Strong Agreement of Nationally Recommended Retention Measures from the Institute of Medicine and Department of Health and Human Services

Objective

We sought to quantify agreement between Institute of Medicine (IOM) and Department of Health and Human Services (DHHS) retention indicators, which have not been compared in the same population, and assess clinical retention within the largest HIV cohort collaboration in the U.S.

Design

Observational study from 2008–2010, using clinical cohort data in the North American AIDS Cohort Collaboration on Research and Design (NA-ACCORD).

Methods

Retention definitions used HIV primary care visits. The IOM retention indicator was: ≥2 visits, ≥90 days apart, each calendar year. This was extended to a 2-year period; retention required meeting the definition in both years. The DHHS retention indicator was: ≥1 visit each semester over 2 years, each ≥60 days apart. Kappa statistics detected agreement between indicators and C statistics (areas under Receiver-Operating Characteristic curves) from logistic regression analyses summarized discrimination of the IOM indicator by the DHHS indicator.

Results

Among 36,769 patients in 2008–2009 and 34,017 in 2009–2010, there were higher percentages of participants retained in care under the IOM indicator than the DHHS indicator (80% vs. 75% in 2008–2009; 78% vs. 72% in 2009–2010, respectively) (p<0.01), persisting across all demographic and clinical characteristics (p<0.01). There was high agreement between indicators overall (κ = 0.83 in 2008–2009; κ = 0.79 in 2009–2010, p<0.001), and C statistics revealed a very strong ability to predict retention according to the IOM indicator based on DHHS indicator status, even within characteristic strata.

Conclusions

Although the IOM indicator consistently reported higher retention in care compared with the DHHS indicator, there was strong agreement between IOM and DHHS retention indicators in a cohort demographically similar to persons living with HIV/AIDS in the U.S. Persons with poorer retention represent subgroups of interest for retention improvement programs nationally, particularly in light of the White House Executive Order on the HIV Care Continuum.     

A large-scale survey of genetic copy number variations among Han Chinese residing in Taiwan

Background

Winter migration of immature brown trout (Salmo trutta) into freshwater rivers has been hypothesized to result from physiologically stressful combinations of high salinity and low temperature in the sea.

Results

We sampled brown trout from two Danish populations entering different saline conditions and quantified expression of the hsp70 and Na/K-ATPases α 1b genes following acclimation to freshwater and full-strength seawater at 2°C and 10°C. An interaction effect of low temperature and high salinity on expression of both hsp70 and Na/K-ATPase α 1b was found in trout from the river entering high saline conditions, while a temperature independent up-regulation of both genes in full-strength seawater was found for trout entering marine conditions with lower salinities.

Conclusion

Overall our results support the hypothesis that physiologically stressful conditions in the sea drive sea-run brown trout into freshwater rivers in winter. However, our results also demonstrate intra-specific differences in expression of important stress and osmoregulative genes most likely reflecting adaptive differences between trout populations on a regional scale, thus strongly suggesting local adaptations driven by the local marine environment.     

Mycorrhizal-induced growth depression in plants

As plant mutualists, one would not expect arbuscular mycorrhizal fungi (AMF) to cause growth depression of their host plants. The mechanism responsible for negative effects of AMF is still debated and so here we review the possible abiotic and biotic reasons for AMF-induced growth depression in plants: 1) The Phytocentric explanations, include: a) AMF and non-mycotrophic plants, b) different growth stages of plants. 2) The Mycocentric explanations, include: a) Low effective AMF species, b) The existence of vesicles, c) Genetic variability of AMF, and d) Geographic origin of AMF. 3) Unbalanced C-for-nutrient-trade, involving both partners and 4) Indirect effects of other organisms. We note deficiencies in previous studies and suggest improvements in experimental designs such as the use of realistic mixtures of AM fungal species, and growing plants in mixtures in field situations, rather than single pot studies, with and without fungi. Determining whether and how AM fungi cheat on their hosts will enable a better understanding of their roles in natural communities and their use as biofertilizers in agriculture.     

Beyond CHELP: improved potential derived charges for sugars

The partitioning of the overall molecular charge distribution into atom centered monopole charges, while quantum mechanically ill-defined, is nevertheless a technique which finds applications in several broad classes of chemical problems. Charges derived from fits to electrostatic potentials have an intuitive appeal since, in principle, these could be derived from either theoretical or experimental data. It has been noted, however, that such potential derived charges can be conformationally dependent in ways that do not appear to reflect the changes in the molecular wavefunction. Both the algorithm used for selecting points at which the molecular electrostatic potential will be fit and the density of points used in the fit have been suggested to influence the resultant charges. Recently [Stouch TR, Williams DE (1992) J Comp Chem 13: 622–32; Stouch TR, Williams DE (1993) J Comp Chem 14: 858–66] it has been noted that numerical difficulties may make it impossible to fit all the atomic charges in a molecule. Singular value decomposition (SVD) of the linear least squares matrices used in fitting atom based monopoles to molecular electrostatic potentials provides a tool for evaluating the integrity of the calculated charges. Based on the SVD analysis for a selected group of molecules we have noted particularly that increasing the molecular size reduces the fraction of charges which can be validly assigned. Users of PD derived charges, especially those who are using those charges for tasks other than reproduction of the MEP, should be aware that there is a high probability that a significant portion of those charges are statistically unreliable. Therefore, charges in many biological molecules, such as sugars, prove to be difficult to obtain by potential derived (PD) methods such as CHELP or CHELPG. Results from the SVD can be used to both assess PD charges and to generate an improved, albeit incomplete, set. Improved PD fits are presented for a series of simple saccharides. Abbreviations: HF, Hartree-Fock; LLS, linear least squares; MEP, molecular electrostatic potential; PD, potential derived; SVD, singular value decomposition This revised version was published online in November 2006 with corrections to the Cover Date.     

