Ranking relations using analogies in biological and information networks

Analogical reasoning depends fundamentally on the ability to learn and generalize about relations between objects. We develop an approach to relational learning which, given a set of pairs of objects $\mathbf{S}=\{A^{(1)}:B^{(1)},A^{(2)}:B^{(2)},\ldots,A^{(N)}:B ^{(N)}\}$, measures how well other pairs A:B fit in with the set $\mathbf{S}$. Our work addresses the following question: is the relation between objects A and B analogous to those relations found in $\mathbf{S}$? Such questions are particularly relevant in information retrieval, where an investigator might want to search for analogous pairs of objects that match the query set of interest. There are many ways in which objects can be related, making the task of measuring analogies very challenging. Our approach combines a similarity measure on function spaces with Bayesian analysis to produce a ranking. It requires data containing features of the objects of interest and a link matrix specifying which relationships exist; no further attributes of such relationships are necessary. We illustrate the potential of our method on text analysis and information networks. An application on discovering functional interactions between pairs of proteins is discussed in detail, where we show that our approach can work in practice even if a small set of protein pairs is provided.Comment: Published in at http://dx.doi.org/10.1214/09-AOAS321 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Decrease in water clarity of the southern and central North Sea during the 20th century

Light in the marine environment is a key environmental variable coupling physics to marine biogeochemistry and ecology. Weak light penetration reduces light available for photosynthesis, changing energy fluxes through the marine food web. Based on published and unpublished data, this study shows that the central and southern North Sea has become significantly less clear over the second half of the 20th century. In particular, in the different regions and seasons investigated, the average Secchi depth pre-1950 decreased between 25% and 75% compared to the average Secchi depth post-1950. Consequently, in summer pre-1950, most (74%) of the sea floor in the permanently mixed area off East Anglia was within the photic zone. For the last 25+ years, changes in water clarity were more likely driven by an increase in the concentration of suspended sediments, rather than phytoplankton. We suggest that a combination of causes have contributed to this increase in suspended sediments such as changes in sea-bed communities and in weather patterns, decreased sink of sediments in estuaries, and increased coastal erosion. A predicted future increase in storminess (Beniston et al., 2007; Kovats et al., 2014) could enhance the concentration of suspended sediments in the water column and consequently lead to a further decrease in clarity, with potential impacts on phytoplankton production, CO2 fluxes, and fishery production

Interplay of Orbital Degeneracy and Superconductivity in a Molecular Conductor

We study electron propagation in a molecular lattice model. Each molecular site involves doubly degenerate electronic states coupled to doubly degenerate molecular vibration, leading to a so--called E-e type of Jahn-Teller Hamiltonian. For weak electron-phonon coupling and in the anti-adiabatic limit we find that the orbital degeneracy induces an intersite pairing mechanism which is absent in the standard non-degenerate polaronic model. In this limit we analyse the model in the presence of an additional on-site repulsion and we determine, within BCS mean field theory, the region of stability of superconductivity. In one dimension, where powerful analytical techniques are available, we are able to calculate the phase diagram of the model both for weak and for strong electron-phonon coupling.Comment: 11 pages, REVTEX style, 3 compressed figures adde

The Phase Diagram of Correlated Electrons in a Lattice of Berry Molecules

A model for correlated electrons in a lattice with local additional spin--1 degrees of freedom inducing constrained hopping, is studied both in the low density limit and at quarter filling. We show that in both 1D and 2D two particles form a bound state even in presence of a repulsive U<U_c. A picture of a dilute Bose gas, leading to off-diagonal long range order (LRO) in 2D (quasi-LRO in 1D), is supported by quantitative calculations in 1D which allow for a determination of the phase diagram.Comment: 7 pages + 2 ps figures, published versio

Electro-fluid dynamics of aqueous humor production: simulations and new directions.

Purpose: to theoretically investigate the role of bicarbonate ion (HCO− 3 ) on the nonpigmented transepithelial potential di erence Vm, the sodium potassium pump (Na/K) and the active secretion of aqueous humor. Methods: a three-dimensional mathematical model is proposed to isolate the roles of HCO− 3 and Na+, which are di icult to investigate experimentally. The model combines the velocity-extended Poisson-Nernst-Planck equations to describe ion electrodi usion and the Stokes equations to describe aqueous humor flow into the basolateral space adjacent to the nonpigmented ephitelial cells. Results: Computations show that Vm is close to baseline experimental measurements (on monkeys) in the range [−2.7, −2.3]mV only if HCO− 3 is included in the simulation. The model is also capable of reproducing the flow of Na+ exiting the cell and the flow of K+ entering the cell, in accordance with the physiology of the Na/K pump. The simulated Na/K ratio is 1.53, which is in very good agreement with the theoretical value of 1.5. Conclusion: Model simulations suggest that HCO− 3 inhibition may prevent physiologically correct baseline values of the nonpigmented transepithelial potential di erence and Na/K ATPase function. This may provide useful indication in the design of medications that decrease the active secretion of aqueous humor, and supports the advantage of using mathematical models as a noninvasive complement of animal models

A need-based, multi-level, cross-sectoral framework to explain variations in satisfaction of care needs among people living with dementia

YesBACKGROUND: Provision of care and support for people with dementia and family carers is complex, given variation in how dementia manifests, progresses and affects people, co-morbidities associated with ageing, as well as individual preferences, needs, and circumstances. The traditional service-led approach, where individual needs are assessed against current service provision, has been recognised as unfit to meet such complexity. As a result, people with dementia and family members often fail to receive adequate support, with needs remaining unmet. Current research lacks a conceptual framework for explaining variation in satisfaction of care needs. This work develops a conceptual framework mapped onto the care delivery process to explain variations in whether, when and why care needs of people with dementia are met and to expose individual-, service-, system-level factors that enable or hinder needs satisfaction. METHODS: Data collected through 24 in-depth interviews and two focus groups (10 participants) with people with dementia and family carers living in the North East of England (UK) were analysed thematically to develop a typology of care needs. The need most frequently reported for people with dementia (i.e. for support to go out and about) was analysed using themes stemming from the conceptual framework which combined candidacy and discrepancy theories. RESULTS: The operationalisation of the framework showed that satisfaction of the need to go out was first determined at the point of service access, affected by issues about navigation, adjudication, permeability, users' resistance to offers, users' appearance, and systems-level operating conditions, and, subsequently, at the point of service use, when factors related to service structure and care process determined (dis)satisfaction with service and, hence, further contributed to met or unmet need. CONCLUSION: The conceptual framework pinpoints causes of variations in satisfaction of care needs which can be addressed when designing interventions and service improvements.We gratefully acknowledge financial support from the Health Foundation (grant number 1274233)