Distance and intersection number in the curve graph of a surface

In this work, we study the cellular decomposition of $S$ induced by a filling pair of curves $v$ and $w$, $Dec_{v,w}(S) = S - (v \cup w)$, and its connection to the distance function $d(v,w)$ in the curve graph of a closed orientable surface $S$ of genus $g$. Efficient geodesics were introduced by the first author in joint work with Margalit and Menasco in 2016, giving an algorithm that begins with a pair of non-separating filling curves that determine vertices $(v,w)$ in the curve graph of a closed orientable surface $S$ and computing from them a finite set of {\it efficient} geodesics. We extend the tools of efficient geodesics to study the relationship between distance $d(v,w)$, intersection number $i(v,w)$, and $Dec_{v,w}(S)$. The main result is the development and analysis of particular configurations of rectangles in $Dec_{v,w}(S)$ called \textit{spirals}. We are able to show that, in some special cases, the efficient geodesic algorithm can be used to build an algorithm that reduces $i(v,w)$ while preserving $d(v,w)$. At the end of the paper, we note a connection of our work to the notion of extending geodesics.Comment: 20 pages, 17 figures. Changes: A key lemma (Lemma 5.6) was revised to be more precise, an irrelevant proposition (Proposition 2.1) and example were removed, unnecessary background material was taken out, some of the definitions and cited results were clarified (including added figures,) and Proposition 5.7 and Theorem 5.8 have been merged into a single theorem, Theorem 4.

A Quantitative Prioritisation of Human and Domestic Animal Pathogens in Europe

Disease or pathogen risk prioritisations aid understanding of infectious agent impact within surveillance or mitigation and biosecurity work, but take significant development. Previous work has shown the H-(Hirsch-)index as an alternative proxy. We present a weighted risk analysis describing infectious pathogen impact for human health (human pathogens) and well-being (domestic animal pathogens) using an objective, evidence-based, repeatable approach; the H-index. This study established the highest H-index European pathogens. Commonalities amongst pathogens not included in previous surveillance or risk analyses were examined. Differences between host types (humans/animals/zoonotic) in pathogen H-indices were explored as a One Health impact indicator. Finally, the acceptability of the H-index proxy for animal pathogen impact was examined by comparison with other measures. 57 pathogens appeared solely in the top 100 highest H-indices (1) human or (2) animal pathogens list, and 43 occurred in both. Of human pathogens, 66 were zoonotic and 67 were emerging, compared to 67 and 57 for animals. There were statistically significant differences between H-indices for host types (humans, animal, zoonotic), and there was limited evidence that H-indices are a reasonable proxy for animal pathogen impact. This work addresses measures outlined by the European Commission to strengthen climate change resilience and biosecurity for infectious diseases. The results include a quantitative evaluation of infectious pathogen impact, and suggest greater impacts of human-only compared to zoonotic pathogens or scientific under-representation of zoonoses. The outputs separate high and low impact pathogens, and should be combined with other risk assessment methods relying on expert opinion or qualitative data for priority setting, or could be used to prioritise diseases for which formal risk assessments are not possible because of data gaps

Computational science and re-discovery: open-source implementations of ellipsoidal harmonics for problems in potential theory

We present two open-source (BSD) implementations of ellipsoidal harmonic expansions for solving problems of potential theory using separation of variables. Ellipsoidal harmonics are used surprisingly infrequently, considering their substantial value for problems ranging in scale from molecules to the entire solar system. In this article, we suggest two possible reasons for the paucity relative to spherical harmonics. The first is essentially historical---ellipsoidal harmonics developed during the late 19th century and early 20th, when it was found that only the lowest-order harmonics are expressible in closed form. Each higher-order term requires the solution of an eigenvalue problem, and tedious manual computation seems to have discouraged applications and theoretical studies. The second explanation is practical: even with modern computers and accurate eigenvalue algorithms, expansions in ellipsoidal harmonics are significantly more challenging to compute than those in Cartesian or spherical coordinates. The present implementations reduce the "barrier to entry" by providing an easy and free way for the community to begin using ellipsoidal harmonics in actual research. We demonstrate our implementation using the specific and physiologically crucial problem of how charged proteins interact with their environment, and ask: what other analytical tools await re-discovery in an era of inexpensive computation?Comment: 25 pages, 3 figure

Cosmic Origins Spectrograph Observations of the Chemical Composition of LMC N132D

We present new far-ultraviolet spectra of an oxygen-rich knot in the Large Magellanic Cloud supernova remnant N132D, obtained with the Hubble Space Telescope/Cosmic Origins Spectrograph. Moderate resolution (v~200 km/s) spectra in the HST far-ultraviolet bandpass (1150 - 1750 A) show emission from several ionization states of oxygen as well as trace amounts of other species. We use the improvements in sensitivity and resolving power offered by COS to separate contributions from different velocity components within the remnant, as well as emission from different species within the oxygen-rich knot itself. This is the first time that compositional and velocity structure in the ultraviolet emission lines from N132D has been resolved, and we use this to assess the chemical composition of the remnant. No nitrogen is detected in N132D and multiple carbon species are found at velocities inconsistent with the main oxygen component. We find helium and silicon to be associated with the oxygen-rich knot, and use the reddening-corrected line strengths of OIII], OIV], OV, and SiIV to constrain the composition and physical characteristics of this oxygen-rich knot. We find that models with a silicon-to-oxygen abundance ratio of N(Si)/N(O) = 0.01 can reproduce the observed emission for a shock velocity of ~130 km/s, implying a mass of ~50 solar masses for the N132D progenitor star.Comment: 5 pages, 4 figures. Submitted to ApJ

Preserving the impossible: conservation of soft-sediment hominin footprint sites and strategies for three-dimensional digital data capture.

