Retained in HIV Care But Not on Antiretroviral Treatment: A Qualitative Patient-Provider Dyadic Study

Background

Patients retained in HIV care but not on antiretroviral therapy (ART) represent an important part of the HIV care cascade in the United States. Even in an era of more tolerable and efficacious ART, decision making in regards to ART offer and uptake remains complex and calls for exploration of both patient and provider perspectives. We sought to understand reasons for lack of ART usage in patients meeting the Health Resources Services Administration definition of retention as well as what motivated HIV primary care appointment attendance in the absence of ART.

Methods and Findings

We conducted a qualitative study consisting of 70 in-depth interviews with ART-naïve and ART-experienced patients off ART and their primary care providers in two urban safety-net HIV clinics in San Francisco and New York. Twenty patients and their providers were interviewed separately at baseline, and 15 dyads were interviewed again after at least 3 mo and another clinic visit in order to understand any ART use in the interim. We applied dyadic analysis to our data. Nearly all patients were willing to consider ART, and 40% of the sample went on ART, citing education on newer antiretroviral drugs, acceptance of HIV diagnosis, social support, and increased confidence in their ability to adhere as facilitators. However, the strength of the provider recommendation of ART played an important role. Many patients had internalized messages from providers that their health was too good to warrant ART. In addition, providers, while demonstrating patient-centered care through sensitivity to patients experiencing psychosocial instability, frequently muted the offer of ART, at times unintentionally. In the absence of ART, lab monitoring, provider relationships, access to social services, opiate pain medications, and acute symptoms motivated care. The main limitations of this study were that treatment as prevention was not explored in depth and that participants were recruited from academic HIV clinics in the US, making the findings most generalizable to this setting.

Conclusions

Provider communication with regard to ART is a key focus for further exploration and intervention in order to increase ART uptake for those retained in HIV care.     

Two theories of origin of the land-plant sporophyte: Which is left standing?

Questions concerning the two competing theories of the development of alternating generations in land plants, the homologous theory and the antithetic theory, have never been fully resolved. In the majority of recent accounts there appears to have been increasing de facto support (if one considers the ontogenetic processes and phylogenetic consequences discussed) for the antithetic theory. However, this preference is usually not plainly stated (as such) in these discussions, and some support has also continued for the homologous theory. The crux of both theories (homologous and antithetic) centers upon how the sporophyte may have originated in the life cycle. One problem with the homologous theory is that it is not made explicit how the development of a dependent sporophyte could have occurred in the life cycle (when the precedent organisms are considered to have had free-living, putatively similar, gametophytes and sporophytes). The antithetic theory, by contrast, offers a definite ontogenetic mechanism or process (retention of the zygote on the gametophyte, delay of zygotic meiosis, with zygotic mitoses occurring first) by which a dependent sporophyte might have originated and persisted, in the context of a life cycle formerly lacking a sporophyte generation. Also, a review of a variety of evidence (morphological, cytological, biochemical, etc.) would appear to lend more support to the antithetic theory than to the homologous theory. In discussing types of algae now known to be most clearly related to land plants (i.e., charophytes, particularly advanced forms), the type of life cycle exhibited by these particular algae (haplontic, with zygotic meiosis; no sporophyte present) suggests that only an antithetic origin of the sporophyte in land plants is actually feasible.     

Sequencing of the Dutch Elm Disease Fungus Genome Using the Roche/454 GS-FLX Titanium System in a Comparison of Multiple Genomics Core Facilities

