A Topological Characterization Of Knots and Links Arising From Site-Specific Recombination

We develop a topological model of knots and links arising from a single (or multiple processive) round(s) of recombination starting with an unknot, unlink, or (2,m)-torus knot or link substrate. We show that all knotted or linked products fall into a single family, and prove that the size of this family grows linearly with the cube of the minimum number of crossings. Additionally, we prove that the only possible products of an unknot substrate are either clasp knots and links or (2,m)-torus knots and links. Finally, in the (common) case of (2,m)-torus knot or link substrates whose products have minimal crossing number m+1, we prove that the types of products are tightly prescribed, and use this to examine previously uncharacterized experimental data.Comment: 18 pages, 3 tables, 18 figures. See also arXiv:0707.3775v1 for biological evidence for and applications of the model developed her

Topological Gaseous Plasmon Polariton in Realistic Plasma

Nontrivial topology in bulk matter has been linked with the existence of topologically protected interfacial states. We show that a gaseous plasmon polariton (GPP), an electromagnetic surface wave existing at the boundary of magnetized plasma and vacuum, has a topological origin that arises from the nontrivial topology of magnetized plasma. Because a gaseous plasma cannot sustain a sharp interface with discontinuous density, one must consider a gradual density falloff with scale length comparable to or longer than the wavelength of the wave. We show that the GPP may be found within a gapped spectrum in present-day laboratory devices, suggesting that platforms are currently available for experimental investigation of topological wave physics in plasmas

Found: High Surface Brightness Compact Galaxies

We are using the 2dF spectrograph to make a survey of all objects (`stars' and `galaxies') in a 12 sq.deg region towards the Fornax cluster. We have discovered a population of compact emission-line galaxies unresolved on photographic sky survey plates and therefore missing in most galaxy surveys based on such material. These galaxies are as luminous as normal field galaxies. Using H-alpha to estimate star formation they contribute at least an additional 5 per cent to the local star formation rate.Comment: To appear in "The Low Surface Brightness Universe", IAU Coll 171, eds. J.I. Davies et al., A.S.P. Conference Series. 3 pages, LaTex, 1 encapsulated ps-figure, requires paspconf.st

Nontrivial topology in the continuous spectrum of a magnetized plasma

Classification of matter through topological phases and topological edge states between distinct materials has been a subject of great interest recently. While lattices have been the main setting for these studies, a relatively unexplored realm for this physics is that of continuum fluids. In the typical case of a fluid model with a point spectrum, nontrivial topology and associated edge modes have been observed previously. However, another possibility is that a continuous spectrum can coexist with the point spectrum. Here we demonstrate that a fluid plasma model can harbor nontrivial topology within its continuous spectrum, and that there are boundary modes at the interface between topologically distinct regions. We consider the ideal magnetohydrodynamics (MHD) model. In the presence of magnetic shear, we find nontrivial topology in the Alfvén continuum. For strong shear, the Chern number is ±1, depending on the sign of the shear. If the magnetic shear changes sign within the plasma, a topological phase transition occurs, and bulk-boundary correspondence then suggests a mode localized to the layer of zero magnetic shear. We confirm the existence of this mode numerically. Moreover, this reversed-shear Alfvén eigenmode (RSAE) is well known within magnetic fusion as it has been observed in several tokamaks. In examining how the MHD model might be regularized at small scales, we also consider the electron limit of Hall MHD. We show that the whistler band, which plays an important role in planetary ionospheres, has nontrivial topology. More broadly, this work raises the possibility that fusion devices could be carefully tailored to produce other topological states with potentially useful behavior

ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations.

Environmental DNA (eDNA) metabarcoding is becoming a core tool in ecology and conservation biology, and is being used in a growing number of education, biodiversity monitoring, and public outreach programs in which professional research scientists engage community partners in primary research. Results from eDNA analyses can engage and educate natural resource managers, students, community scientists, and naturalists, but without significant training in bioinformatics, it can be difficult for this diverse audience to interact with eDNA results. Here we present the R package ranacapa, at the core of which is a Shiny web app that helps perform exploratory biodiversity analyses and visualizations of eDNA results. The app requires a taxonomy-by-sample matrix and a simple metadata file with descriptive information about each sample. The app enables users to explore the data with interactive figures and presents results from simple community ecology analyses. We demonstrate the value of ranacapa to two groups of community partners engaging with eDNA metabarcoding results