Human footprints provide some of the most publically emotive and tangible evidence of our ancestors. To the scientific community they provide evidence of stature, presence, behaviour and in the case of early hominins potential evidence with respect to the evolution of gait. While rare in the geological record the number of footprint sites has increased in recent years along with the analytical tools available for their study. Many of these sites are at risk from rapid erosion, including the Ileret footprints in northern Kenya which are second only in age to those at Laetoli (Tanzania). Unlithified, soft-sediment footprint sites such these pose a significant geoconservation challenge. In the first part of this paper conservation and preservation options are explored leading to the conclusion that to 'record and digitally rescue' provides the only viable approach. Key to such strategies is the increasing availability of three-dimensional data capture either via optical laser scanning and/or digital photogrammetry. Within the discipline there is a developing schism between those that favour one approach over the other and a requirement from geoconservationists and the scientific community for some form of objective appraisal of these alternatives is necessary. Consequently in the second part of this paper we evaluate these alternative approaches and the role they can play in a 'record and digitally rescue' conservation strategy. Using modern footprint data, digital models created via optical laser scanning are compared to those generated by state-of-the-art photogrammetry. Both methods give comparable although subtly different results. This data is evaluated alongside a review of field deployment issues to provide guidance to the community with respect to the factors which need to be considered in digital conservation of human/hominin footprints

Draft genome sequences of two extensively drug-resistant strains of acinetobacter baumannii isolated from clinical samples in Pakistan

Infections in immunocompromised patients that are caused by extensively drug-resistant (XDR) Acinetobacter baumannii strains have been increasingly reported worldwide. In particular, carbapenem-resistant A. baumannii strains are a prominent cause of health care-associated infections. Here, we report draft genome assemblies for two clinical XDR A. baumannii isolates obtained from hospitalized patients in Pakistan

Challenges to the development of antigen-specific breast cancer vaccines

Continued progress in the development of antigen-specific breast cancer vaccines depends on the identification of appropriate target antigens, the establishment of effective immunization strategies, and the ability to circumvent immune escape mechanisms. Methods such as T cell epitope cloning and serological expression cloning (SEREX) have led to the identification of a number target antigens expressed in breast cancer. Improved immunization strategies, such as using dendritic cells to present tumor-associated antigens to T lymphocytes, have been shown to induce antigen-specific T cell responses in vivo and, in some cases, objective clinical responses. An outcome of successful tumor immunity is the evolution of antigen-loss tumor variants. The development of a polyvalent breast cancer vaccine, directed against a panel of tumor-associated antigens, may counteract this form of immune escape

Effect of scavenger receptor BI antagonist ITX5061 in patients with hepatitis C virus infection undergoing liver transplantation

Hepatitis C virus (HCV) entry inhibitors have been hypothesized to prevent infection of the liver after transplantation. ITX5061 is a Scavenger Receptor B-I (SR-BI) antagonist that blocks HCV entry and infection in vitro. We assessed the safety and efficacy of ITX5061 to limit HCV infection of the graft. The study included 23 HCV infected patients undergoing liver transplantation. The first 13 "control" patients did not receive drug. The subsequent 10 patients received ITX5061 150 mg immediately pre- and post-transplant, and daily for 1 week thereafter. ITX5061 pharmacokinetics and plasma HCV RNA were quantified. Viral genetic diversity was measured by ultradeep pyrosequencing. ITX5061 was well tolerated with measurable plasma concentrations during therapy. Whilst the median HCV RNA reduction was greater in ITX treated patients at all time points in the first week after transplantation there was no difference in the overall change in the area over the HCV RNA curve in the 7-day treatment period. However, in genotype 1 infected patients treatment was associated with a sustained reduction in HCV RNA levels compared to the control group (area over the HCV RNA curve analysis, p=0.004). Ultradeep pyrosequencing revealed a complex and evolving pattern of HCV variants infecting the graft during the first week. ITX5061 significantly limited viral evolution where the median divergence between day 0 and day 7 was 3.5% in the control group compared to 0.1% in the treated group.CONCLUSIONS: ITX5061 reduces plasma HCV RNA post transplant notably in genotype 1 infected patients and slows viral evolution. Following liver transplantation the likely contribution of extrahepatic reservoirs of HCV necessitates combining entry inhibitors such as ITX5061 with inhibitors of replication in future studies. Clinicaltrials.gov NCT01292824. This article is protected by copyright. All rights reserved.</p

On the Inequivalence of Weak-Localization and Coherent Backscattering

We define a current-conserving approximation for the local conductivity tensor of a disordered system which includes the effects of weak localization. Using this approximation we show that the weak localization effect in conductance is not obtained simply from the diagram corresponding to the coherent back-scattering peak observed in optical experiments. Other diagrams contribute to the effect at the same order and decrease its value. These diagrams appear to have no semiclassical analogues, a fact which may have implications for the semiclassical theory of chaotic systems. The effects of discrete symmetries on weak localization in disordered conductors is evaluated and and compared to results from chaotic scatterers.Comment: 24 pages revtex + 12 figures on request; hub.94.