADHM data, we prove the existence of a charge seven instanton with icosahedral symmetry. By computing the holonomy of this instanton we obtain a Skyrme field which approximates the minimal energy charge seven Skyrmion. We also present a one parameter family of tetrahedrally symmetric instantons whose holonomy gives a family of Skyrme fields which models a Skyrmion scattering process, where seven well-separated Skyrmions collide to form the icosahedrally symmetric Skyrmion.Comment: 22 pages plus 1 figure in GIF forma

Predicting the outcomes of assisted reproductive technology treatments : a systematic review and quality assessment of prediction models

Objective Predicting the outcomes of assisted reproductive technology (ART) treatments is desirable, but adopting prediction models into clinical practice remains limited. We aimed to review available prediction models for ART treatments by conducting a systematic review of the literature to identify the best performing models for their accuracy, generalisability and applicability. Evidence review We searched electronic databases (MEDLINE, EMBASE, and CENTRAL) until June 2020. We included studies reporting on the development or evaluation of models predicting the reproductive outcomes before (pre-ART) or after starting (Intra-ART) treatment in couples undergoing any ART treatment. We evaluated the models’ discrimination, calibration, type of validation, and any implementation tools for clinical practice. Results We included 69 cohort studies reporting on 120 unique prediction models. Half the studies reported on pre-ART (48%) and half on intra-ART (56%) prediction models. The commonest predictors used were maternal age (90%), tubal factor subfertility (50%), and embryo quality (60%). Only fourteen models were externally-validated (14/120, 12%) including eight pre-ART models (Templeton, Nelson, LaMarca, McLernon, Arvis, and the Stolwijk A/I,C,II models), and five intra-ART models (Cai, Hunault, van Loendersloot, Meijerink, Stolwijk B, and the McLernon post-treatment model) with a reported c-statistics ranging from 0.50 to 0.78. Ten of these models provided implementation tools for clinical practice with only two reported online calculators. Conclusion We identified externally validated prediction models that could be used to advise couples undergoing ART treatments on their reproductive outcomes. The quality of available models remains limited and more research is needed to improve their generalizability and applicability into clinical practice

Continent-Wide Survey Reveals Massive Decline in African Savannah Elephants

African elephants (Loxodonta africana) are imperiled by poaching and habitat loss. Despite global attention to the plight of elephants, their population sizes and trends are uncertain or unknown over much of Africa. To conserve this iconic species, conservationists need timely, accurate data on elephant populations. Here, we report the results of the Great Elephant Census (GEC), the first continent-wide, standardized survey of African savannah elephants. We also provide the first quantitative model of elephant population trends across Africa. We estimated a population of 352,271 savannah elephants on study sites in 18 countries, representing approximately 93% of all savannah elephants in those countries. Elephant populations in survey areas with historical data decreased by an estimated 144,000 from 2007 to 2014, and populations are currently shrinking by 8% per year continent-wide, primarily due to poaching. Though 84% of elephants occurred in protected areas, many protected areas had carcass ratios that indicated high levels of elephant mortality. Results of the GEC show the necessity of action to end the African elephants’ downward trajectory by preventing poaching and protecting habitat

A tetrapeptide class of biased analgesics from an Australian fungus targets the μ-opioid receptor

An Australian estuarine isolate ofPenicilliumsp. MST-MF667 yielded3 tetrapeptides named the bilaids with an unusual alternating LDLDchirality. Given their resemblance to known short peptide opioidagonists, we elucidated that they were weak (Kilow micromolar)μ-opioid agonists, which led to the design of bilorphin, a potent andselectiveμ-opioid receptor (MOPr) agonist (Ki1.1 nM). In sharp con-trast to all-natural product opioid peptides that efficaciously recruitβ-arrestin, bilorphin is G protein biased, weakly phosphorylatingthe MOPr and marginally recruitingβ-arrestin, with no receptorinternalization. Importantly, bilorphin exhibits a similar G proteinbias to oliceridine, a small nonpeptide with improved overdosesafety. Molecular dynamics simulations of bilorphin and thestrongly arrestin-biased endomorphin-2 with the MOPr indicatedistinct receptor interactions and receptor conformations thatcould underlie their large differences in bias. Whereas bilorphinis systemically inactive, a glycosylated analog, bilactorphin, isorally active with similar in vivo potency to morphine. Bilorphinis both a unique molecular tool that enhances understanding ofMOPr biased signaling and a promising lead in the development ofnext generation analgesics

Evidence for a vector charmonium-like state in e+e−→Ds+Ds2∗(2573)−+c.c.e^+e^- \to D^+_sD^*_{s2}(2573)^-+c.c.

We report the measurement of $e^+e^- \to D^+_sD^*_{s2}(2573)^-+c.c.$ via initial-state radiation using a data sample of an integrated luminosity of 921.9 fb$^{-1}$ collected with the Belle detector at the $\Upsilon(4S)$ and nearby. We find evidence for an enhancement with a 3.4$\sigma$ significance in the invariant mass of $D^+_sD^*_{s2}(2573)^- +c.c.$ The measured mass and width are $(4619.8^{+8.9}_{-8.0}({\rm stat.})\pm2.3({\rm syst.}))~{\rm MeV}/c^{2}$ and $(47.0^{+31.3}_{-14.8}({\rm stat.})\pm4.6({\rm syst.}))~{\rm MeV}$, respectively. The mass, width, and quantum numbers of this enhancement are consistent with the charmonium-like state at 4626 MeV/$c^2$ recently reported by Belle in $e^+e^-\to D^+_sD_{s1}(2536)^-+c.c.$ The product of the $e^+e^-\to D^+_sD^*_{s2}(2573)^-+c.c.$ cross section and the branching fraction of $D^*_{s2}(2573)^-\to{\bar D}^0K^-$ is measured from $D^+_sD^*_{s2}(2573)^-$ threshold to 5.6 GeV.Comment: 9 pages, 4 figure