Centre-specific bacterial pathogen typing affects infection-control decision making

Whole-genome sequencing is becoming the de facto standard for bacterial outbreak surveillance and infection prevention. This is accompanied by a variety of bioinformatic tools and needs bioinformatics expertise for implementation. However, little is known about the concordance of reported outbreaks when using different bioinformatic workflows. In this multi-centre proficiency testing among 13 major Dutch healthcare-affiliated centres, bacterial whole-genome outbreak analysis was assessed. Centres who participated obtained two randomized bacterial datasets of Illumina sequences, a Klebsiella pneumoniae and a Vancomycin-resistant Enterococcus faecium, and were asked to apply their bioinformatic workflows. Centres reported back on antimicrobial resistance, multi-locus sequence typing (MLST), and outbreak clusters. The reported clusters were analysed using a method to compare landscapes of phylogenetic trees and calculating Kendall–Colijn distances. Furthermore, fasta files were analysed by state-of-the-art single nucleotide polymorphism (SNP) analysis to mitigate the differences introduced by each centre and determine standardized SNP cut-offs. Thirteen centres participated in this study. The reported outbreak clusters revealed discrepancies between centres, even when almost identical bioinformatic workflows were used. Due to stringent filtering, some centres failed to detect extended-spectrum beta-lactamase genes and MLST loci. Applying a standardized method to determine outbreak clusters on the reported de novo assemblies, did not result in uniformity of outbreak-cluster composition among centres

Theory of anyon excitons: Relation to excitons of nu=1/3 and nu=2/3 incompressible liquids

Elementary excitations of incompressible quantum liquids (IQL's) are anyons, i.e., quasiparticles carrying fractional charges and obeying fractional statistics. To find out how the properties of these quasiparticles manifest themselves in the optical spectra, we have developed the anyon exciton model (AEM) and compared the results with the finite-size data for excitons of nu=1/3 and nu=2/3 IQL's. The model considers an exciton as a neutral composite consisting of three quasielectrons and a single hole. The AEM works well when the separation between electron and hole confinement planes, h, is larger than the magnetic length l. In the framework of the AEM an exciton possesses momentum k and two internal quantum numbers, one of which can be chosen as the angular momentum, L, of the k=0 state. Existence of the internal degrees of freedom results in the multiple branch energy spectrum, crater-like electron density shape and 120 degrees density correlations for k=0 excitons, and the splitting of the electron shell into bunches for non-zero k excitons. For h larger than 2l the bottom states obey the superselection rule L=3m (m are integers starting from 2), all of them are hard core states. For h nearly 2l there is one-to-one correspondence between the low-energy spectra found for the AEM and the many- electron exciton spectra of the nu=2/3 IQL, whereas some states are absent from the many-electron spectra of the nu=1/3 IQL. We argue that this striking difference in the spectra originates from the different populational statistics of the quasielectrons of charge conjugate IQL's and show that the proper account of the statistical requirements eliminates excessive states from the spectrum. Apparently, this phenomenon is the first manifestation of the exclusion statistics in the anyon bound states.Comment: 26 pages with 9 figures, typos correcte

Anorgasmia in women

This article reports on the etiology and treatment of anorgasmia. Etiological factors include childhood and adolescent experiences, current individual attitudes, and lifestyle factors, as well as the quality and dynamics of past and present committed relationships. It is important to assess the nature of each of the previously mentioned factors in determining the nature of the orgasmic dysfunction as well as assisting in the development of a treatment plan. Treatment approaches for anorgasmia need to address individual factors (e.g., performance anxiety, poor body image) as well as interpersonal problems. A systemic treatment framework would appear to be the most useful approach to treat this sexual dysfunction, as this type of strategy identifies and treats the difficulties experienced by the anorgasmic woman within the total context of her life. Of course, this approach necessitates the involvement of the partner in therapy, and treatment is unlikely to be effective unless the problems experienced by both the woman and her partner are addressed. Limitations of past research in terms of inadequate evaluation of treatment, low sample sizes, and poorly defined interventions are discussed. Finally, directions for future research to advance our understanding of the most effective treatments for anorgasmia are considered. <br /