Barley aleurone cells contain two types of vacuoles. Characterization Of lytic organelles by use of fluorescent probes

Light microscopy was used to study the structure and function of vacuoles in living protoplasts of barley (Hordeum vulgare cv Himalaya) aleurone. Light microscopy showed that aleurone protoplasts contain two distinct types of vacuole: the protein storage vacuole and a lysosome-like organelle, which we have called the secondary vacuole. Fluorescence microscopy using pH-sensitive fluorescent probes and a fluorogenic substrate for cysteine proteases showed that both protein storage vacuoles and secondary vacuoles are acidic, lytic organelles. Ratio imaging showed that the pH of secondary vacuoles was lower in aleurone protoplasts incubated in gibberellic acid than in those incubated in abscisic acid. Uptake of fluorescent probes into intact, isolated protein storage vacuoles and secondary vacuoles required ATP and occurred via at least two types of vanadate-sensitive, ATP-dependent tonoplast transporters. One transporter catalyzed the accumulation of glutathione-conjugated probes, and another transported probes not conjugated to glutathione.     

Identifying rare and common disease associated variants in genomic data using Parkinson’s disease as a model

Background

Genome-wide association studies have been successful in identifying common genetic variants for human diseases. However, much of the heritable variation associated with diseases such as Parkinson’s disease remains unknown suggesting that many more risk loci are yet to be identified. Rare variants have become important in disease association studies for explaining missing heritability. Methods for detecting this type of association require prior knowledge on candidate genes and combining variants within the region. These methods may suffer from power loss in situations with many neutral variants or causal variants with opposite effects.

Results

We propose a method capable of scanning genetic variants to identify the region most likely harbouring disease gene with rare and/or common causal variants. Our method assigns a score at each individual variant based on our scoring system. It uses aggregate scores to identify the region with disease association. We evaluate performance by simulation based on 1000 Genomes sequencing data and compare with three commonly used methods. We use a Parkinson’s disease case–control dataset as a model to demonstrate the application of our method.Our method has better power than CMC and WSS and similar power to SKAT-O with well-controlled type I error under simulation based on 1000 Genomes sequencing data. In real data analysis, we confirm the association of α-synuclein gene (SNCA) with Parkinson’s disease (p = 0.005). We further identify association with hyaluronan synthase 2 (HAS2, p = 0.028) and kringle containing transmembrane protein 1 (KREMEN1, p = 0.006). KREMEN1 is associated with Wnt signalling pathway which has been shown to play an important role for neurodegeneration in Parkinson’s disease.

Conclusions

Our method is time efficient and less sensitive to inclusion of neutral variants and direction effect of causal variants. It can narrow down a genomic region or a chromosome to a disease associated region. Using Parkinson’s disease as a model, our method not only confirms association for a known gene but also identifies two genes previously found by other studies. In spite of many existing methods, we conclude that our method serves as an efficient alternative for exploring genomic data containing both rare and common variants.

Electronic supplementary material

The online version of this article (doi:10.1186/s12929-014-0088-9) contains supplementary material, which is available to authorized users.     

An ecological comparison of Impatiens glandulifera Royle in the native and introduced range

Understanding the ecology of plant species in their whole range (native and introduced) can provide insights into those that become problematic weeds in the introduced range despite being benign components of the vegetative community in the native range. We studied the morphological traits of Impatiens glandulifera in the native (Indian Himalayas) and introduced (UK) range and evaluated what influences natural enemies and arbuscular mycorrhizal fungi (AMF) have on plant performance. We compared height, total leaf area, root: shoot ratio, natural enemy damage and the colonisation of AMF from individual plants within and between ranges twice in 2010 during the months of June and August. In addition, in August 2010, we estimated the number of reproductive units (expressed as the sum of flowers, seed capsule and seeds) at each site. We found that all morphological traits varied between populations and countries, though in general introduced populations, and the semi-natural population in India, showed higher performance compared to natural native populations. There was only an indication that natural enemy damage, which was significantly higher in the native range, negatively affected reproductive units. Within the introduced range, the percentage colonisation of AMF was negatively associated with plant performance indicating that I. glandulifera may associate with an incompatible AMF species incurring a cost to invasive populations. We conclude that species which are heavily regulated in the native range, though still show high levels of performance, should be considered undesirable introductions into similar ecoclimatic ranges due to the potential that these species will become highly invasive species.     

Impact of temperature on Na2Sr(PO4)F:Eu3+ phosphor

In this article, we report the synthesis of Na₂Sr_1‐x(PO₄)F:Eu_x phosphor via a combustion method. The influence of different annealing temperatures on the photoluminescence properties was investigated. The phosphor was excited at both 254 and 393 nm. Na₂Sr_1‐x(PO₄)F:Eu_x³⁺ phosphors emit strong orange and red color at 593 and 612 nm, respectively, under both excitation wavelengths. Na₂Sr_1‐x(PO₄)F:Eu_x³⁺ phosphors annealed at 1050°C showed stronger emission intensity compared with 600, 900 and 1200°C. Moreover, Na₂Sr_1‐x(PO₄)F:Eu_x³⁺ phosphor was found to be more intense when compared with commercial Y₂O₃:Eu³⁺ phosphor. Copyright © 2013 John Wiley & Sons, Ltd.