On the Feasibility of Maintenance Algorithms in Dynamic Graphs

Near ubiquitous mobile computing has led to intense interest in dynamic graph theory. This provides a new and challenging setting for algorithmics and complexity theory. For any graph-based problem, the rapid evolution of a (possibly disconnected) graph over time naturally leads to the important complexity question: is it better to calculate a new solution from scratch or to adapt the known solution on the prior graph to quickly provide a solution of guaranteed quality for the changed graph? In this paper, we demonstrate that the former is the best approach in some cases, but that there are cases where the latter is feasible. We prove that, under certain conditions, hard problems cannot even be approximated in any reasonable complexity bound --- i.e., even with a large amount of time, having a solution to a very similar graph does not help in computing a solution to the current graph. To achieve this, we formalize the idea as a maintenance algorithm. Using r-Regular Subgraph as the primary example we show that W[1]-hardness for the parameterized approximation problem implies the non-existence of a maintenance algorithm for the given approximation ratio. Conversely we show that Vertex Cover, which is fixed-parameter tractable, has a 2-approximate maintenance algorithm. The implications of NP-hardness and NPO-hardness are also explored

Novel norovirus recombinants detected in South Africa

BACKGROUND: Noroviruses (NoV) are the leading cause of viral gastroenteritis worldwide. Recombination frequently occurs within and between NoV genotypes and recombinants have been implicated in sporadic cases, outbreaks and pandemics of NoV. There is a lack of data on NoV recombinants in Africa and therefore their presence and diversity was investigated in South Africa (SA). RESULTS: Between 2010 and 2013, eleven types of NoV recombinants were identified in SA. Amplification of the polymerase/capsid region spanning the ORF1/2 junction and phylogenetic analysis confirmed each of the recombinant types. SimPlot and maximum x(2) analysis indicated that all recombinants had a breakpoint in the region of the ORF1/2 junction (P < 0.05). The majority (9/11) were intergenotype recombinants, but two intragenotype GII.4 recombinants were characterised. Three combinations represent novel recombinants namely GII.P not assigned (NA)/GII.3, GII.P4 New Orleans 2009/GII.4 NA and GII.P16/GII.17. Several widely reported recombinants were identified and included GII.P21/GII.2, GII.P21/GII.3, GII.Pe/GII.4 Sydney 2012, and GII.Pg/GII.12. Other recombinants that were identified were GII.Pg/GII.1, GII.Pe/GII.4 Osaka 2007, GII.P4 New Orleans 2009/GII.4 Sydney 2012, GII.P7/GII.6. To date these recombinant types all have a reportedly restricted geographic distribution. This is the first report of the GII.P4 New Orleans 2009/GII.4 Sydney 2012 recombinant in Africa. CONCLUSIONS: Over the past four years, remarkably diverse NoV recombinants have been circulating in SA. Pandemic strains such as the GII.Pe/GII.4 Sydney 2012 recombinant co-circulated with novel and emerging recombinant strains. Combined polymerase- and capsid-based NoV genotyping is essential to determine the true diversity and global prevalence of these viruses

Ixodes ricinus Tick Lipocalins: Identification, Cloning, Phylogenetic Analysis and Biochemical Characterization

BACKGROUND: During their blood meal, ticks secrete a wide variety of proteins that interfere with their host's defense mechanisms. Among these proteins, lipocalins play a major role in the modulation of the inflammatory response. METHODOLOGY/PRINCIPAL FINDINGS: Screening a cDNA library in association with RT-PCR and RACE methodologies allowed us to identify 14 new lipocalin genes in the salivary glands of the Ixodes ricinus hard tick. A computational in-depth structural analysis confirmed that LIRs belong to the lipocalin family. These proteins were called LIR for "Lipocalin from I. ricinus" and numbered from 1 to 14 (LIR1 to LIR14). According to their percentage identity/similarity, LIR proteins may be assigned to 6 distinct phylogenetic groups. The mature proteins have calculated pM and pI varying from 21.8 kDa to 37.2 kDa and from 4.45 to 9.57 respectively. In a western blot analysis, all recombinant LIRs appeared as a series of thin bands at 50-70 kDa, suggesting extensive glycosylation, which was experimentally confirmed by treatment with N-glycosidase F. In addition, the in vivo expression analysis of LIRs in I. ricinus, examined by RT-PCR, showed homogeneous expression profiles for certain phylogenetic groups and relatively heterogeneous profiles for other groups. Finally, we demonstrated that LIR6 codes for a protein that specifically binds leukotriene B4. CONCLUSIONS/SIGNIFICANCE: This work confirms that, regarding their biochemical properties, expression profile, and sequence signature, lipocalins in Ixodes hard tick genus, and more specifically in the Ixodes ricinus species, are segregated into distinct phylogenetic groups suggesting potential distinct function. This was particularly demonstrated by the ability of LIR6 to scavenge leukotriene B4. The other LIRs did not bind any of the ligands tested, such as 5-hydroxytryptamine, ADP, norepinephrine, platelet activating factor, prostaglandins D2 and E2, and finally leukotrienes B4 and C4.Journal ArticleResearch Support, Non-U.S. Gov'tSCOPUS: ar.jinfo:eu-repo/semantics/publishe