As part of the DNA Sequencing Research Group of the Association of Biomolecular Resource Facilities, we have tested the reproducibility of the Roche/454 GS-FLX Titanium System at five core facilities. Experience with the Roche/454 system ranged from <10 to >340 sequencing runs performed. All participating sites were supplied with an aliquot of a common DNA preparation and were requested to conduct sequencing at a common loading condition. The evaluation of sequencing yield and accuracy metrics was assessed at a single site. The study was conducted using a laboratory strain of the Dutch elm disease fungus Ophiostoma novo-ulmi strain H327, an ascomycete, vegetatively haploid fungus with an estimated genome size of 30–50 Mb. We show that the Titanium System is reproducible, with some variation detected in loading conditions, sequencing yield, and homopolymer length accuracy. We demonstrate that reads shorter than the theoretical minimum length are of lower overall quality and not simply truncated reads. The O. novo-ulmi H327 genome assembly is 31.8 Mb and is comprised of eight chromosome-length linear scaffolds, a circular mitochondrial conti of 66.4 kb, and a putative 4.2-kb linear plasmid. We estimate that the nuclear genome encodes 8613 protein coding genes, and the mitochondrion encodes 15 genes and 26 tRNAs.     

Seasonal patterns in rainforest litterfall: Detecting endogenous and environmental influences from long‐term sampling

Tropical rainforests play an important role in the storage and cycling of global terrestrial carbon. In the carbon cycle, net primary productivity of forests is linked to soil respiration through the production and decomposition of forest litter. Climate seasonality appears to influence the production of litter although there is considerable variability within and across forests that makes accurate estimates challenging. We explored the effects of climate seasonality on litterfall dynamics in a lowland humid rainforest over a 7‐year period from 2007 to 2013, including an El Niño/La Niña cycle in 2010/2011. Litterfall was sampled fortnightly in 24 traps of 0.50 m diameter within a 1‐ha forest plot. Total mean litterfall was 10.48 ± 1.32 (±SD, dry weight) Mg ha^?1 year^?1 and seasonal in distribution. The different components of litterfall were divided into L_Leaf (63.5%), L_Wood (27.7%) and L_{FF[flowers & fruit]} (8.8%), which all demonstrated seasonal dynamics. Peak falls in L_Leaf and L_Wood were highly predictable, coinciding with maximum daily temperatures and 1 and 2 months prior to maximum monthly rainfall. The El Niño/La Niña cycle coincided with elevated local winter temperatures and peak falls of L_Leaf and L_Wood. Importantly, we establish how sampling length and generalized additive models eliminate the requirement for extensive within‐site sampling when the intention is to describe dynamics in litterfall patterns. Further, a greater understanding of seasonal cycles in litterfall allows us to distinguish between endogenous controls and environmental factors, such as El Niño events, which may have significant impacts on biochemical cycles.     

Epitope mapping with a recombinant human 68-kDa (U1) ribonucleoprotein antigen reveals heterogeneous autoantibody profiles in human autoimmune sera

Several cDNA fragments encoding parts of the (U1)RNP specific 68-kDa autoantigen were expressed in Escherichia coli and the fusion proteins were used as substrate for localization of the autoreactive epitopes. We have identified a region of approximately 30 amino acids reacting with more than 90% (16 of 17) of all human anti-p68 sera tested, regions which carry only a few and a region with no autoepitopes. Comparative analysis of epitopes recognized on partially degraded fusion proteins indicated that the anti-p68 autoimmune response is polyclonal. It involves generation of antibodies to several epitopes including one in a region with retroviral gag protein homology speculated to play a role in the initiation of the autoimmune response. Each of the 17 sera tested contained a different set of autoantibody specificities. These data are not consistent with random mutation as a sole mechanism of anti-p68 autoantibody induction and argue for an Ag-driven autoimmune response.     

Do energetic demands constrain incubation scheduling in a biparental species?

