Chaos game representation for comparison of whole genomes

BACKGROUND: Chaos game representation of genome sequences has been used for visual representation of genome sequence patterns as well as alignment-free comparisons of sequences based on oligonucleotide frequencies. However the potential of this representation for making alignment-based comparisons of whole genome sequences has not been exploited. RESULTS: We present here a fast algorithm for identifying all local alignments between two long DNA sequences using the sequence information contained in CGR points. The local alignments can be depicted graphically in a dot-matrix plot or in text form, and the significant similarities and differences between the two sequences can be identified. We demonstrate the method through comparison of whole genomes of several microbial species. Given two closely related genomes we generate information on mismatches, insertions, deletions and shuffles that differentiate the two genomes. CONCLUSION: Addition of the possibility of large scale sequence alignment to the repertoire of alignment-free sequence analysis applications of chaos game representation, positions CGR as a powerful sequence analysis tool

26Postoperative diagnosis and outcome in patients with revision arthroplasty for aseptic loosening

BACKGROUND: The most common cause of implant failure is aseptic loosening (AL), followed by prosthetic joint infection (PJI). This study evaluates the incidence of PJI among patients operated with suspected AL and whether the diagnosis of PJI was predictive of subsequent implant failure including re-infection, at 2 years of follow up. METHODS: Patients undergoing revision hip or knee arthroplasty due to presumed AL from February 2009 to September 2011 were prospectively evaluated. A sonication fluid of prosthesis and tissue samples for microbiology and histopathology at the time of the surgery were collected. Implant failure include recurrent or persistent infection, reoperation for any reason or need for chronic antibiotic suppression. RESULTS: Of 198 patients with pre-and intraoperative diagnosis of AL, 24 (12.1 %) had postoperative diagnosis of PJI. After a follow up of 31 months (IQR: 21 to 38 months), 9 (37.5 %) of 24 patients in the PJI group had implant failure compared to only 1 (1.1 %) in the 198 of AL group (p 20 CFU) and peri-prosthetic tissue culture were 87.5 % vs 66.7 %, respectively. Specificities were 100 % for both techniques (95 % CI, 97.9-100 %). A greater number of patients with PJI (79.1 %) had previous partial arthroplasty revisions than those patients in the AL group (56.9 %) (p = 0.04). In addition, 5 (55.5 %) patients with PJI and implant failure had more revision arthroplasties during the first year after the last implant placement than those patients with PJI without implant failure (1 patient; 6.7 %) (RR 3.8; 95 % CI 1.4-10.1; p = 0.015). On the other hand, 6 (25 %) patients finally diagnosed of PJI were initially diagnosed of AL in the first year after primary arthroplasty, whereas it was only 16 (9.2 %) patients in the group of true AL (RR 2.7; 95 % CI 1.2-6.1; p = 0.03). CONCLUSIONS: More than one tenth of patients with suspected AL are misdiagnosed PJI. Positive histology and positive peri-implant tissue and sonicate fluid cultures are highly predictive of implant failure in patients with PJI. Patients with greater number of partial hip revisions for a presumed AL had more risk of PJI. Early loosening is more often caused by hidden PJI than late loosening

Negotiating the transition from adolescence to motherhood: Coping with prenatal and parenting stress in teenage mothers in Mulago hospital, Uganda

<p>Abstract</p> <p>Background</p> <p>Adolescence is a transitional stage from childhood to adulthood that is characterized by physical, physiological, psychosocial and behavioral changes that are influenced to a large extent by the age, culture and socialization of the individual. To explore what adolescent mothers perceive as their struggles during the period of transition from childhood to parenthood (through motherhood) and to describe strategies employed in coping with stress of pregnancy, motherhood and parenthood.</p> <p>Methods</p> <p>Longitudinal qualitative study involving twenty two in-depth interviews and six focus group discussions among pregnant adolescents who were followed from pregnant to delivery, from January 2004 to August 2005. Participant were selected by theoretical sampling and data was analyzed using grounded theory.</p> <p>Results</p> <p>Overall, young adolescents reported more anxiety, loss of self esteem (when they conceived), difficulty in accessing financial, moral and material support from parents or partners and stigmatization by health workers when they sought care from health facilities. Three strategies by which adolescent mothers cope with parenting and pregnancy stress that were described as utilizing opportunities (thriving), accommodating the challenges (bargaining and surviving), or failure (despairing), and varied in the extent to which they enabled adolescents to cope with the stress.</p> <p>Conclusion</p> <p>Adolescents on the transition to motherhood have variable needs and aspirations and utilize different strategies to cope with the stress of pregnancy and parenthood.</p

Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe

Shigella are human-adapted Escherichia coli that have gained the ability to invade the human gut mucosa and cause dysentery1,2, spreading efficiently via low-dose fecal-oral transmission3,4. Historically, S. sonnei has been predominantly responsible for dysentery in developed countries, but is now emerging as a problem in the developing world, apparently replacing the more diverse S. flexneri in areas undergoing economic development and improvements in water quality4-6. Classical approaches have shown S. sonnei is genetically conserved and clonal7. We report here whole-genome sequencing of 132 globally-distributed isolates. Our phylogenetic analysis shows that the current S. sonnei population descends from a common ancestor that existed less than 500 years ago and has diversified into several distinct lineages with unique characteristics. Our analysis suggests the majority of this diversification occurred in Europe, followed by more recent establishment of local pathogen populations in other continents predominantly due to the pandemic spread of a single, rapidly-evolving, multidrug resistant lineage

Dynamics of Immune System Gene Expression upon Bacterial Challenge and Wounding in a Social Insect (Bombus terrestris)

The innate immune system which helps individuals to combat pathogens comprises a set of genes representing four immune system pathways (Toll, Imd, JNK and JAK/STAT). There is a lack of immune genes in social insects (e.g. honeybees) when compared to Diptera. Potentially, this might be compensated by an advanced system of social immunity (synergistic action of several individuals). The bumble bee, Bombus terrestris, is a primitively eusocial species with an annual life cycle and colonies headed by a single queen. We used this key pollinator to study the temporal dynamics of immune system gene expression in response to wounding and bacterial challenge

Time separation as a hidden variable to the Copenhagen school of quantum mechanics

The Bohr radius is a space-like separation between the proton and electron in the hydrogen atom. According to the Copenhagen school of quantum mechanics, the proton is sitting in the absolute Lorentz frame. If this hydrogen atom is observed from a different Lorentz frame, there is a time-like separation linearly mixed with the Bohr radius. Indeed, the time-separation is one of the essential variables in high-energy hadronic physics where the hadron is a bound state of the quarks, while thoroughly hidden in the present form of quantum mechanics. It will be concluded that this variable is hidden in Feynman's rest of the universe. It is noted first that Feynman's Lorentz-invariant differential equation for the bound-state quarks has a set of solutions which describe all essential features of hadronic physics. These solutions explicitly depend on the time separation between the quarks. This set also forms the mathematical basis for two-mode squeezed states in quantum optics, where both photons are observable, but one of them can be treated a variable hidden in the rest of the universe. The physics of this two-mode state can then be translated into the time-separation variable in the quark model. As in the case of the un-observed photon, the hidden time-separation variable manifests itself as an increase in entropy and uncertainty.Comment: LaTex 10 pages with 5 figure. Invited paper presented at the Conference on Advances in Quantum Theory (Vaxjo, Sweden, June 2010), to be published in one of the AIP Conference Proceedings serie

Using Intervention Mapping to develop an occupational advice intervention to aid return to work following hip and knee replacement in the United Kingdom

