Effects of memory on the shapes of simple outbreak trees

Genomic tools, including phylogenetic trees derived from sequence data, are increasingly used to understand outbreaks of infectious diseases. One challenge is to link phylogenetic trees to patterns of transmission. Particularly in bacteria that cause chronic infections, this inference is affected by variable infectious periods and infectivity over time. It is known that non-exponential infectious periods can have substantial effects on pathogens’ transmission dynamics. Here we ask how this non-Markovian nature of an outbreak process affects the branching trees describing that process, with particular focus on tree shapes. We simulate Crump-Mode-Jagers branching processes and compare different patterns of infectivity over time. We find that memory (non-Markovian-ness) in the process can have a pronounced effect on the shapes of the outbreak’s branching pattern. However, memory also has a pronounced effect on the sizes of the trees, even when the duration of the simulation is fixed. When the sizes of the trees are constrained to a constant value, memory in our processes has little direct effect on tree shapes, but can bias inference of the birth rate from trees. We compare simulated branching trees to phylogenetic trees from an outbreak of tuberculosis in Canada, and discuss the relevance of memory to this dataset

Exploring the processes of change facilitated by musical activities on mental wellness

While the benefits of music to people’s mental health have long been recognized, the process of how it works requires further investigation. This paper is based on the results of a community-based music project offered to a group of mental health service users by a Hong Kong social service centre. A six-dimensional framework, which contains emotional, psychological, social, cognitive, behavioural and spiritual dimensions, is constructed for understanding how musical activities may produce benefits for mental health service users. Through conducting 23 interview sessions for the participants (N = 47), who suffered from mental health problems, including schizophrenia and other psychotic disorders, mood disorders and anxiety disorders, of the music project, this study examines the processes of change within musical activities. Feedback was solicited from them by listening to their first-hand experiences as service users of the musical activities. Recorded interviews were transcribed and analysed to generate themes that correspond to the six dimensions the researchers proposed. This study shows that the clinical effects elicited by the musical activities described fit closely with the needs of mental health service users. Its findings suggest that community-based musical activities have clear potential for supporting mental health service users in recovery, which deserve further promotion

Linear scaling computation of the Fock matrix. IX. Parallel computation of the Coulomb matrix

We present parallelization of a quantum-chemical tree-code [J. Chem. Phys. {\bf 106}, 5526 (1997)] for linear scaling computation of the Coulomb matrix. Equal time partition [J. Chem. Phys. {\bf 118}, 9128 (2003)] is used to load balance computation of the Coulomb matrix. Equal time partition is a measurement based algorithm for domain decomposition that exploits small variation of the density between self-consistent-field cycles to achieve load balance. Efficiency of the equal time partition is illustrated by several tests involving both finite and periodic systems. It is found that equal time partition is able to deliver 91 -- 98 % efficiency with 128 processors in the most time consuming part of the Coulomb matrix calculation. The current parallel quantum chemical tree code is able to deliver 63 -- 81% overall efficiency on 128 processors with fine grained parallelism (less than two heavy atoms per processor).Comment: 7 pages, 6 figure

Chow's Method of Optimal Control: A Numerical Solution

Method

Fixing the Farm Bill: Using the Permanent Provisions in Agricultural Law to Achieve WTO Compliance

Agricultural policy in the United States over the past three-quarters of a century has involved supporting farmers in the unpredictable business of growing crops. Until 1973, such domestic supports took the form of a loan-based system that controlled crop prices. The current payment-based system, put into place after 1973, has encouraged over-production and run afoul of WTO trade rules. Moving back to a loan-based system, or incorporating elements of such a system into U.S. agricultural legislation, could potentially cure problems of overproduction and other domestic ills. A loan-based system could also bring the United States back into alignment with WTO trade rules, protecting it from potentially expensive sanctions by other countries. Furthermore, it is important to understand the ramifications of such a loan-based system because all farm bills since 1949 are simply modifications to loan-based “permanent provisions,” and in the absence of new legislation, these provisions take effect

Analytical method for designing grating compensated dispersion-managed soliton systems

This paper was published in Journal of Optical Society of America B and is made available as an electronic reprint with the permission of OSA. The paper can be found at the following URL on the OSA website: http://www.opticsinfobase.org/abstract.cfm?URI=JOSAB-21-4-706. Systematic or multiple reproduction or distribution to multiple locations via electronic or other means is prohibited and is subject to penalties under law. © 2004 The Optical Society.Peer reviewedPublisher PD

Modeling T Tauri Winds from He I 10830 Profiles

The high opacity of He I 10830 makes it an exceptionally sensitive probe of the inner wind geometry of accreting T Tauri stars. In this line blueshifted absorption below the continuum results from simple scattering of stellar photons, a situation which is readily modeled without definite knowledge of the physical conditions and recourse to multi-level radiative transfer. We present theoretical line profiles for scattering in two possible wind geometries, a disk wind and a wind emerging radially from the star, and compare them to observed He I 10830 profiles from a survey of classical T Tauri stars. The comparison indicates that subcontinuum blueshifted absorption is characteristic of disk winds in ~30% of the stars and of stellar winds in ~40%. We further conclude that for many stars the emission profile of helium likely arises in stellar winds, increasing the fraction of accreting stars inferred to have accretion-powered stellar winds to ~60%. Stars with the highest disk accretion rates are more likely to have stellar wind than disk wind signatures and less likely to have redshifted absorption from magnetospheric funnel flows. This suggests the possibility that when accretion rates are high, disks can extend closer to the star, magnetospheric accretion zones can be reduced in size and conditions arise that favor radially outflowing stellar winds.Comment: 41 pages, 11 figures. Accepted by Astrophysical Journa

Ontogenetic changes in cutaneous and branchial ionocytes and morphology in yellowfin tuna (Thunnus albacares) larvae.

The development of osmoregulatory and gas exchange organs was studied in larval yellowfin tuna (Thunnus albacares) from 2 to 25 days post-hatching (2.9-24.5 mm standard length, SL). Cutaneous and branchial ionocytes were identified using Na+/K+-ATPase immunostaining and scanning electron microscopy. Cutaneous ionocyte abundance significantly increased with SL, but a reduction in ionocyte size and density resulted in a significant decrease in relative ionocyte area. Cutaneous ionocytes in preflexion larvae had a wide apical opening with extended microvilli; however, microvilli retracted into an apical pit from flexion onward. Lamellae in the gill and pseudobranch were first detected ~ 3.3 mm SL. Ionocytes were always present on the gill arch, first appeared in the filaments and lamellae of the pseudobranch at 3.4 mm SL, and later in gill filaments at 4.2 mm SL, but were never observed in the gill lamellae. Unlike the cutaneous ionocytes, gill and pseudobranch ionocytes had a wide apical opening with extended microvilli throughout larval development. The interlamellar fusion, a specialized gill structure binding the lamellae of ram-ventilating fish, began forming by ~ 24.5 mm SL and contained ionocytes, a localization never before reported. Ionocytes were retained on the lamellar fusions and also found on the filament fusions of larger sub-adult yellowfin tuna; however, sub-adult gill ionocytes had apical pits. These results indicate a shift in gas exchange and NaCl secretion from the skin to branchial organs around the flexion stage, and reveal novel aspects of ionocyte localization and morphology in ram-ventilating fishes