Theory of Photoluminescence of the ν=1\nu=1 Quantum Hall State: Excitons, Spin-Waves and Spin-Textures

We study the theory of intrinsic photoluminescence of two-dimensional electron systems in the vicinity of the $\nu=1$ quantum Hall state. We focus predominantly on the recombination of a band of initial ``excitonic states'' that are the low-lying energy states of our model at $\nu=1$. It is shown that the recombination of excitonic states can account for recent observations of the polarization-resolved spectra of a high-mobility GaAs quantum well. The asymmetric broadening of the spectral line in the $\sigma_-$ polarization is explained to be the result of the ``shake-up'' of spin-waves upon radiative recombination of excitonic states. We derive line shapes for the recombination of excitonic states in the presence of long-range disorder that compare favourably with the experimental observations. We also discuss the stabilities and recombination spectra of other (``charged'') initial states of our model. An additional high-energy line observed in experiment is shown to be consistent with the recombination of a positively-charged state. The recombination spectrum of a negatively-charged initial state, predicted by our model but not observed in the present experiments, is shown to provide a direct measure of the formation energy of the smallest ``charged spin-texture'' of the $\nu=1$ state.Comment: 23 pages, 7 postscript figures included. Revtex with epsf.tex and multicol.sty. The revised version contains slightly improved numerical results and a few additional discussions of the result

Multi-drug resistant Vibrio cholerae O1 variant El Tor isolated in northern Vietnam between 2007 and 2010

Since 2007, there has been a re-emergence of cholera outbreaks in northern Vietnam. To understand the molecular epidemiological relatedness and determine the antibiotic susceptibility profiles of responsible V. cholerae O1 outbreak strains, a representative collection of 100 V. cholerae O1 strains was characterized. V. cholerae O1 strains isolated from diarrhoeal patients in northern Vietnam between 2007 and 2010 were investigated for antibiotic susceptibility and characterized by using phenotypic and genotypic tests, including PFGE analysis. Ten clinical V. cholerae O1 isolates from Bangladesh and Zimbabwe were included for comparison. The results revealed that all isolates were resistant to co-trimoxazole and nalidixic acid, 29 % were resistant to tetracycline and 1 % were resistant to azithromycin. All strains were susceptible to ampicillin–sulbactam, doxycycline, chloramphenicol and ciprofloxacin and 95 % were susceptible to azithromycin. MIC values did show reduced susceptibility to fluoroquinolones and 63 % of the strains were intermediately resistant to tetracycline. The isolates expressed phenotypic traits of both serogroup O1 Ogawa and El Tor and harboured an rstR El Tor and ctxB classical biotype. Among the outbreak isolates, only a single PFGE pattern was observed throughout the study period. This study shows that multi-drug resistant V. cholerae altered El Tor producing classical CT strains are now predominant in northern Vietnam

Energy spectra of fractional quantum Hall systems in the presence of a valence hole

The energy spectrum of a two-dimensional electron gas (2DEG) in the fractional quantum Hall regime interacting with an optically injected valence band hole is studied as a function of the filling factor $\nu$ and the separation $d$ between the electron and hole layers. The response of the 2DEG to the hole changes abruptly at $d$ of the order of the magnetic length $\lambda$. At $d<\lambda$, the hole binds electrons to form neutral ($X$) or charged ($X^-$) excitons, and the photoluminescence (PL) spectrum probes the lifetimes and binding energies of these states rather than the original correlations of the 2DEG. The ``dressed exciton'' picture (in which the interaction between an exciton and the 2DEG was proposed to merely enhance the exciton mass) is questioned. Instead, the low energy states are explained in terms of Laughlin correlations between the constituent fermions (electrons and $X^-$'s) and the formation of two-component incompressible fluid states in the electron--hole plasma. At $d>2\lambda$, the hole binds up to two Laughlin quasielectrons (QE) of the 2DEG to form fractionally charged excitons $h$QE$_n$. The previously found ``anyon exciton'' $h$QE$_3$ is shown to be unstable at any value of $d$. The critical dependence of the stability of different $h$QE$_n$ complexes on the presence of QE's in the 2DEG leads to the observed discontinuity of the PL spectrum at $\nu={1\over3}$ or ${2\over3}$.Comment: 16 pages, 14 figures, submitted to PR