Development of a tool to predict outcome of Autologous Chondrocyte Implantation

Objective. The study had 2 objectives: first, to evaluate the success of autologous chondrocyte implantation (ACI) in terms of incidence of surgical re-intervention, including arthroplasty, and investigate predictors of successful treatment outcome. The second objective was to derive a tool predicting a patient’s arthroplasty risk following ACI. Design. In this Level II, prognostic study, 170 ACI-treated patients (110 males [aged 36.8 ± 9.4 years]; 60 females [aged 38.1 ± 10.2 years]) completed a questionnaire about further surgery on their knee treated with ACI 10.9 ± 3.5 years previously. Factors commonly assessed preoperatively (age, gender, defect location and number, previous surgery at this site, and the preoperative Lysholm score) were used as independent factors in regression analyses. Results. At final follow-up (maximum of 19 years post-ACI), 40 patients (23.5%) had undergone surgical re-intervention following ACI. Twenty-six patients (15.3%) underwent arthroplasty, more commonly females (25%) than males (10%; P = 0.001). Cox regression analyses identified 4 factors associated with re-intervention: age at ACI, multiple operations before ACI, patellar defects, and lower pretreatment Lysholm scores (Nagelkerke’s R2 = 0.20). Six predictive items associated with risk of arthroplasty following ACI (Nagelkerke’s R2 = 0.34) were used to develop the Oswestry Risk of Knee Arthroplasty index with internal crossvalidation. Conclusion. In a single-center study, we have identified 6 factors (age, gender, location and number of defects, number of previous operations, and Lysholm score before ACI) that appear to influence the likelihood of ACI patients progressing to arthroplasty. We have used this information to propose a formula or “tool” that could aid treatment decisions and improve patient selection for ACI

The Test Your Memory for Mild Cognitive Impairment (TYM-MCI)

BACKGROUND: To validate a short cognitive test: the Test Your Memory for Mild Cognitive Impairment (TYM-MCI) in the diagnosis of patients with amnestic mild cognitive impairment or mild Alzheimer’s disease (aMCI/AD). METHODS: Two hundred and two patients with mild memory problems were recruited. All had ‘passed’ the Mini-Mental State Examination (MMSE). Patients completed the TYM-MCI, the Test Your Memory test (TYM), MMSE and revised Addenbrooke’s Cognitive Examination (ACE-R), had a neurological examination, clinical diagnostics and multidisciplinary team review. RESULTS: As a single test, the TYM-MCI performed as well as the ACE-R in the distinction of patients with aMCI/AD from patients with subjective memory impairment with a sensitivity of 0.79 and specificity of 0.91. Used in combination with the ACE-R, it provided additional value and identified almost all cases of aMCI/AD. The TYM-MCI correctly classified most patients who had equivocal ACE-R scores. Integrated discriminant improvement analysis showed that the TYM-MCI added value to the conventional memory assessment. Patients initially diagnosed as unknown or with subjective memory impairment who were later rediagnosed with aMCI/AD scored poorly on their original TYM-MCI. CONCLUSION: The TYM-MCI is a powerful short cognitive test that examines verbal and visual recall and is a valuable addition to the assessment of patients with aMCI/AD. It is simple and cheap to administer and requires minimal staff time and training.JBR was supported by the Wellcome Trust (103838)

Exploring the components, asymmetry and distribution of relationship quality in wild Barbary macaques (Macaca sylvanus)

Social relationships between group members are a key feature of many animal societies. The quality of social relationships has been described by three main components: value, compatibility and security, based on the benefits, tenure and stability of social exchanges. We aimed to analyse whether this three component structure could be used to describe the quality of social relationships in wild Barbary macaques (Macaca sylvanus). Moreover, we examined whether relationship quality was affected by the sex, age and rank differences between social partners, and investigated the asymmetric nature of social relationships. We collected over 1,900 hours of focal data on seven behavioural variables measuring relationship quality, and used principal component analysis to investigate how these variables clustered together. We found that relationship quality in wild Barbary macaques can be described by a three component structure that represents the value, compatibility and security of a relationship. Female-female dyads had more valuable relationships and same-age dyads more compatible relationships than any other dyad. Rank difference had no effect on the quality of a social relationship. Finally, we found a high degree of asymmetry in how members of a dyad exchange social behaviour. We argue that the asymmetry of social relationships should be taken into account when exploring the pattern and function of social behaviour in animal societies

Grooming coercion and the post-conflict trading of social services in wild Barbary macaques

In animal and human societies, social services such as protection from predators are often exchanged between group members. The tactics that individuals display to obtain a service depend on its value and on differences between individuals in their capacity to aggressively obtain it. Here we analysed the exchange of valuable social services (i.e. grooming and relationship repair) in the aftermath of a conflict, in wild Barbary macaques (Macaca sylvanus). The relationship repair function of post-conflict affiliation (i.e. reconciliation) was apparent in the victim but not in the aggressor. Conversely, we found evidence for grooming coercion by the aggressor; when the victim failed to give grooming soon after a conflict they received renewed aggression from the aggressor. We argue that post-conflict affiliation between former opponents can be better described as a trading of social services rather than coercion alone, as both animals obtain some benefits (i.e. grooming for the aggressor and relationship repair for the victim). Our study is the first to test the importance of social coercion in the aftermath of a conflict. Differences in competitive abilities can affect the exchange of services and the occurrence of social coercion in animal societies. This may also help explain the variance between populations and species in their social behaviour and conflict management strategies