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The presence of bacterial DNA in Dientamoeba fragilis DNA extracts from culture poses a substantial challenge to sequencing the D. fragilis genome. However, elimination of bacteria from D. fragilis cultures has proven difficult in the past, presumably due to its dependence on some unknown prokaryote/s. This study explored options for removal of bacteria from D. fragilis cultures and for the generation of genome sequence data from D. fragilis. DNA was extracted from human faecal samples and xenic D. fragilis cultures. Extracts were subjected to 16S ribosomal DNA bacterial diversity profiling. Xenic D. fragilis cultures were then subject to antibiotic treatment regimens that systematically removed bacterial species depending on their membrane structure (Gram-positive or Gram-negative) and aerobic requirements. The impact of these treatments on cultures was assessed by 16S amplicon sequencing. Prior to antibiotic treatment, the cultures were dominated by Gram-negative bacteria. Addition of meropenem to cultures eliminated anaerobic Gram-negative bacteria, but it also led to protozoan death after 5 days incubation. The seeding of meropenem resistant Klebsiella pneumoniae strain KPC-2 into cultures before treatment by meropenem prevented death of D. fragilis cells beyond this 5 day period, suggesting that one or more species of Gram-negative bacteria may be an essential nutritional requirement for D. fragilis. Gram-positive cells were completely eliminated using vancomycin without affecting trophozoite growth. Finally, this study shows that genome sequencing of D. fragilis is feasible following bacterial elimination from cultures as the result of the major advances occurring in bioinformatics. We provide evidence on this fact by successfully sequencing the D. fragilis 28S large ribosomal DNA subunit gene using culture-derived DNA.
The article begins with the journey towards knowledge of the infinite that is traced out in Descartes's Meditations. Drawing on Levinas's construal of the argument in the Third Meditation, I argue that Descartes's reflections on God as infinite can be a starting point for deepening our understanding of the religious quest – the paradoxical human search for that which, by its very nature, is incomprehensible to the human mind. The second half of the article argues that this search is from first to last structured by desire and longing, and that something prima facie non-cognitive and non-epistemic, namely the desire for God, has a cognitive and epistemic role to play. Perhaps desire can be our human way, or a human way, whereby we can (in Descartes's words) ‘in a certain manner attain to’ the infinite perfection that is God.
Born and bred in Keighley, Carole Rawcliffe is a proud Yorkshirewoman and when minded to do so can express herself in broad Yorkshire. She studied History at Sheffield University and graduated with a first-class degree. This outstanding achievement would not cause much comment now. In 1967, however, she was one of only five History graduates there to have been awarded such a degree since 1952. She stayed at Sheffield to undertake research for her PhD under the supervision of Dr Robin Jeffs on the subject of the Stafford earls of Stafford and dukes of Buckingham, but left in 1971 to join the Royal Commission on Historical Manuscripts. The Historical Manuscripts Commission, as it is usually known, had been established in 1869 with the remit of surveying and reporting on those records, both public and private, that were not legally categorised as ‘Public Records’, and on the repositories where they were held. The Commission was then situated in Quality Court, off Chancery Lane, just 300 yards north of the Public Record Office, and when Carole arrived it was presided over as Secretary by Roger Ellis, a gentleman scholar with a distinguished war record and a delightful manner.
In many ways the HMC proved an excellent training ground, providing Carole with valuable opportunities to broaden her experience. The material in the Commission's published reports was exceptionally diverse both in content and in chronological range, and much of the work undertaken by its staff focused on the National Register of Archives, which had been established within the HMC in 1945 and contained many thousands of published and unpublished lists and catalogues of archival collections relating to all aspects of British history. These provided details of documents held in local authority, business and private archives across Great Britain and in repositories throughout the world. Relatively little medieval material was listed in the NRA catalogues, but the range and interest of the post-medieval material was very wide indeed, covering political, literary, scientific, diplomatic and ecclesiastical history as well as the records of commerce and industry and great family and estate collections.