Seroprevalence of SARS-CoV-2 antibodies among healthcare workers in Dutch hospitals after the 2020 first wave:a multicentre cross-sectional study with prospective follow-up

BACKGROUND: We aimed to estimate the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seroprevalence and describe its determinants and associated symptoms among unvaccinated healthcare workers (HCWs) after the first wave of the pandemic.METHODS: HCWs from 13 Dutch hospitals were screened for antibodies against the spike protein of SARS-CoV-2 in June-July 2020 and after three months. Participants completed a retrospective questionnaire on determinants for occupational and community exposure to SARS-CoV-2 and symptoms suggestive of COVID-19 experienced since January 2020. The seroprevalence was calculated per baseline characteristic and symptom at baseline and after follow-up. Adjusted odds ratios (aOR) for seropositivity were determined using logistic regression.RESULTS: Among 2328 HCWs, 323 (13.9%) were seropositive at enrolment, 49 of whom (15%) reported no previous symptoms suggestive of COVID-19. During follow-up, only 1% of the tested participants seroconverted. Seroprevalence was higher in younger HCWs compared to the mid-age category (aOR 1.53, 95% CI 1.07-2.18). Nurses (aOR 2.21, 95% CI 1.34-3.64) and administrative staff (aOR 1.87, 95% CI 1.02-3.43) had a higher seroprevalence than physicians. The highest seroprevalence was observed in HCWs in the emergency department (ED) (aOR 1.79, 95% CI 1.10-2.91), the lowest in HCWs in the intensive, high, or medium care units (aOR 0.47, 95% CI 0.31-0.71). Chronic respiratory disease, smoking, and having a dog were independently associated with a lower seroprevalence, while HCWs with diabetes mellitus had a higher seroprevalence. In a multivariable model containing all self-reported symptoms since January 2020, altered smell and taste, fever, general malaise/fatigue, and muscle aches were positively associated with developing antibodies, while sore throat and chills were negatively associated.CONCLUSIONS: The SARS-CoV-2 seroprevalence in unvaccinated HCWs of 13 Dutch hospitals was 14% in June-July 2020 and remained stable after three months. A higher seroprevalence was observed in the ED and among nurses, administrative and young staff, and those with diabetes mellitus, while a lower seroprevalence was found in HCWs in intensive, high, or medium care, and those with self-reported lung disease, smokers, and dog owners. A history of altered smell or taste, fever, muscle aches and fatigue were independently associated with the presence of SARS-CoV-2 antibodies in unvaccinated HCWs.</p

Enterprise Education Competitions: A Theoretically Flawed Intervention?

The demand for including enterprise in the education system, at all levels and for all pupils is now a global phenomenon. Within this context, the use of competitions and competitive learning activities is presented as a popular and effective vehicle for learning. The purpose of this chapter is to illustrate how a realist method of enquiry – which utilises theory as the unit of analysis – can shed new light on the assumed and unintended outcomes of enterprise education competitions. The case developed here is that there are inherent flaws in assuming that competitions will ‘work’ in the ways set out in policy and guidance. Some of the most prevalent stated outcomes – that competitions will motivate and reward young people, that they will enable the development of entrepreneurial skills, and that learners will be inspired by their peers – are challenged by theory from psychology and education. The issue at stake is that the expansion of enterprise education policy into primary and secondary education increases the likelihood that more learners will be sheep dipped in competitions, and competitive activities, without a clear recognition of the potential unintended effects. In this chapter, we employ a realist-informed approach to critically evaluate the theoretical basis that underpins the use of competitions and competitive learning activities in school-based enterprise education. We believe that our findings and subsequent recommendations will provide those who promote and practice the use of competitions with a richer, more sophisticated picture of the potential flaws within such activities.Peer reviewedFinal Published versio

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types