Prognosis of HIV-1-infected patients up to 5 years after initiation of HAART: collaborative analysis of prospective studies

OBJECTIVE: To estimate the prognosis over 5 years of HIV-1-infected, treatment-naive patients starting HAART, taking into account the immunological and virological response to therapy. DESIGN: A collaborative analysis of data from 12 cohorts in Europe and North America on 20,379 adults who started HAART between 1995 and 2003. METHODS: Parametric survival models were used to predict the cumulative incidence at 5 years of a new AIDS-defining event or death, and death alone, first from the start of HAART and second from 6 months after the start of HAART. Data were analysed by intention-to-continue-treatment, ignoring treatment changes and interruptions. RESULTS: During 61 798 person-years of follow-up, 1005 patients died and an additional 1303 developed AIDS. A total of 10 046 (49%) patients started HAART either with a CD4 cell count of less than 200 cells/microl or with a diagnosis of AIDS. The 5-year risk of AIDS or death (death alone) from the start of HAART ranged from 5.6 to 77% (1.8-65%), depending on age, CD4 cell count, HIV-1-RNA level, clinical stage, and history of injection drug use. From 6 months the corresponding figures were 4.1-99% for AIDS or death and 1.3-96% for death alone. CONCLUSION: On the basis of data collected routinely in HIV care, prognostic models with high discriminatory power over 5 years were developed for patients starting HAART in industrialized countries. A risk calculator that produces estimates for progression rates at years 1 to 5 after starting HAART is available from www.art-cohort-collaboration.org.

Influence of beveling and ultrasound application on marginal adaptation of box-only Class II (slot) resin composite restorations

A laboratory study was performed to assess the influence of beveling the margins of cavities and the effects on marginal adaptation of the application of ultrasound during setting and initial light curing. After minimal access cavities had been prepared with an 80 microm diamond bur, 80 box-only Class II cavities were prepared mesially and distally in 40 extracted human molars using four different oscillating diamond coated instruments: (A) a U-shaped PCS insert as the non-beveled control (EMS), (B) Bevelshape (Intensiv), (C) SonicSys (KaVo) and (D) SuperPrep (KaVo). In groups B-D, the time taken for additional bevel finishing was measured. The cavities were filled with a hybrid composite material in three increments. Ultrasound was also applied to one cavity per tooth before and during initial light curing (10 seconds). The specimens were subjected to thermomechanical stress in a computer-controlled masticator device. Marginal quality was assessed by scanning electron microscopy and the results were compared statistically. The additional time required for finishing was B > D > C (p < or = 0.05). In all groups, thermomechanical loading resulted in a decrease in marginal quality. Beveling resulted in higher values for "continuous" margins compared with that of the unbeveled controls. The latter showed better marginal quality at the axial walls when ultrasound was used. Beveling seems essential for good marginal adaptation but requires more preparation time. The use of ultrasonic vibrations may improve the marginal quality of unbeveled fillings and warrants further investigation.

Distinguishing phenotypes of childhood wheeze and cough using latent class analysis

Airway disease in childhood comprises a heterogeneous group of disorders. Attempts to distinguish different phenotypes have generally considered few disease dimensions. The present study examines phenotypes of childhood wheeze and chronic cough, by fitting a statistical model to data representing multiple disease dimensions. From a population-based, longitudinal cohort study of 1,650 preschool children, 319 with parent-reported wheeze or chronic cough were included. Phenotypes were identified by latent class analysis using data on symptoms, skin-prick tests, lung function and airway responsiveness from two preschool surveys. These phenotypes were then compared with respect to outcome at school age. The model distinguished three phenotypes of wheeze and two phenotypes of chronic cough. Subsequent wheeze, chronic cough and inhaler use at school age differed clearly between the five phenotypes. The wheeze phenotypes shared features with previously described entities and partly reconciled discrepancies between existing sets of phenotype labels. This novel, multidimensional approach has the potential to identify clinically relevant phenotypes, not only in paediatric disorders but also in adult obstructive airway diseases, where phenotype definition is an equally important issue.

