Combining Thesaurus Knowledge and Probabilistic Topic Models

In this paper we present the approach of introducing thesaurus knowledge into probabilistic topic models. The main idea of the approach is based on the assumption that the frequencies of semantically related words and phrases, which are met in the same texts, should be enhanced: this action leads to their larger contribution into topics found in these texts. We have conducted experiments with several thesauri and found that for improving topic models, it is useful to utilize domain-specific knowledge. If a general thesaurus, such as WordNet, is used, the thesaurus-based improvement of topic models can be achieved with excluding hyponymy relations in combined topic models.Comment: Accepted to AIST-2017 conference (http://aistconf.ru/). The final publication will be available at link.springer.co

Model diagnostics and refinement for phylodynamic models

<div><p>Phylodynamic modelling, which studies the joint dynamics of epidemiological and evolutionary processes, has made significant progress in recent years due to increasingly available genomic data and advances in statistical modelling. These advances have greatly improved our understanding of transmission dynamics of many important pathogens. Nevertheless, there remains a lack of effective, targetted diagnostic tools for systematically detecting model mis-specification. Development of such tools is essential for model criticism, refinement, and calibration. The idea of utilising <i>latent residuals</i> for model assessment has already been exploited in general spatio-temporal epidemiological settings. Specifically, by proposing appropriately designed non-centered, re-parameterizations of a given epidemiological process, one can construct latent residuals with known sampling distributions which can be used to quantify evidence of model mis-specification. In this paper, we extend this idea to formulate a novel model-diagnostic framework for phylodynamic models. Using simulated examples, we show that our framework may effectively detect a particular form of mis-specification in a phylodynamic model, particularly in the event of superspreading. We also exemplify our approach by applying the framework to a dataset describing a local foot-and-mouth (FMD) outbreak in the UK, eliciting strong evidence against the assumption of no within-host-diversity in the outbreak. We further demonstrate that our framework can facilitate model calibration in real-life scenarios, by proposing a within-host-diversity model which appears to offer a better fit to data than one that assumes no within-host-diversity of FMD virus.</p></div

Space-charge-limited flows in the quantum regime

This paper reviews the recent developments of space-charge-limited (SCL) flow or Child-Langmuir (CL) law in the quantum regime. According to the classical CL law for planar diodes, the current density scales as 3/23∕2’s power of gap voltage and to the inverse squared power of gap spacing. When the electron de Broglie wavelength is comparable or larger than the gap spacing, the classical SCL current density is enhanced by a large factor due to electron tunneling and exchange-correlation effects, and there is a new quantum scaling for the current density, which is proportional to the 1/21∕2’s power of gap voltage, and to the inverse fourth-power of gap spacing. It is also found that the classical concepts of the SCL flow such as bipolar flow, transit time, beam-loaded capacitance, emitted charge density, and magnetic insulation are no longer valid in quantum regime. In the quantum regime, there exists a minimum transit time of the SCL flows, in contrast to the classical solution. By including the surface properties of the emitting surface, there is a threshold voltage that is required to obtain the quantum CL law. The implications of the Fowler-Nordheim-like field emission in the presence of intense space charge over the nanometer scale is discussed.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/87757/2/056701_1.pd

Dendritic Cells: A Spot on Sialic Acid

Glycans decorating cell surface and secreted proteins and lipids occupy the juncture where critical host–host and host-pathogen interactions occur. The role of glycan epitopes in cell–cell and cell-pathogen adhesive events is already well-established, and cell surface glycan structures change rapidly in response to stimulus and inflammatory cues. Despite the wide acceptance that glycans are centrally implicated in immunity, exactly how glycans and their changes contribute to the overall immune response remains poorly defined. Sialic acids are unique sugars that usually occupy the terminal position of the glycan chains and may be modified by external factors, such as pathogens, or upon specific physiological cellular events. At cell surface, sialic acid-modified structures form the key fundamental determinants for a number of receptors with known involvement in cellular adhesiveness and cell trafficking, such as the Selectins and the Siglec families of carbohydrate recognizing receptors. Dendritic cells (DCs) preside over the transition from innate to the adaptive immune repertoires, and no other cell has such relevant role in antigen screening, uptake, and its presentation to lymphocytes, ultimately triggering the adaptive immune response. Interestingly, sialic acid-modified structures are involved in all DC functions, such as antigen uptake, DC migration, and capacity to prime T cell responses. Sialic acid content changes along DC differentiation and activation and, while, not yet fully understood, these changes have important implications in DC functions. This review focuses on the developmental regulation of DC surface sialic acids and how manipulation of DC surface sialic acids can affect immune-critical DC functions by altering antigen endocytosis, pathogen and tumor cell recognition, cell recruitment, and capacity for T cell priming. The existing evidence points to a potential of DC surface sialylation as a therapeutic target to improve and diversify DC-based therapies

Generalised dimensions of measures on almost self-affine sets

We establish a generic formula for the generalised q-dimensions of measures supported by almost self-affine sets, for all q>1. These q-dimensions may exhibit phase transitions as q varies. We first consider general measures and then specialise to Bernoulli and Gibbs measures. Our method involves estimating expectations of moment expressions in terms of `multienergy' integrals which we then bound using induction on families of trees

