String Matching and 1d Lattice Gases

We calculate the probability distributions for the number of occurrences $n$ of a given $l$ letter word in a random string of $k$ letters. Analytical expressions for the distribution are known for the asymptotic regimes (i) $k \gg r^l \gg 1$ (Gaussian) and $k,l \to \infty$ such that $k/r^l$ is finite (Compound Poisson). However, it is known that these distributions do now work well in the intermediate regime $k \gtrsim r^l \gtrsim 1$. We show that the problem of calculating the string matching probability can be cast into a determining the configurational partition function of a 1d lattice gas with interacting particles so that the matching probability becomes the grand-partition sum of the lattice gas, with the number of particles corresponding to the number of matches. We perform a virial expansion of the effective equation of state and obtain the probability distribution. Our result reproduces the behavior of the distribution in all regimes. We are also able to show analytically how the limiting distributions arise. Our analysis builds on the fact that the effective interactions between the particles consist of a relatively strong core of size $l$, the word length, followed by a weak, exponentially decaying tail. We find that the asymptotic regimes correspond to the case where the tail of the interactions can be neglected, while in the intermediate regime they need to be kept in the analysis. Our results are readily generalized to the case where the random strings are generated by more complicated stochastic processes such as a non-uniform letter probability distribution or Markov chains. We show that in these cases the tails of the effective interactions can be made even more dominant rendering thus the asymptotic approximations less accurate in such a regime.Comment: 44 pages and 8 figures. Major revision of previous version. The lattice gas analogy has been worked out in full, including virial expansion and equation of state. This constitutes the main part of the paper now. Connections with existing work is made and references should be up to date now. To be submitted for publicatio

The Sight Loss and Vision Priority Setting Partnership (SLV-PSP): overview and results of the research prioritisation survey process

Objectives: The Sight Loss and Vision Priority Setting Partnership aimed to identify research priorities relating to sight loss and vision through consultation with patients, carers and clinicians. These priorities can be used to inform funding bodies’ decisions and enhance the case for additional research funding. Design: Prospective survey with support from the James Lind Alliance. Setting: UK-wide National Health Service (NHS) and non-NHS. Participants: Patients, carers and eye health professionals. Academic researchers were excluded solely from the prioritisation process. The survey was disseminated by patient groups, professional bodies, at conferences and through the media, and was available for completion online, by phone, by post and by alternative formats (Braille and audio). Outcome measure: People were asked to submit the questions about prevention, diagnosis and treatment of sight loss and eye conditions that they most wanted to see answered by research. Returned survey questions were reviewed by a data assessment group. Priorities were established across eye disease categories at final workshops. Results: 2220 people responded generating 4461 submissions. Sixty-five per cent of respondents had sight loss and/or an eye condition. Following initial data analysis, 686 submissions remained which were circulated for interim prioritisation (excluding cataract and ocular cancer questions) to 446 patients/carers and 218 professionals. The remaining 346 questions were discussed at final prioritisation workshops to reach agreement of top questions per category. Conclusions: The exercise engaged a diverse community of stakeholders generating a wide range of conditions and research questions. Top priority questions were established across 12 eye disease categories. This is an Open Access article distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 3.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial

Optical application and measurement of torque on microparticles of isotropic nonabsorbing material

We show how it is possible to controllably rotate or align microscopic particles of isotropic nonabsorbing material in a TEM00 Gaussian beam trap, with simultaneous measurement of the applied torque using purely optical means. This is a simple and general method of rotation, requiring only that the particle is elongated along one direction. Thus, this method can be used to rotate or align a wide range of naturally occurring particles. The ability to measure the applied torque enables the use of this method as a quantitative tool--the rotational equivalent of optical tweezers based force measurement. As well as being of particular value for the rotation of biological specimens, this method is also suitable for the development of optically-driven micromachines.Comment: 8 pages, 6 figure

Immunological Sex Differences in Socially Promiscuous African Ground Squirrels

Differences in how males and females respond to foreign antigens are common across taxa. Such sexual differences in the immune system are predicted to be greater in species with high promiscuity and sociality as these factors increase the likelihood of disease transmission. Intense sperm competition is thought to further this sexual dichotomy as increased investment in spermatogenesis likely incurs additional immunological costs. Xerus inauris, a ground squirrel found throughout southern Africa, is extremely social and promiscuous with one of the highest male reproductive investments among rodents. These life-history attributes suggest males and females should demonstrate a large dichotomy in immunity. Contrary to our prediction, we found no difference in spleen mass between the sexes. However, we did find significant biases in leukocyte types and red blood cell counts, possibly reflecting responses to parasite types. Among males, we predicted greater investments in spermatogenesis would result in reduced immunological investments. We found a negative association between testes and spleen size and a positive relationship between testes and number of lice suggesting trade-offs in reproductive investment possibly due to the costs associated with spermatogenesis and immunity. We suggest when measuring sexual differences in immunity it is important to consider the effects of reproductive pressures, parasite types, and life history costs

How reliably can we predict the reliability of protein structure predictions?

