Post-processing partitions to identify domains of modularity optimization

We introduce the Convex Hull of Admissible Modularity Partitions (CHAMP) algorithm to prune and prioritize different network community structures identified across multiple runs of possibly various computational heuristics. Given a set of partitions, CHAMP identifies the domain of modularity optimization for each partition ---i.e., the parameter-space domain where it has the largest modularity relative to the input set---discarding partitions with empty domains to obtain the subset of partitions that are "admissible" candidate community structures that remain potentially optimal over indicated parameter domains. Importantly, CHAMP can be used for multi-dimensional parameter spaces, such as those for multilayer networks where one includes a resolution parameter and interlayer coupling. Using the results from CHAMP, a user can more appropriately select robust community structures by observing the sizes of domains of optimization and the pairwise comparisons between partitions in the admissible subset. We demonstrate the utility of CHAMP with several example networks. In these examples, CHAMP focuses attention onto pruned subsets of admissible partitions that are 20-to-1785 times smaller than the sets of unique partitions obtained by community detection heuristics that were input into CHAMP.Comment: http://www.mdpi.com/1999-4893/10/3/9

Molecular confirmation of Sarcocystis fayeri in a donkey

Sarcocystis fayeri is a canine protozoan parasite with an equine intermediate host. Historically classified as an incidental pathogen, recent literature has described the toxic effects of Sarcocystis fayeri in human food poisoning, and highlighted potential involvement in equine neuromuscular disease. Until now, horses were believed to be the exclusive intermediate host. This study reports the first molecular confirmation of S. fayeri in a donkey, and gives rise to the consideration of donkeys being a potential reservoir for the parasite. This finding is of particular importance in understanding the epidemiology of this disease

A co-evolutionary arms race: trypanosomes shaping the human genome, humans shaping the trypanosome genome

<i>Trypanosoma brucei</i> is the causative agent of African sleeping sickness in humans and one of several pathogens that cause the related veterinary disease Nagana. A complex co-evolution has occurred between these parasites and primates that led to the emergence of trypanosome-specific defences and counter-measures. The first line of defence in humans and several other <i>catarrhine</i> primates is the trypanolytic protein apolipoprotein-L1 (APOL1) found within two serum protein complexes, trypanosome lytic factor 1 and 2 (TLF-1 and TLF-2). Two sub-species of <i>T. Brucei</i> have evolved specific mechanisms to overcome this innate resistance, <i>Trypanosoma brucei gambiense</i> and <i>Trypanosoma brucei rhodesiense</i>. In <i>T. b. Rhodesiense</i>, the presence of the serum resistance associated (SRA) gene, a truncated variable surface glycoprotein (VSG), is sufficient to confer resistance to lysis. The resistance mechanism of <i>T. b. Gambiense</i> is more complex, involving multiple components: reduction in binding affinity of a receptor for TLF, increased cysteine protease activity and the presence of the truncated VSG, <i>T. b. Gambiense</i>-specific glycoprotein <i>(TgsGP)</i>. In a striking example of co-evolution, evidence is emerging that primates are responding to challenge by <i>T. b. Gambiense</i> and <i>T. b. Rhodesiense</i>, with several populations of humans and primates displaying resistance to infection by these two sub-species

Cysteine proteinase C1A paralog profiles correspond with phylogenetic lineages of pathogenic piroplasmids

Piroplasmid parasites comprising of Babesia, Theileria, and Cytauxzoon are transmitted by ticks to farm and pet animals and have a significant impact on livestock industries and animal health in tropical and subtropical regions worldwide. In addition, diverse Babesia spp. infect humans as opportunistic hosts. Molecular phylogeny has demonstrated at least six piroplasmid lineages exemplified by B. microti, B. duncani, C. felis, T. equi, Theileria sensu stricto (T. annulata, T. parva, and T. orientalis) and Babesia sensu stricto (B. bovis, B. bigemina, and B. ovis). C1A cysteine-proteinases (C1A-Cp) are papain-like enzymes implicated in pathogenic and vital steps of the parasite life cycle such as nutrition and host cell egress. An expansion of C1A-Cp of T. annulata and T. parva with respect to B. bovis and B. ovis was previously described. In the present work, C1A-Cp paralogs were identified in available genomes of species pertaining to each piroplasmid lineage. Phylogenetic analysis revealed eight C1A-Cp groups. The profile of C1A-Cp paralogs across these groups corroborates and defines the existence of six piroplasmid lineages. C. felis, T. equi and Theileria s.s. each showed characteristic expansions into extensive families of C1A-Cp paralogs in two of the eight groups. Underlying gene duplications have occurred as independent unique evolutionary events that allow distinguishing these three piroplasmid lineages. We hypothesize that C1A-Cp paralog families may be associated with the advent of the schizont stage. Differences in the invertebrate tick host specificity and/or mode of transmission in piroplasmid lineages might also be associated with the observed C1A-Cp paralog profiles

Use of hyaluronidase in the comparison between manual and automated hematology analysis with the ADVIA 120 to improve analysis of feline body cavity effusions