The high energetic demands of incubation in birds may be animportant ecological factor limiting the evolution of life-historytraits, such as clutch size. In biparental species, however,the demands of incubation may not be a major constraint becausethere may always be sufficient feeding time available for theoff-duty bird to regain energy used during an incubation bout.We investigated whether the energetic demands of incubationconstrain optimum incubation bout length in a biparental incubatorby decreasing the energetic demands of incubation. We put aninsulated cup around the lining of semipalmated sandpiper nestsso that the rate of cooling of eggs was reduced by 21%. Semipalmatedsandpipers responded by increasing their mean incubation boutlength of around 11.1 h by about 10%. Bout lengths in unmanipulatednatural nests became longer as hatch approached (incubationstage), and this was independent of weather. Bout lengths mayhave decreased with increasing rainfall and were independentof time of day. The results suggest that bout length in semipalmatedsandpipers is constrained by their cumulative energetic expenditureduring an incubation bout, and this is determined partly bythe high costs of steady-state incubation. The results alsosuggest that the incubating bird determines the bout lengthrather than the returning bird. Semipalmated sandpipersmay havemaximized incubation bout length to minimize changeovers duringincubation because these probably increasepredation risk. Selectionto minimize the frequency of changeover may then be a factorcontributing to the evolution ofbiparental care and life-historytraits in semipalmated sandpipers.     

Which genetic loci have greater population assignment power?

SUMMARY: WHICHLOCI is a program that determines the relative discriminatory power of alternate genetic loci and loci combinations for population assignment of individuals. AVAILABILITY: http://www.oregonstate.edu/dept/comes/genetics/software.htm     

Changes in forest understory associated with Juniperus encroachment in Oklahoma,USA

Question: Does understory vegetation cover and richness decline along a gradient of increasing Juniperus virginiana midstory canopy cover and is that decline best correlated with litter accumulation? Location: Cross Timbers Forest in Payne County, OK, USA. Methods: We measured vegetation in forest gaps as well as forest areas without J. virginiana, at the inner and outer edge of J. virginiana canopies and near J. virginiana trunks (200 plots) and compared vegetation differences among location to light, litter, soil and microclimate variables. Results: Species richness (11 spp m^?2 to 6 spp m^?2) and summer vegetation cover (53.3% to 12.7%) declined with proximity to trunks. Regression indicated that richness declines (R²=0.08) and cover (R²=0.18) were best correlated with J. virginiana litter accumulation. Partial canonical correspondence analysis (pCCA) revealed two strong canonical axes, one related to litter/light and another to cover of Quercus spp. versus J. virginiana. Tree seedlings and woody vines dominated near J. virginiana. Forbs, graminoids and Quercus spp. seedlings were more common in areas without J. virginiana. Conclusions: Increasing J. virginiana and consequent litter additions alter understory biomass and composition and, through inhibiting Quercus spp. recruitment, may lead to changes in overstory composition. Decreases in herbaceous litter, which historically contributed to fuel accumulation, may have positive feedback effects on midstory encroachment by reducing the potential for prescribed burning.     

Characterization of novel SF3b and 17S U2 snRNP proteins,including a human Prp5p homologue and an SF3b DEAD-box protein

Mass spectrometry was used to identify novel proteins associated with the human 17S U2 snRNP and one of its stable subunits, SF3b. Several additional proteins were identified, demonstrating that 17S U2 snRNPs are significantly more complex than previously thought. Two of the newly identified proteins, namely the DEAD-box proteins SF3b125 and hPrp5 (a homologue of Saccharomyces cerevisiae Prp5p) were characterized further. Immunodepletion experiments with HeLa nuclear extract indicated that hPrp5p plays an important role in pre-mRNA splicing, acting during or prior to prespliceosome assembly. The SF3b-associated protein SF3b125 dissociates at the time of 17S U2 formation, raising the interesting possibility that it might facilitate the assembly of the 17S U2 snRNP. Finally, immunofluorescence/FISH studies revealed a differential subnuclear distribution of U2 snRNA, hPrp5p and SF3b125, which were enriched in Cajal bodies, versus SF3b155 and SF3a120, which were not; a model for 17S U2 snRNP assembly based on these findings is presented. Taken together, these studies provide new insight into the composition of the 17S U2 snRNP and the potential function of several of its proteins.