Parasites of the genera Plasmodium and Haemoproteus (Apicomplexa: Haemosporida) are a diverse group of pathogens that infect birds nearly worldwide. Despite their ubiquity, the ecological and evolutionary factors that shape the diversity and distribution of these protozoan parasites among avian communities and geographic regions are poorly understood. Based on a survey throughout the Neotropics of the haemosporidian parasites infecting manakins (Pipridae), a family of Passerine birds endemic to this region, we asked whether host relatedness, ecological similarity and geographic proximity structure parasite turnover between manakin species and local manakin assemblages. We used molecular methods to screen 1343 individuals of 30 manakin species for the presence of parasites. We found no significant correlations between manakin parasite lineage turnover and both manakin species turnover and geographic distance. Climate differences, species turnover in the larger bird community and parasite lineage turnover in non-manakin hosts did not correlate with manakin parasite lineage turnover. We also found no evidence that manakin parasite lineage turnover among host species correlates with range overlap and genetic divergence among hosts. Our analyses indicate that host switching (turnover among host species) and dispersal (turnover among locations) of haemosporidian parasites in manakins are not constrained at this scale.
Dense, controlled-impedance, superconducting cables with small cross-sections are desirable, especially for quantum computing applications. In this study, superconductivity properties, rf microwave response and mechanical reliability performance of embedded Nb dc cables and Nb microstrip transmission line resonators with different thicknesses of polyimide PI-2611 encapsulation layers (0, 4 and 8 μm) have been investigated. Critical temperature (Tc) and critical current (Ic) of embedded Nb dc cables are ∼ 8.2 K and ∼ 0.2 A, respectively. Embedded Nb resonators yield high loaded quality factor (QL), with values as high as 14481 at ∼ 1.2 K and at a fundamental resonance of ∼ 2 GHz. From mechanical fatigue testing, we have observed that a polyimide encapsulation layer can effectively enhance the mechanical reliability of superconducting Nb flexible cables.
Aberrant microbiota composition and function have been linked to several pathologies, including type 2 diabetes. In animal models, prebiotics induce favourable changes in the intestinal microbiota, intestinal permeability (IP) and endotoxaemia, which are linked to concurrent improvement in glucose tolerance. This is the first study to investigate the link between IP, glucose tolerance and intestinal bacteria in human type 2 diabetes. In all, twenty-nine men with well-controlled type 2 diabetes were randomised to a prebiotic (galacto-oligosaccharide mixture) or placebo (maltodextrin) supplement (5·5 g/d for 12 weeks). Intestinal microbial community structure, IP, endotoxaemia, inflammatory markers and glucose tolerance were assessed at baseline and post intervention. IP was estimated by the urinary recovery of oral 51Cr-EDTA and glucose tolerance by insulin-modified intravenous glucose tolerance test. Intestinal microbial community analysis was performed by high-throughput next-generation sequencing of 16S rRNA amplicons and quantitative PCR. Prebiotic fibre supplementation had no significant effects on clinical outcomes or bacterial abundances compared with placebo; however, changes in the bacterial family Veillonellaceae correlated inversely with changes in glucose response and IL-6 levels (r −0·90, P=0·042 for both) following prebiotic intake. The absence of significant changes to the microbial community structure at a prebiotic dosage/length of supplementation shown to be effective in healthy individuals is an important finding. We propose that concurrent metformin treatment and the high heterogeneity of human type 2 diabetes may have played a significant role. The current study does not provide evidence for the role of prebiotics in the treatment of type 2 diabetes.
There is limited evidence of the prevalence of enteric protozoon infections in developed settings. We estimated the prevalence of enteric protozoa and evaluated the outcome of testing algorithms used in hospital settings in Sydney, Australia. This retrospective study assessed microbiological data from four public clinical laboratories. Pooled data from the four hospitals revealed the most common enteric protozoon detected was Blastocystis spp. in an average of 5·4% of cases, followed by Giardia intestinalis (1·1%) and Dientamoeba fragilis (0·8%). Protozoon detection rates between hospitals were significantly different and could be based on multiple factors. The modified iron haematoxylin staining method, consistently detected higher rates of Blastocystis spp., and G. intestinalis in comparison with microscopy of wet preparations, as well as higher rates of G. intestinalis and Cryptosporidium when compared with enzyme immunoassay. The study concludes that there are multiple factors that contribute to the variability in protozoa detection rates in metropolitan hospitals, including widespread variability in the testing protocols for enteric protozoa, individual and population characteristics. A gold standard approach for diagnosis of enteric protozoa is recommended. Molecular diagnostic methods such as polymerase chain reaction would provide consistency across laboratories and yield more reliable estimates of the actual prevalence of enteric protozoa.