The effect of orientation of retinal configuration upon accommodation and convergence

The effect of orientation of retinal configuration upon accommodation and convergenc

WhatsApp-propriate? A retrospective content analysis of WhatsApp use and potential breaches in confidentiality among a team of doctors at a district hospital, South Africa

Background. There has been a steady increase in the use of electronic media and instant messaging among healthcare professionals, where it has been almost universally adopted in the workplace. The use of WhatsApp and its perceived benefits in healthcare have been extensively studied; however, there are concerns regarding the potential for ethical breaches in confidentiality through shared electronic patient information.Objectives. To identify the usage characteristics and incidence of shared patient information with WhatsApp use in a team of medical doctors in an unobserved and unregulated setting.Methods. We conducted a retrospective cross-sectional content analysis of WhatsApp messages (n=3 340) among a team of 20 doctors in a South African district hospital over 6 months. All messages found within this time period were allocated unique identifiers. The text and image messages were thematically grouped into four categories, i.e. clinical care, resource allocation, social and administrative. Messages that contained patient-identifying information were included in the analysis.Results. Of a total of 3 340 messages sent, 220 (6.6%) contained patient-identifying information. Of these, 109 (3.3%) contained non-anonymised patient information, while in 111 (3.3%) messages, the information was anonymised. The likelihood of sharing patient identifiers was proportionally much higher in shared images (odds ratio (OR) 5.1; 95% confidence interval (CI) 3.2 - 8.2; p&lt;0.0001) compared with text messages, and in messages that related to clinical care (OR 9.3; 95% CI 2.2 - 38.8; p=0.0023) compared with those sent for resource allocation, and social or administrative purposes.Conclusions. Non-anonymised patient identifiers were found in 3.3% of messages, constituting the potential for breaching patient confidentiality. While WhatsApp groups have significant utility in co-ordinating aspects of clinical care, resource allocation, as well as social and administrative functions, the safe use of WhatsApp should be promoted to ensure that patient confidentiality is maintained

Operations concurrentes et files de priorite

Projet PARADISRésumé disponible dans le fichier PD

First detection of human sapoviruses in river water in South Africa

Over a 2-year period, from January 2009 to December 2010, water samples were collected from three rivers (Klip, Rietspruit and Suikerbosrand) in the Vaal River System, South Africa. Enteric viruses were recovered by a glass wool adsorption–elution method and concentrated using polyethylene glycol/sodium chloride precipitation. Sapoviruses (SaVs) were detected using published sapovirus (SaV)-specific primers and Taqman probes in a two-step real-time reverse transcription-polymerase chain reaction assay. Based on sequence analysis of the 50-end of the capsid gene, SaVs were genotyped. In 2009, SaVs were detected in 39% (15/38) of samples from the Klip river, 83% (5/6) from the Rietspruit and 14% (1/7) of samples from the Suikerbosrand river. In 2010, SaVs were detected in 54% (14/26) of Klip river samples, 92% (11/12) from the Rietspruit and 20% (2/10) of samples from the Suikerbosrand river. SaV strains identified in the water samples were characterised into several GI and GII genotypes. The presence of SaVs in these rivers indicates human faecal contamination which may pose a potential health risk to persons exposed to these water sources during domestic or recreational activities.Poliomyelitis Research Foundation and National Research Foundation (NRF), Iliso Consulting and the Medical Research Council of South Africahttp://www.iwaponline.comhb201

Human calicivirus diversity in wastewater in South Africa

AIM : To investigate the diversity of human caliciviruses (HuCVs) in wastewater from small- to medium-sized communities in five provinces of South Africa (SA). METHODS AND RESULTS : Wastewater samples (51) were screened for norovirus (NoV) GI, GII, GIV and sapovirus (SaV) using real-time reverse transcription (RT)-PCR. Partial capsid nucleotide sequences were analysed for genotyping. At least one HuCV was detected in 42 samples (82%) with NoV GI being detected in 15 (29%), NoV GII in 32 (63%) and SaV in 37 (73%) samples. NoV GIV was not detected. Five NoV GI genotypes (GI.1, GI.3, GI.4, GI.8 and GI.unassigned), eight NoV GII genotypes (GII.2, GII.3, GII.4, GII.6, GII.7, GII.12, GII.13 and GII.17) and six SaV genotypes (GI.2, GI.3, GI.6, GI.7, GII.1 and GII.2) were characterized. CONCLUSIONS : Many NoV and SaV genotypes were detected in wastewater, demonstrating a high genetic diversity of HuCVs in the surrounding communities. Caliciviruses were characterized from several provinces in SA, indicating widespread occurrence in the country. SIGNIFICANCE AND THE IMPACT OF THE STUDY : This study provides valuable new data on CVs circulating in SA, including the first data on SaV strains from wastewater in Africa. Environmental surveillance is especially important in countries like SA where outbreak reporting systems or routine HuCV surveillance is lackinghttp://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1365-2672hb2013ay201