Background There are increasing numbers of total hip replacements (THR) and total knee replacements (TKR) being performed in patients of working age. Providing patients undergoing TKR and THR with return to work advice might facilitate return to work. The aim of this paper is to report on the process used to systematically develop an occupational advice intervention to be delivered in hospital for those undergoing arthroplasty. Methods The six-step Intervention Mapping (IM) approach to development, implementation and evaluation of a theory and evidence-based interventions was followed. This paper reports on the development of the intervention covered by steps 1 to 4 of the IM process. Steps 1-3 gathered data on current practice and barriers to change using a mixed methods approach (cohort study of patients undergoing THR or TKR, stakeholder interviews, survey of practice, evidence synthesis) and provided a theoretical framework for intervention development. Step 4 used information from steps 1-3 in combination with a Delphi consensus process to develop the intervention and the associated tools and materials to facilitate its delivery. Results The final intervention identified included a number of core principles including: early patient identification; delivery of key information to patients and their employers; assessment and support by a member of the orthopaedic team; procedures for escalation based on patient need; mechanisms to support communication; and training and support for the clinical teams delivering care. A total of 13 patient and 20 staff performance objectives as delivery requirements, supported by a range of tools, roles and training resources. The intervention addressed outcomes based at the individual and interpersonal levels of the ecological model. Conclusions Following the IM approach resulted in a structured and justified occupational intervention for delivery in secondary care for patients undergoing total hip and knee replacement. The feasibility of the intervention will subsequently be tested alongside further investigation to establish its effectiveness and cost-effectiveness. Key Words Intervention Mapping Return to Work Occupational advice Arthroplasty Hip Kne

Post-injection delirium/sedation syndrome in patients with schizophrenia treated with olanzapine long-acting injection, I: analysis of cases

<p>Abstract</p> <p>Background</p> <p>An advance in the treatment of schizophrenia is the development of long-acting intramuscular formulations of antipsychotics, such as olanzapine long-acting injection (LAI). During clinical trials, a post-injection syndrome characterized by signs of delirium and/or excessive sedation was identified in a small percentage of patients following injection with olanzapine LAI.</p> <p>Methods</p> <p>Safety data from all completed and ongoing trials of olanzapine LAI were reviewed for possible cases of this post-injection syndrome. Descriptive analyses were conducted to characterize incidence, clinical presentation, and outcome. Regression analyses were conducted to assess possible risk factors.</p> <p>Results</p> <p>Based on approximately 45,000 olanzapine LAI injections given to 2054 patients in clinical trials through 14 October 2008, post-injection delirium/sedation syndrome occurred in approximately 0.07% of injections or 1.4% of patients (30 cases in 29 patients). Symptomatology was consistent with olanzapine overdose (e.g., sedation, confusion, slurred speech, altered gait, or unconsciousness). However, no clinically significant decreases in vital signs were observed. Symptom onset ranged from immediate to 3 to 5 hours post injection, with a median onset time of 25 minutes post injection. All patients recovered within 1.5 to 72 hours, and the majority continued to receive further olanzapine LAI injections following the event. No clear risk factors were identified.</p> <p>Conclusions</p> <p>Post-injection delirium/sedation syndrome can be readily identified based on symptom presentation, progression, and temporal relationship to the injection, and is consistent with olanzapine overdose following probable accidental intravascular injection of a portion of the olanzapine LAI dose. Although there is no specific antidote for olanzapine overdose, patients can be treated symptomatically as needed. Special precautions include use of proper injection technique and a post-injection observation period.</p> <p>Trial Registration</p> <p>ClinicalTrials.gov ID; URL: <url>http://http//www.clinicaltrials.gov/</url>: NCT00094640, NCT00088478, NCT00088491, NCT00088465, and NCT00320489.</p

Interaction Between Convection and Pulsation

This article reviews our current understanding of modelling convection dynamics in stars. Several semi-analytical time-dependent convection models have been proposed for pulsating one-dimensional stellar structures with different formulations for how the convective turbulent velocity field couples with the global stellar oscillations. In this review we put emphasis on two, widely used, time-dependent convection formulations for estimating pulsation properties in one-dimensional stellar models. Applications to pulsating stars are presented with results for oscillation properties, such as the effects of convection dynamics on the oscillation frequencies, or the stability of pulsation modes, in classical pulsators and in stars supporting solar-type oscillations.Comment: Invited review article for Living Reviews in Solar Physics. 88 pages, 14 figure