Communicability across evolving networks

Many natural and technological applications generate time ordered sequences of networks, defined over a fixed set of nodes; for example time-stamped information about ‘who phoned who’ or ‘who came into contact with who’ arise naturally in studies of communication and the spread of disease. Concepts and algorithms for static networks do not immediately carry through to this dynamic setting. For example, suppose A and B interact in the morning, and then B and C interact in the afternoon. Information, or disease, may then pass from A to C, but not vice versa. This subtlety is lost if we simply summarize using the daily aggregate network given by the chain A-B-C. However, using a natural definition of a walk on an evolving network, we show that classic centrality measures from the static setting can be extended in a computationally convenient manner. In particular, communicability indices can be computed to summarize the ability of each node to broadcast and receive information. The computations involve basic operations in linear algebra, and the asymmetry caused by time’s arrow is captured naturally through the non-mutativity of matrix-matrix multiplication. Illustrative examples are given for both synthetic and real-world communication data sets. We also discuss the use of the new centrality measures for real-time monitoring and prediction

Googling the brain: discovering hierarchical and asymmetric network structures, with applications in neuroscience

Hierarchical organisation is a common feature of many directed networks arising in nature and technology. For example, a well-defined message-passing framework based on managerial status typically exists in a business organisation. However, in many real-world networks such patterns of hierarchy are unlikely to be quite so transparent. Due to the nature in which empirical data is collated the nodes will often be ordered so as to obscure any underlying structure. In addition, the possibility of even a small number of links violating any overall “chain of command” makes the determination of such structures extremely challenging. Here we address the issue of how to reorder a directed network in order to reveal this type of hierarchy. In doing so we also look at the task of quantifying the level of hierarchy, given a particular node ordering. We look at a variety of approaches. Using ideas from the graph Laplacian literature, we show that a relevant discrete optimization problem leads to a natural hierarchical node ranking. We also show that this ranking arises via a maximum likelihood problem associated with a new range-dependent hierarchical random graph model. This random graph insight allows us to compute a likelihood ratio that quantifies the overall tendency for a given network to be hierarchical. We also develop a generalization of this node ordering algorithm based on the combinatorics of directed walks. In passing, we note that Google’s PageRank algorithm tackles a closely related problem, and may also be motivated from a combinatoric, walk-counting viewpoint. We illustrate the performance of the resulting algorithms on synthetic network data, and on a real-world network from neuroscience where results may be validated biologically

Photosystem II Peripheral Accessory Chlorophyll Mutants in Chlamydomonas reinhardtii. Biochemical Characterization and Sensitivity to Photo-Inhibition

In addition to the four chlorophylls (Chls) involved in primary charge separation, the photosystem II (PSII) reaction center polypeptides, D1 and D2, coordinate a pair of symmetry-related, peripheral accessory Chls. These Chls are axially coordinated by the D1-H118 and D2-H117 residues and are in close association with the proximal Chl antennae proteins, CP43 and CP47. To gain insight into the function(s) of each of the peripheral Chls, we generated site-specific mutations of the amino acid residues that coordinate these Chls and characterized their energy and electron transfer properties. Our results demonstrate that D1-H118 and D2-H117 mutants differ with respect to: (a) their relative numbers of functional PSII complexes, (b) their relative ability to stabilize charge-separated states, (c) light-harvesting efficiency, and (d) their sensitivity to photo-inhibition. The D2-H117N and D2-H117Q mutants had reduced levels of functional PSII complexes and oxygen evolution capacity as well as reduced light-harvesting efficiencies relative to wild-type cells. In contrast, the D1-H118Q mutant was capable of near wild-type rates of oxygen evolution at saturating light intensities. The D1-H118Q mutant also was substantially more resistant to photo-inhibition than wild type. This reduced sensitivity to photo-inhibition is presumably associated with a reduced light-harvesting efficiency in this mutant. Finally, it is noted that the PSII peripheral accessory Chls have similarities to a to a pair of Chls also present in the PSI reaction center complex

What's in a virus? Folk understandings of hepatitis C infection and infectiousness among injecting drug users in Kings Cross, Sydney

BACKGROUND: To explore folk understandings of blood borne virus infection and infectiousness among injecting drug users in Kings Cross, Sydney. METHODS: Observational fieldwork was conducted in Kings Cross over a four month period. In-depth interviews with 24 current injectors and 4 key informants recruited from King Cross were undertaken. RESULTS: Hepatitis C (HCV) generated different meanings from HIV. HIV was considered "the dreaded" and generated fear of infection and dire disease progression. Whereas HCV was considered non-desirable but less threatening than HIV. The risks of transmitting HCV through sharing injecting paraphernalia was poorly understood. Some believed HCV infection was linked to poor hygiene and dirty water. Jaundice was mistakenly thought to indicate HCV infection and was used to gauge infectiousness. Many were confused about their current hepatitis C serostatus. Some participants thought they had a "dormant antibody" or that they had a "mild case" of infection. Participants were unsure what this meant for their own health or for their potential to infect others. CONCLUSION: Participants displayed confusion about transmission risks for hepatitis C, conflating blood awareness and hygiene health promotion messages. Participants' reliance on the symptom of jaundice to gauge serostatus places them at risk of transmitting and contracting HCV. Participants were confused about what a positive HCV diagnosis meant for their own health and their ability to infect others. Education is needed to debunk misconceptions about jaundice and clarify medical terms such as 'antibody' at the time of diagnosis. Further clarification of messages about injecting hygiene and blood awareness are also required