Multivariate modelling of responses to conditional items: New possibilities for latent class analysis

Questionnaire data may contain missing values because certain questions do not apply to all respondents. For instance, questions addressing particular attributes of a symptom, such as frequency, triggers or seasonality, are only applicable to those who have experienced the symptom, while for those who have not, responses to these items will be missing. This missing information does not fall into the category 'missing by design', rather the features of interest do not exist and cannot be measured regardless of survey design. Analysis of responses to such conditional items is therefore typically restricted to the subpopulation in which they apply. This article is concerned with joint multivariate modelling of responses to both unconditional and conditional items without restricting the analysis to this subpopulation. Such an approach is of interest when the distributions of both types of responses are thought to be determined by common parameters affecting the whole population. By integrating the conditional item structure into the model, inference can be based both on unconditional data from the entire population and on conditional data from subjects for whom they exist. This approach opens new possibilities for multivariate analysis of such data. We apply this approach to latent class modelling and provide an example using data on respiratory symptoms (wheeze and cough) in children. Conditional data structures such as that considered here are common in medical research settings and, although our focus is on latent class models, the approach can be applied to other multivariate models.

Guidelines for the use and interpretation of assays for monitoring cell death in higher eukaryotes

Cell death is essential for a plethora of physiological processes, and its deregulation characterizes numerous human diseases. Thus, the in-depth investigation of cell death and its mechanisms constitutes a formidable challenge for fundamental and applied biomedical research, and has tremendous implications for the development of novel therapeutic strategies. It is, therefore, of utmost importance to standardize the experimental procedures that identify dying and dead cells in cell cultures and/or in tissues, from model organisms and/or humans, in healthy and/or pathological scenarios. Thus far, dozens of methods have been proposed to quantify cell death-related parameters. However, no guidelines exist regarding their use and interpretation, and nobody has thoroughly annotated the experimental settings for which each of these techniques is most appropriate. Here, we provide a nonexhaustive comparison of methods to detect cell death with apoptotic or nonapoptotic morphologies, their advantages and pitfalls. These guidelines are intended for investigators who study cell death, as well as for reviewers who need to constructively critique scientific reports that deal with cellular demise. Given the difficulties in determining the exact number of cells that have passed the point-of-no-return of the signaling cascades leading to cell death, we emphasize the importance of performing multiple, methodologically unrelated assays to quantify dying and dead cells.

Immuno-detection of anthrose containing tetrasaccharide in the exosporium of Bacillus anthracis and Bacillus cereus strains

AIMS: Bacillus anthracis strains of various origins were analysed with the view to describe intrinsic and persistent structural components of the Bacillus collagen-like protein of anthracis glycoprotein associated anthrose containing tetrasaccharide in the exosporium. METHODS AND RESULTS: The tetrasaccharide consists of three rhamnose residues and an unique monosaccharide--anthrose. As anthrose was not found in spores of related strains of bacteria, we envisioned the detection of B. anthracis spores based on antibodies against anthrose-containing polysaccharides. Carbohydrate-protein conjugates containing the synthetic tetrasaccharide, an anthrose-rhamnose disaccharide or anthrose alone were employed to immunize mice. All three formulations were immunogenic and elicited IgG responses with different fine specificities. All sera and monoclonal antibodies derived from tetrasaccharide immunized mice cross-reacted not only with spore lysates of a panel of virulent B. anthracis strains, but also with some of the B. cereus strains tested. CONCLUSIONS: Our results demonstrate that antibodies to synthetic carbohydrates are useful tools for epitope analyses of complex carbohydrate antigens and for the detection of particular target structures in biological specimens. SIGNIFICANCE AND IMPACT OF THE STUDY: Although not strictly specific for B. anthracis spores, antibodies against the tetrasaccharide may have potential as immuno-capturing components for a highly sensitive spore detection system.