On completeness of orbits of Killing vector fields

A Theorem is proved which reduces the problem of completeness of orbits of Killing vector fields in maximal globally hyperbolic, say vacuum, space--times to some properties of the orbits near the Cauchy surface. In particular it is shown that all Killing orbits are complete in maximal developements of asymptotically flat Cauchy data, or of Cauchy data prescribed on a compact manifold. This result gives a significant strengthening of the uniqueness theorems for black holes.Comment: 16 pages, Latex, preprint NSF-ITP-93-4

A novel two‐beam accelerator (twobetron)

A new configuration is analyzed wherein a low current beam is accelerated to high energies (10’s of amps, 10’s of MeV) by a driver beam of high current and low energy (a few kiloamps, <1 MeV). The annular driver beam excites the TM020 cavity mode of an accelerating structure which transfers its rf power to the on‐axis secondary beam. Systematic variation of the driver beam radius provides the secondary beam with phase focusing and adjustable acceleration gradient. A proof‐of‐principle experiment is suggested. Various issues, such as the scaling laws, transverse and longitudinal instabilities, rf coupling among cavities, etc., are examined. © 1995 American Institute of PHysics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/87548/2/451_1.pd

Lagrangian Floer superpotentials and crepant resolutions for toric orbifolds

We investigate the relationship between the Lagrangian Floer superpotentials for a toric orbifold and its toric crepant resolutions. More specifically, we study an open string version of the crepant resolution conjecture (CRC) which states that the Lagrangian Floer superpotential of a Gorenstein toric orbifold $\mathcal{X}$ and that of its toric crepant resolution $Y$ coincide after analytic continuation of quantum parameters and a change of variables. Relating this conjecture with the closed CRC, we find that the change of variable formula which appears in closed CRC can be explained by relations between open (orbifold) Gromov-Witten invariants. We also discover a geometric explanation (in terms of virtual counting of stable orbi-discs) for the specialization of quantum parameters to roots of unity which appears in Y. Ruan's original CRC ["The cohomology ring of crepant resolutions of orbifolds", Gromov-Witten theory of spin curves and orbifolds, 117-126, Contemp. Math., 403, Amer. Math. Soc., Providence, RI, 2006]. We prove the open CRC for the weighted projective spaces $\mathcal{X}=\mathbb{P}(1,\ldots,1,n)$ using an equality between open and closed orbifold Gromov-Witten invariants. Along the way, we also prove an open mirror theorem for these toric orbifolds.Comment: 48 pages, 1 figure; v2: references added and updated, final version, to appear in CM

Thoracoscopic repair of congenital diaphragmatic hernia: two centres’ experience with 60 patients

© 2014, Springer-Verlag Berlin Heidelberg. Methods: All patients who underwent thoracoscopic repair of congenital diaphragmatic hernia between 2010 and 2013 at the two tertiary referral centres were identified. Medical records were retrospectively reviewed. Data including patients’ demographics, peri-operative outcomes, length of hospitalisation and post-operative complications were extracted and analysed. Introduction: Congenital diaphragmatic hernia is a potentially life-threatening neonatal condition which required surgical intervention. With the advances in endosurgical instruments and techniques, thoracoscopic approach is gaining popularity as a standard procedure in the treatment of this condition. In this study, we reviewed our two centres’ experience with thoracoscopic repair of congenital diaphragmatic hernia in recent years. Conclusion: Thoracoscopic repair of congenital diaphragmatic hernia can be performed safely in specialised centres. The post-operative recovery and cosmesis are excellent. Diaphragmatic hernia with large defect remains a challenge for surgeons. Results: 60 patients were identified over the study period, with 46 males and 14 females. 48 patients received operation within the first 7 days of life. There were seven patients with delayed presentation and were operated after 1 month old. The average body weight was 3.03 kg. Left-sided hernia was more prevalent (n = 50). The mean operative time was 88.5 min (range 31–194 min). No conversion to open thoracotomy or laparotomy was required in any of the patients. All patients except one were intubated and paralysed in neonatal intensive care units for at least 3 days after operation. Average hospital stay was 14.6 days. There was no mortality in this series. There were five recurrences, one being the patient without post-operative paralysis, and the others with deficient posterior muscle rim. No musculoskeletal deformity was noted on follow-up examination.postprin

Atom-photon coupling from nitrogen-vacancy centres embedded in tellurite microspheres

We have developed a technique for creating high quality tellurite microspheres with embedded nanodiamonds (NDs) containing nitrogen-vacancy (NV) centres. This hybrid method allows fluorescence of the NVs in the NDs to be directly, rather than evanescently, coupled to the whispering gallery modes of the tellurite microspheres at room temperature. As a demonstration of its sensing potential, shifting of the resonance peaks is also demonstrated by coating a sphere surface with a liquid layer. This new approach is a robust way of creating cavities for use in quantum and sensing applications