Background: Comparative methods have been the standard techniques for in silico protein structure prediction. The prediction is based on a multiple alignment that contains both reference sequences with known structures and the sequence whose unknown structure is predicted. Intensive research has been made to improve the quality of multiple alignments, since misaligned parts of the multiple alignment yield misleading predictions. However, sometimes all methods fail to predict the correct alignment, because the evolutionary signal is too weak to find the homologous parts due to the large number of mutations that separate the sequences. Results: Stochastic sequence alignment methods define a posterior distribution of possible multiple alignments. They can highlight the most likely alignment, and above that, they can give posterior probabilities for each alignment column. We made a comprehensive study on the HOMSTRAD database of structural alignments, predicting secondary structures in four different ways. We showed that alignment posterior probabilities correlate with the reliability of secondary structure predictions, though the strength of the correlation is different for different protocols. The correspondence between the reliability of secondary structure predictions and alignment posterior probabilities is the closest to the identity function when the secondary structure posterior probabilities are calculated from the posterior distribution of multiple alignments. The largest deviation from the identity function has been obtained in the case of predicting secondary structures from a single optimal pairwise alignment. We also showed that alignment posterior probabilities correlate with the 3D distances between C α amino acids in superimposed tertiary structures. Conclusion: Alignment posterior probabilities can be used to a priori detect errors in comparative models on the sequence alignment level. </p

Extending conceptual understanding : how interprofessional education influences affective domain development

Background: Interprofessional learning (IPL) can influence affective domain development of students, through teaching activities that facilitate learning with, from and about other professions. Current quantitative evidence offers limited explanation of how this learning is achieved within IPL programmes. This original paper tests a conceptual framework drawn from theories on IPL and affective domain development (attitudes, values and behaviours) to explain what works for whom, when and in what circumstances. Methods: The objectives of the study were twofold: to evaluate the impact of the IPL programme on the student’s attitudes and values, and identify behaviour changes in clinical practice towards interprofessional working. Using an action research approach, based in practice, an IPL programme was delivered over six weeks. Students from five professional disciplines: nursing, radiography, physiotherapy, social work, and podiatry (n=63) participated over the two action research cycles and in semi structured focus groups (n=37). Results: The recorded personal experiences of the IPL activities on the students were examined in relation to the: type of activity; impact on the affective domain of learning (attitude, value, or behaviour) and self-reported outcome on application to their practice. Modification in affective domain development was measured to identification or internalisation stage for 30 of the students. Self-reported outcomes on application to practice included direct impact on patient care, personal resilience building, improved communication and ability to challenge practice. Conclusion: This paper presents a conceptual framework not evident in current research, in regards to what IPL works for whom, in what circumstances and when. IPL Activities that address a personal reward or incentive and are delivered over 4 weeks, imitating ‘circles of care,’ that explore self-assessment, team building and reflection can lead to sustained change in values, attitudes and behaviours. Keywords: Action Research, Interprofessional Education, Interprofessional learning, Health and Social care, Collaboration

DIAGNOSTIC AND PREVENTIVE SERVICES IN A NATIONAL INCREMENTAL DENTAL PLAN FOR CHILDREN

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/65579/1/j.1752-7325.1977.tb02874.x.pd

Financial considerations in the conduct of multi-centre randomised controlled trials: evidence from a qualitative study.

National Coordinating Centre for Research Methodology; Medical Research Council, UK Department of Health; Chief Scientist OfficeNot peer reviewedPublisher PD

Using Structure to Explore the Sequence Alignment Space of Remote Homologs

Protein structure modeling by homology requires an accurate sequence alignment between the query protein and its structural template. However, sequence alignment methods based on dynamic programming (DP) are typically unable to generate accurate alignments for remote sequence homologs, thus limiting the applicability of modeling methods. A central problem is that the alignment that is “optimal” in terms of the DP score does not necessarily correspond to the alignment that produces the most accurate structural model. That is, the correct alignment based on structural superposition will generally have a lower score than the optimal alignment obtained from sequence. Variations of the DP algorithm have been developed that generate alternative alignments that are “suboptimal” in terms of the DP score, but these still encounter difficulties in detecting the correct structural alignment. We present here a new alternative sequence alignment method that relies heavily on the structure of the template. By initially aligning the query sequence to individual fragments in secondary structure elements and combining high-scoring fragments that pass basic tests for “modelability”, we can generate accurate alignments within a small ensemble. Our results suggest that the set of sequences that can currently be modeled by homology can be greatly extended