Proceedings of the Twelfth Annual Biochemical Engineering Symposium

This work presents the proceedings of the twelfth symposium which was held at Kansas State University on April 24, 1982. Since a number of the contributions will be published in detail elsewhere, only brief reports are included here. Some of the reports describe current progress with respect to ongoing projects. Requests for further information should be directed to Dr. Peter Reilly at Iowa State University, Dr. V. G. Murphy at Colorado State University, Dr. Rakesh Bajpai at University of Missouri, Dr. Ed Clausen at University of Arkansas, Dr. L. T. Fan and Dr. L. E. Erickson at Kansas State University. ContentsA Kinetic Analysis of Oleaginous Yeast Fermentation by Candida curvata on Whey Permeate, B.D. Brown and K.H. Hsu, Iowa State University Kinetics of Biofouling in Simulated Water Distribution Systems Using CSTR, T.M. Prakash, University of Missouri Kinetics of Gas Production by C. acetobutylicum, Michael Doremus, Colorado State University Large Scale Production of Methane from Agricultural Residues, O.P. Doyle, G.C. Magruder, E.C. Clausen, and J.L. Gaddy, University of Arkansas The Optimal Process Design for Enzymatic Hydrolysis of Wheat Straw, M.M Gharpuray and L.T. Fan, Kansas State University Extractive Butanol Fermentation, Michael Sierks, Colorado State University Yields Associated with Ethyl Alcohol Production, M.D. Oner, Kansas State University Estimation of Growth Yield and Maintenance Parameters for Microbial Growth on Corn Dust, B.O. Solomon, Kansas State University Milling of Ensiled Corn, Andrzej Neryng, Iowa State University Protein Extraction from Alfalfa, Ravidranath Joshi, Colorado State University Analysis of Disaccharides by Capillary Gas Chromatography, Z.L. Nikolov, Iowa State University Characterization of High Viscosity Fermentations in Tower Fermentors, S.A. Patel and C.H. Lee, Kansas State University Utilization of Sugars in Sorghum Molasses by Clostridium acetobutylicum B. Hong, K.C. Shin, and L.T. Fan, Kansas State University

Flavor-phenomenology of two-Higgs-doublet models with generic Yukawa structure

In this article, we perform an extensive study of flavor observables in a two-Higgs-doublet model with generic Yukawa structure (of type III). This model is interesting not only because it is the decoupling limit of the minimal supersymmetric standard model but also because of its rich flavor phenomenology which also allows for sizable effects not only in flavor-changing neutral-current (FCNC) processes but also in tauonic B decays. We examine the possible effects in flavor physics and constrain the model both from tree-level processes and from loop observables. The free parameters of the model are the heavy Higgs mass, tanβ (the ratio of vacuum expectation values) and the “nonholomorphic” Yukawa couplings ϵfij(f=u,d,ℓ). In our analysis we constrain the elements ϵfij in various ways: In a first step we give order of magnitude constraints on ϵfij from ’t Hooft’s naturalness criterion, finding that all ϵfij must be rather small unless the third generation is involved. In a second step, we constrain the Yukawa structure of the type-III two-Higgs-doublet model from tree-level FCNC processes (Bs,d→μ+μ−, KL→μ+μ−, D¯¯¯0→μ+μ−, ΔF=2 processes, τ−→μ−μ+μ−, τ−→e−μ+μ− and μ−→e−e+e−) and observe that all flavor off-diagonal elements of these couplings, except ϵu32,31 and ϵu23,13, must be very small in order to satisfy the current experimental bounds. In a third step, we consider Higgs mediated loop contributions to FCNC processes [b→s(d)γ, Bs,d mixing, K−K¯¯¯ mixing and μ→eγ] finding that also ϵu13 and ϵu23 must be very small, while the bounds on ϵu31 and ϵu32 are especially weak. Furthermore, considering the constraints from electric dipole moments we obtain constrains on some parameters ϵu,ℓij. Taking into account the constraints from FCNC processes we study the size of possible effects in the tauonic B decays (B→τν, B→Dτν and B→D∗τν) as well as in D(s)→τν, D(s)→μν, K(π)→eν, K(π)→μν and τ→K(π)ν which are all sensitive to tree-level charged Higgs exchange. Interestingly, the unconstrained ϵu32,31 are just the elements which directly enter the branching ratios for B→τν, B→Dτν and B→D∗τν. We show that they can explain the deviations from the SM predictions in these processes without fine-tuning. Furthermore, B→τν, B→Dτν and B→D∗τν can even be explained simultaneously. Finally, we give upper limits on the branching ratios of the lepton flavor-violating neutral B meson decays (Bs,d→μe, Bs,d→τe and Bs,d→τμ) and correlate the radiative lepton decays (τ→μγ, τ→eγ and μ→eγ) to the corresponding neutral current lepton decays (τ−→μ−μ+μ−, τ−→e−μ+μ− and μ−→e−e+e−). A detailed Appendix contains all relevant information for the considered processes for general scalar-fermion-fermion couplings.