Molecular cloning and transcriptional activity of a new Petunia calreticulin gene involved in pistil transmitting tract maturation, progamic phase, and double fertilization

Calreticulin (CRT) is a highly conserved and ubiquitously expressed Ca2+-binding protein in multicellular eukaryotes. As an endoplasmic reticulum-resident protein, CRT plays a key role in many cellular processes including Ca2+ storage and release, protein synthesis, and molecular chaperoning in both animals and plants. CRT has long been suggested to play a role in plant sexual reproduction. To begin to address this possibility, we cloned and characterized the full-length cDNA of a new CRT gene (PhCRT) from Petunia. The deduced amino acid sequence of PhCRT shares homology with other known plant CRTs, and phylogenetic analysis indicates that the PhCRT cDNA clone belongs to the CRT1/CRT2 subclass. Northern blot analysis and fluorescent in situ hybridization were used to assess PhCRT gene expression in different parts of the pistil before pollination, during subsequent stages of the progamic phase, and at fertilization. The highest level of PhCRT mRNA was detected in the stigma–style part of the unpollinated pistil 1 day before anthesis and during the early stage of the progamic phase, when pollen is germinated and tubes outgrow on the stigma. In the ovary, PhCRT mRNA was most abundant after pollination and reached maximum at the late stage of the progamic phase, when pollen tubes grow into the ovules and fertilization occurs. PhCRT mRNA transcripts were seen to accumulate predominantly in transmitting tract cells of maturing and receptive stigma, in germinated pollen/growing tubes, and at the micropylar region of the ovule, where the female gametophyte is located. From these results, we suggest that PhCRT gene expression is up-regulated during secretory activity of the pistil transmitting tract cells, pollen germination and outgrowth of the tubes, and then during gamete fusion and early embryogenesis

Is gynaecological surgical training a cause for concern? A questionnaire survey of trainees and trainers

<p>Astract</p> <p>Background</p> <p>Concerns have been raised as to whether the current postgraduate training programme for gynaecological surgery is being detrimentally affected by changes in working practices, in particular the European Working Time Directive (EWTD). The purpose of this study was to investigate the surgical activity of obstetrics and gynaecology trainees and to explore trainees' and trainers' opinions on the current barriers and potential solutions to surgical training.</p> <p>Methods</p> <p>Two questionnaire surveys were conducted, one to obstetrics and gynaecology trainees working within the West Midlands Deanery and a second to consultant gynaecologists in the West Midlands region.</p> <p>Results</p> <p>One hundred and four trainees (64.3%) and 66 consultant gynaecologists (55.0%) responded. Sixty-six trainees (66.7%) reported attending up to one operating list per week. However, 28.1% reported attending up to one list every two weeks or less and 5 trainees stated that they had not attended a list at all over the preceding 8 weeks. Trainees working in a unit with less than 3999 deliveries attended significantly more theatre sessions compared to trainees in units with over 4000 deliveries (p = 0.007), as did senior trainees (p = 0.032) and trainees attached to consultants performing major gynaecological surgery (p = 0.022). In the previous 8 weeks, only 6 trainees reported performing a total abdominal hysterectomy independently, all were senior trainees (ST6 and above). In the trainers' survey, only two respondents (3.0%) agreed that the current program produces doctors competent in general gynaecological surgery by the end of training, compared to 48 (73.8%) respondents who disagreed.</p> <p>Conclusions</p> <p>Trainees' concerns over a lack of surgical training appear to be justified. The main barriers to training are perceived to be a lack of team structure and a lack of theatre time.</p

Demographic, risk behaviour and personal network variables associated with prevalent hepatitis C, hepatitis B, and HIV infection in injection drug users in Winnipeg, Canada

BACKGROUND: Previous studies have used social network variables to improve our understanding of HIV transmission. Similar analytic approaches have not been undertaken for hepatitis C (HCV) or B (HBV), nor used to conduct comparative studies on these pathogens within a single setting. METHODS: A cross-sectional survey consisting of a questionnaire and blood sample was conducted on injection drug users in Winnipeg between December 2003 and September 2004. Logistic regression analyses were used to correlate respondent and personal network data with HCV, HBV and HIV prevalence. RESULTS: At the multivariate level, pathogen prevalence was correlated with both respondent and IDU risk network variables. Pathogen transmission was associated with several distinct types of high-risk networks formed around specific venues (shooting galleries, hotels) or within users who are linked by their drug use preferences. Smaller, isolated pockets of IDUs also appear to exist within the larger population where behavioural patterns pose a lesser risk, unless or until, a given pathogen enters those networks. CONCLUSION: The findings suggest that consideration of both respondent and personal network variables can assist in understanding the transmission patterns of HCV, HBV, and HIV. It is important to assess these effects for multiple pathogens within one setting as the associations identified and the direction of those associations can differ between pathogens