Classification of body cavity effusions is an important step in the investigation and diagnosis of disease in cats. Feline inflammatory effusions are often highly proteinaceous and viscous, which can cause clumping of white cells and subsequently inaccurate nucleated cell counts (NCCs) using automated and manual methods. Microscopic assessment of cellularity can also be difficult given the variable thickness of smears and cell clumping, which skews white cell distribution. The ADVIA 120 uses 2 white cell–counting channels, the basophil/lobularity (WBC/baso) and differential/peroxidase channels, which can provide quite different results in highly viscous feline samples and often disagree with smear assessment of cellularity. We investigated the effects of pre-incubation of feline effusion samples with hyaluronidase and its effects on NCCs and cellularity assessment. NCCs were obtained by automated analysis using the ADVIA 120 and by manual counting methods. Agreement was assessed using a Bland–Altman chart. Pretreatment of samples with hyaluronidase resulted in good agreement between the ADVIA basophil channel and manual counting methods in all samples in the study. However, improvements in NCCs after hyaluronidase treatment were significantly greater in clumped samples, and cell distribution of these samples on direct smears was also improved. Therefore, when nucleated cell clumping is observed on a direct smear, pretreatment of the sample with hyaluronidase prior to analysis on an automated analyzer is advised, with the WBC/baso channel displaying the most accurate NCC

Characterization of HSP90 isoforms in transformed bovine leukocytes infected with Theileria annulata

HSP90 chaperones are essential regulators of cellular function, as they ensure the appropriate conformation of multiple key client proteins. Four HSP90 isoforms were identified in the protozoan parasite Theileria annulata. Partial characterisation was undertaken for three and localisation confirmed for cytoplasmic (TA12105); endoplasmic reticulum (TA06470) and apicoplast (TA10720) forms. ATPase activity and binding to the HSP90 inhibitor geldanamycin, were demonstrated for recombinant TA12105 and all three native forms could be isolated to varying extents by binding to geldanamycin beads. Because it is essential, HSP90 is considered a potential therapeutic drug target. Resistance to the only specific Theileriacidal drug is increasing and one challenge for design of drugs that target the parasite is to limit the effect on the host. An in vitro cell culture system that allows comparison between uninfected bovine cells and the T. annulata-infected counterpart was utilised to test the effects of geldanamycin and the derivative 17-AAG. T. annulata-infected cells had greater tolerance to geldanamycin than uninfected cells yet exhibited significantly more sensitivity to 17-AAG. These findings suggest that parasite HSP90 isoform (s) can alter the drug sensitivity of infected host cells and that members of the Theileria HSP90 family are potential targets worthy of further investigation

Results from the third Scottish National Prevalence Survey: is a population health approach now needed to prevent healthcare-associated infections?

Summary Background Healthcare associated infections (HAI) are a major public health concern and a significant cause of morbidity and mortality. A robust and current evidence base that is specific to local, national and Europe-wide settings is necessary to inform the development of strategies to reduce HAI and contain antimicrobial resistance (AMR). Aim To measure the prevalence of HAI and antimicrobial prescribing and identify key priority areas for interventions to reduce the burden of infection. Methods A national rolling PPS in National Health Service (NHS) acute, NHS non-acute, NHS paediatric and independent hospitals was carried out between September and November 2016 using the European Centre for Disease Prevention and Control protocol designed for the European PPS. Findings The prevalence of HAI was 4.6%, 2.7% and 3.2% in acute adults, paediatric and non-acute patient groups, respectively. The most common HAI types reported in adult patients were urinary tract infection and pneumonia. The prevalence of antimicrobial prescribing was 35.7%, 29.3% and 13.8% in acute adults, paediatric and non-acute patient groups, respectively. Respiratory, skin and soft tissue, gastrointestinal and urinary tract infections were the most common infections being treated at the time of survey. Conclusion HAI continues to be a public health concern in Scotland. UTI and pneumonia continue to place a significant burden on patients and on healthcare delivery, including those that develop in the community and require hospital admission. A broader population health approach which focuses on reducing the risk of infection upstream would reduce these infections in both community and hospital settings

Loop mediated isothermal amplification (LAMP) of Theileria annulata DNA

In the past three decades, as an alternative to PCR (polymerase chain reaction) new diagnostic techniques like LAMP (loop mediated isothermal amplification) whereby target DNA can be amplified under isothermal conditions without using thermocycler have been developed. The LAMP method allows the synthesis of large amounts of DNA in a short time with high specificity and rapid and easy detection of generated products. In this study, specificity and sensitivity of LAMP method was evaluated for the detection of T. annulata in acute infected and/or carriers cattle using primer pair specifically designed to amplify merozoite surface antigen gene (Mero1), 30 kDa major merozoite surface antigen gene (Tams-1) and cytochrome b gene of T.annulata. Primer pairs with highest sensitivity were used to evaluate the applicability of LAMP to the field samples. Two LAMP primers (CYTOB1 and CYTOB341) targeting cytochrome b gene specifically amplified DNA of different T. annulata isolates successfully while no amplification was seen in other species DNAs and BL20. CYTOB1 primers detected T. annulata Ankara / D7 DNA up to 2 fg, however the detection limit of CYTOB341 was 10 fold lower. The sensitivity of CYTOB1 LAMP assay was same with F3/B3 PCR, however when compared with that of cytob1 PCR a 10 fold lower sensitivity was found. The LAMP product was confirmed by restriction digestion and sequencing. Results obtained from this study indicated that none of the designed primer pairs specific to target genes (Tams-1 and Mero1), except cytochrome b gene was able to specifically and sensitively detect different isolates of T. annulata. Consequently, it was shown that LAMP method using CYTOB1 primers is less effective than the cytob1 PCR in terms of detecting T. annulata in the field sample

Nonlinearly stacked low noise turbofan stator

A nonlinearly stacked low noise turbofan stator vane having a characteristic curve that is characterized by a nonlinear sweep and a nonlinear lean is provided. The stator is in an axial fan or compressor turbomachinery stage that is comprised of a collection of vanes whose highly three-dimensional shape is selected to reduce rotor-stator and rotor-strut interaction noise while maintaining the aerodynamic and mechanical performance of the vane. The nonlinearly stacked low noise turbofan stator vane reduces noise associated with the fan stage of turbomachinery to improve environmental compatibility