SUSYFLAVOR v2: A Computational tool for FCNC and CP-violating processes in the MSSM

We present SUSY_FLAVOR version 2 — a Fortran 77 program that calculates low-energy flavor observables in the general R-parity conserving MSSM. For a set of MSSM parameters as input, the code gives predictions for: 1. Electric dipole moments of the leptons and the neutron. 2. Anomalous magnetic moments (i.e. g − 2) of the leptons. 3. Radiative lepton decays (μ → eγ and τ → μγ , eγ ). 4. Rare Kaon decays (K0 L → π0 ¯νν and K+ → π+ ¯νν). 5. Leptonic B decays (Bs,d → l+l−, B → τ ν and B → Dτ ν). 6. Radiative B decays (B → ¯ Xsγ ). 7. ΔF = 2 processes ( ¯ K0–K0, ¯D–D, ¯Bd–Bd and ¯Bs–Bs mixing). Comparing to SUSY_FLAVOR v1, where the matching conditions were calculated strictly at one-loop level, SUSY_FLAVOR v2 performs the resummation of all chirally enhanced corrections, i.e. takes into account the enhanced effects from tan β and/or large trilinear soft mixing terms to all orders in perturbation theory. Also, in SUSY_FLAVOR v2 new routines calculation of B → (D)τ ν, g − 2, radiative lepton decays and Br(l → l′γ ) were added. All calculations are done using exact diagonalization of the sfermion mass matrices. The program can be obtained from http://www.fuw.edu.pl/susy_flavor.

Addendum: search for ν μ → ν e oscillations with the OPERA experiment in the CNGS beam

A first result of the search for ν ( )μ( ) → ν ( )e( ) oscillations in the OPERA experiment, located at the Gran Sasso Underground Laboratory, is presented. The experiment looked for the appearance of ν ( )e( ) in the CNGS neutrino beam using the data collected in 2008 and 2009. Data are compatible with the non-oscillation hypothesis in the three-flavour mixing model. A further analysis of the same data constrains the non-standard oscillation parameters θ (new) and suggested by the LSND and MiniBooNE experiments. For large values (>0.1 eV(2)), the OPERA 90% C.L. upper limit on sin(2)(2θ (new)) based on a Bayesian statistical method reaches the value 7.2 × 10(−3).