Radiocarbon measurements were begun at Sharp Laboratories in the spring of 1962 with the construction of a complete C14 dating laboratory. This first system used the method described by Fairhall, Schell, and Takashima (1961) for the conversion of CO2 to methane via ruthenium catalyst. This system proved to be fast and reliable, giving overall yields of solid sample to counting gas of better than 90% for the total conversion and purification (the conversion yield of CO2 to methane is quantitative). The detector in present use is 2 L, with construction materials consisting solely of O.F.H.C. copper, teflon, and epoxy resin. The shield consists of 4 in. of high purity lead (specially prepared), 4 in. of borated hydrogenous neutron moderator, a guard counter (cosmic ray detector), and 1 in. of ultra pure mercury. The gross to net ratio obtained with this system averages about 53. The background, for P in cm methane pressure, is:
Angiostrongylus cantonensis is a metastrongyloid nematode found widely in the Asia-Pacific region, and the aetiological agent of angiostrongyliasis; a disease characterized by eosinophilic meningitis. Rattus rats are definitive hosts of A. cantonensis, while intermediate hosts include terrestrial and aquatic molluscs. Humans are dead-end hosts that usually become infected upon ingestion of infected molluscs. A presumptive diagnosis is often made based on clinical features, a history of mollusc consumption, eosinophilic pleocytosis in cerebral spinal fluid, and advanced imaging such as computed tomography. Serological tests are available for angiostrongyliasis, though many tests are still under development. While there is no treatment consensus, therapy often includes a combination of anthelmintics and corticosteroids. Angiostrongyliasis is relatively rare, but is often associated with morbidity and sometimes mortality. Recent reports suggest the parasites’ range is increasing, leading to fatalities in regions previously considered Angiostrongylus-free, and sometimes, delayed diagnosis in newly invaded regions. Increased awareness of angiostrongyliasis would facilitate rapid diagnosis and improved clinical outcomes. This paper summarizes knowledge on the parasites’ life cycle, clinical aspects and epidemiology. The molecular biology of Angiostrongylus spp. is also discussed. Attention is paid to the significance of angiostrongyliasis in Australia, given the recent severe cases reported from the Sydney region.
Cosmology is one of the most dynamically evolving areas of astrophysics today. Twenty years ago the estimates of the amplitude of the primordial fluctuations were about 10-3, almost a factor of 100 off of today’s measurements. Ten years ago we could only hope for high precision measurements of large scale structure, there were less than 5000 redshifts measured, and only a handful of normal galaxies with z > 1 were known. Computer models of structure formation had just begun to consider non-power-law spectra based on physical models like hot/cold dark matter. As a consequence there was considerable freedom in adjusting parameters in the various galaxy formation scenarios. In contrast, many of today’s debates are about factors of 2 and soon we will be arguing about 10% differences. The Harrison-Zeldovich shape of the primordial fluctuation spectrum, first derived from philosophical arguments can now be quantified from detections of fluctuations by COBE. The number of available redshifts is beyond 50,000, and soon we will have redshift surveys surpassing 1 million galaxies. N-body simulations are becoming more sophisticated, of higher resolution, and incorporating complex gas dynamics.
Clostridium difficile infection (CDI) in hospitalized patients is generally attributed to the current stay, but recent studies reveal high C. difficile colonization rates on admission.
To determine the rate of colonization with toxigenic C. difficile among intensive care unit patients upon admission as well as acquired during hospitalization, and the risk of subsequent CDI.
Prospective cohort study from April 15 through July 8, 2013. Adults admitted to an intensive care unit within 48 hours of admission to the Johns Hopkins Hospital, Baltimore, Maryland, were screened for colonization with toxigenic C. difficile. The primary outcome was risk of developing CDI.
Among 542 patients, 17 (3.1%) were colonized with toxigenic C. difficile on admission and an additional 3 patients were found to be colonized during hospitalization. Both colonization with toxigenic C. difficile on admission and colonization during hospitalization were associated with an increased risk for development of CDI (relative risk, 10.29 [95% CI, 2.24–47.40], P=.003; and 15.66 [4.01–61.08], P<.001, respectively). Using multivariable analysis, colonization on admission and colonization during hospitalization were independent predictors of CDI (relative risk, 8.62 [95% CI, 1.48–50.25], P=.017; and 10.93 [1.49–80.20], P=.019, respectively), while adjusting for potential confounders.
In intensive care unit patients, colonization with toxigenic C. difficile is an independent risk factor for development of subsequent CDI. Further studies are needed to identify populations with higher toxigenic C. difficile colonization rates possibly benefiting from screening or avoidance of agents known to promote CDI.