New results on ν μ → ν τ appearance with the OPERA experiment in the CNGS beam

The OPERA neutrino experiment is designed to perform the first observation of neutrino oscillations in direct appearance mode in the νμ→ντ channel, via the detection of the τ-leptons created in charged current ντ interactions. The detector, located in the underground Gran Sasso Laboratory, consists of an emulsion/lead target with an average mass of about 1.2 kt, complemented by electronic detectors. It is exposed to the CERN Neutrinos to Gran Sasso beam, with a baseline of 730 km and a mean energy of 17 GeV. The observation of the first ντ candidate event and the analysis of the 2008-2009 neutrino sample have been reported in previous publications. This work describes substantial improvements in the analysis and in the evaluation of the detection efficiencies and backgrounds using new simulation tools. The analysis is extended to a sub-sample of 2010 and 2011 data, resulting from an electronic detector-based pre-selection, in which an additional ντ candidate has been observed. The significance of the two events in terms of a νμ→ντ oscillation signal is of 2.40 σ.

Polonofilizm i polskość wśród czeskich emancypantek w drugiej połowie XIX wieku: przykład Karoliny Světlej

The awakening of national consciousness went hand in hand in Bohemia with an anxiety about national disappearance. In this context, the recourse to Pan-Slavism was for the Czechs a way to encourage themselves through the idea of belonging to a great Slavic world, while the Slavic Congress organized in Prague in 1848 was an attempt to realize this ideal. The Congress was a failure from the political point of view, but it did have some socio-cultural repercussions: notably, it served as a pretext for the advancement of women's issues in Bohemia. It is indeed in the wake of the Congress that Honorata z Wiśniowskich Zapová, a Polish women settled in Prague after her marriage to a Czech intellectual, founded, under the guise of collaboration between all Slavic women, the first women's association, as well as a (very short-lived) Czech-Polish institute, where Czech, as well as Polish girls, could get a quality education in their mother tongue. Honorata was undoubtedly the source of the polonophilia wind that seemed to blow over the Czech emancipation movement in the second half of the nineteenth century. In particular, Karolina Světlá showed in her Memoirs a great recognition for Honorata's efforts in matters of emancipation and education, and explicitly took up the challenge launched by the latter in founding another women's association and in inaugurating a school for underprivileged girls. But the tribute Světlá paid to Honorata is even more evident in her literary work, where Poland and the Polish woman (who often wears Honorata's features) play a significant role (see for example her short novel Sisters or her story A Few Days in the Life of a Prague Dandy). Světlá was probably the Czech feminist writer who, in her activities and in her work, relied most strongly on the Polish woman as a model for the Czech woman. However, she wasn't alone. In general, it was a characteristic of the Czech feminist movement of the second half of the nineteenth century to have recourse to the Polish woman and to Poland as a landmark for comparison and as a goal to be achieved.

DYPTOP: a cost-efficient TOPMODEL implementation to simulate sub-grid spatio-temporal dynamics of global wetlands and peatlands

Simulating the spatio-temporal dynamics of inundation is key to understanding the role of wetlands under past and future climate change. Earlier modelling studies have mostly relied on fixed prescribed peatland maps and inundation time series of limited temporal coverage. Here, we describe and assess the the Dynamical Peatland Model Based on TOPMODEL (DYPTOP), which predicts the extent of inundation based on a computationally efficient TOPMODEL implementation. This approach rests on an empirical, grid-cell-specific relationship between the mean soil water balance and the flooded area. DYPTOP combines the simulated inundation extent and its temporal persistency with criteria for the ecosystem water balance and the modelled peatland-specific soil carbon balance to predict the global distribution of peatlands. We apply DYPTOP in combination with the LPX-Bern DGVM and benchmark the global-scale distribution, extent, and seasonality of inundation against satellite data. DYPTOP successfully predicts the spatial distribution and extent of wetlands and major boreal and tropical peatland complexes and reveals the governing limitations to peatland occurrence across the globe. Peatlands covering large boreal lowlands are reproduced only when accounting for a positive feedback induced by the enhanced mean soil water holding capacity in peatland-dominated regions. DYPTOP is designed to minimize input data requirements, optimizes computational efficiency and allows for a modular adoption in Earth system models.