Infect. Control Hosp. Epidemiol. 2015;36(11):1324–1329
We compared findings of an audit of New Zealand's version of the second opinion appointed doctor (SOAD) scheme with published information on the equivalent scheme for England and Wales, to consider what might be learnt from the different jurisdictions' experience.
Strong similarities exist between the two schemes in the demographic profile of individuals subject to the SOAD process and rates of approval of compulsory treatment. The clearer legal framework for the English scheme and its supervision by an independent national agency may offer significant advantages in terms of consistency and transparency, compared with the informal, decentralised structure of New Zealand's scheme.
Clinicians may not always favour greater formality or elaborate national structures for administering the Mental Health Act, but there are advantages in promoting clarity and consistency in a mandatory statutory process designed to protect compulsory patients' rights.
In 31 patients, Phaeoacremonium parasiticum was recovered from bronchoscopy specimens (biopsies and aspirates). The pseudo-outbreak was caused by contaminated ice used to control hemorrhage during bronchoscopy and was associated with deficiencies in equipment cleaning. The bronchoscopy technique was modified, the ice dispenser was disinfected, bronchoscope reprocessing was improved, and there were no recurrences.
Infect Control Hosp Epidemiol 2014;35(8):1063–1065
The “methods of barbarism” and the “rights of small nations” are perhaps the most recognizable of British slogans arising out of the wars of the early twentieth century. They are instantly associated with the Boer War and the First World War respectively, but seldom are they associated with each other. However, the Pro-Boer rhetoric of “the methods of barbarism” and the First World War propaganda of “the rights of small nations” are intimately linked through their roots in the pluralist Liberal vision of Britishness.
These slogans and the propaganda campaigns that they epitomized must be understood within the context of a multicultural Britain and opposing notions of British national identity. Defining “barbarism” as the oppression of small nations through the brutal use of force, the Pro-Boers associated the term with the Anglocentric vision of the British nation reflected in the “New Imperialism” of the Conservatives. Through their belief in Anglo-Saxon racial superiority, the Conservative imperialists maintained that small nations like those of the Irish, the Welsh, and the Boers would either be assimilated or swept aside by the historical progress of an expanding Anglo-Saxon nation state. In contrast to this notion of Conservative “barbarism,” the Pro-Boer Liberals drew on the Gladstonian heritage of their party in defining the United Kingdom as a multinational state at the center of a multinational empire. They eschewed the use of force in the maintenance of empire and argued that the bonds of imperialism must be based upon mutual goodwill, voluntarism, and the recognition of the principle of nationality.
When the First World War broke out in 1914, propagandists drew upon these contrasting constructions of Liberal cultural pluralism and Conservative cultural uniformity. In terms similar to those employed by the Pro-Boers, British propagandists depicted the First World War as a struggle against German “barbarism” and as a fight to vindicate the “rights of small nations.” Solidly based upon the Liberal construction of the multicultural and multinational nature of Britishness, Britain's role as the champion of the principle of nationality was proclaimed with an eye not only to the international context of Europe but to the domestic context of the British state and empire as well.
Objective: We sought to determine the prevalence of attention-deficit/hyperactivity disorder in a population of children who underwent neonatal heart surgery involving repair of the aortic arch for Norwood Stage I, interrupted aortic arch, and combined repair of aortic coarctation with ventricular septal defect. Methods: Children between the ages of 5 and 16 were surveyed using the ADHD-IV and the Child Heath Questionnaire-50. Classification as attention-deficit/hyperactivity disorder was defined for this study as either a parent-reported diagnosis of attention-deficit/hyperactivity disorder or ADHD-IV inattention score of ⩾93 percentile. Results: Of the 134 surveys, 57 (43%) were returned completed. A total of 25 (44%) children either had a diagnosis of attention-deficit/hyperactivity disorder and/or ADHD-IV inattention score ⩾93 percentile. Eleven of the 13 (85%) children with interrupted aortic arch, 3 of the 7 (42.9%) children with combined coarctation/ventricular septal defect repair, and 9 of the 33 (27.3%) children with hypoplastic left-heart syndrome were classified as having attention-deficit/hyperactivity disorder. Only 7 of the 25 (28%) children received medical treatment for this condition. Quality of life indicators in the Child Heath Questionnaire-50 Questionnaire were highly correlated with the ADHD-IV scores. Conclusion: The risks for the development of attention-deficit/hyperactivity disorder are multifactorial but are significantly increased in this post-surgical population. This study revealed a low treatment rate for attention-deficit/hyperactivity disorder, and a significant impact on the quality of life in these children.