Local RNA structure alignment with incomplete sequence

Motivation: Accuracy of automated structural RNA alignment is improved by using models that consider not only primary sequence but also secondary structure information. However, current RNA structural alignment approaches tend to perform poorly on incomplete sequence fragments, such as single reads from metagenomic environmental surveys, because nucleotides that are expected to be base paired are missing

THE USE OF PROPENSITY SCORES TO ASSESS THE GENERALIZABILITY OF RESULTS FROM RANDOMIZED TRIALS

Randomized trials remain the most accepted design for estimating the effects of interventions, but they do not necessarily answer a question of primary interest: Will the program be effective in a target population in which it may be implemented? In other words,are the results generalizable? There has been very little statistical research on how to assess the generalizability, or external validity, of randomized trials. We propose the use of propensity-score-based metrics to quantify the similarity of the participants in a randomized trial and a target population. In this setting the propensity score model predicts participation in the randomized trial, given a set of covariates. The resulting propensity scores are used first to quantify the difference between the trial participants and the target population, and then to weight the control group outcomes to the population, assessing how well the weighted outcomes track the outcomes actually observed in the population. These metrics can serve as a first step in assessing the generalizability of results from randomized trials to target populations. This paper lays out these ideas, discusses the assumptions underlying the approach, and illustrates the metrics using data on the evaluation of a schoolwide prevention program called Positive Behavioral Interventions and Supports

Monocyte chemoattractant protein-1 promotes macrophage-mediated tubular injury, but not glomerular injury, in nephrotoxic serum nephritis

Monocyte chemoattractant protein-1 (MCP-1) is upregulated in renal parenchymal cells during kidney disease. To investigate whether MCP-1 promotes tubular and/or glomerular injury, we induced nephrotoxic serum nephritis (NSN) in MCP-1 genetically deficient mice. Mice were analyzed when tubules and glomeruli were severely damaged in the MCP-1–intact strain (day 7). MCP-1 transcripts increased fivefold in MCP-1–intact mice. MCP-1 was predominantly localized within cortical tubules (90%), and most cortical tubules were damaged, whereas few glomerular cells expressed MCP-1 (10%). By comparison, there was a marked reduction (>40%) in tubular injury in MCP-1–deficient mice (histopathology, apoptosis). MCP-1–deficient mice were not protected from glomerular injury (histopathology, proteinuria, macrophage influx). Macrophage accumulation increased adjacent to tubules in MCP-1–intact mice compared with MCP-1–deficient mice (70%, P < 0.005), indicating that macrophages recruited by MCP-1 induce tubular epithelial cell (TEC) damage. Lipopolysaccharide-activated bone marrow macrophages released molecules that induced TEC death that was not dependent on MCP-1 expression by macrophages or TEC. In conclusion, MCP-1 is predominantly expressed by TEC and not glomeruli, promotes TEC and not glomerular damage, and increases activated macrophages adjacent to TEC that damage TEC during NSN. Therefore, we suggest that blockage of TEC MCP-1 expression is a therapeutic strategy for some forms of kidney disease.published_or_final_versio

Transplantation of Human Embryonic Stem Cell-Derived Retinal Pigment Epithelial Cells in Macular Degeneration

PURPOSE: Transplantation of human embryonic stem cell (hESC)-derived retinal pigment epithelial (RPE) cells offers the potential for benefit in macular degeneration. Previous trials have reported improved visual acuity (VA), but lacked detailed analysis of retinal structure and function in the treated area. DESIGN: Phase 1/2 open-label dose-escalation trial to evaluate safety and potential efficacy (clinicaltrials.gov identifier, NCT01469832). PARTICIPANTS: Twelve participants with advanced Stargardt disease (STGD1), the most common cause of macular degeneration in children and young adults. METHODS: Subretinal transplantation of up to 200 000 hESC-derived RPE cells with systemic immunosuppressive therapy for 13 weeks. MAIN OUTCOME MEASURES: The primary end points were the safety and tolerability of hESC-derived RPE cell administration. We also investigated evidence of the survival of transplanted cells and measured retinal structure and function using microperimetry and spectral-domain OCT. RESULTS: Focal areas of subretinal hyperpigmentation developed in all participants in a dose-dependent manner in the recipient retina and persisted after withdrawal of systemic immunosuppression. We found no evidence of uncontrolled proliferation or inflammatory responses. Borderline improvements in best-corrected VA in 4 participants either were unsustained or were matched by a similar improvement in the untreated contralateral eye. Microperimetry demonstrated no evidence of benefit at 12 months in the 12 participants. In one instance at the highest dose, localized retinal thinning and reduced sensitivity in the area of hyperpigmentation suggested the potential for harm. Participant-reported quality of life using the 25-item National Eye Institute Visual Function Questionnaire indicated no significant change. CONCLUSIONS: Subretinal hyperpigmentation is consistent with the survival of viable transplanted hESC-derived RPE cells, but may reflect released pigment in their absence. The findings demonstrate the value of detailed analysis of spatial correlation of retinal structure and function in determining with appropriate sensitivity the impact of cell transplantation and suggest that intervention in early stage of disease should be approached with caution. Given the slow rate of progressive degeneration at this advanced stage of disease, any protection against further deterioration may be evident only after a more extended period of observation

Methodology of a diabetes prevention translational research project utilizing a community-academic partnership for implementation in an underserved Latino community

<p>Abstract</p> <p>Background</p> <p>Latinos comprise the largest racial/ethnic group in the United States and have 2–3 times the prevalence of type 2 diabetes mellitus as Caucasians.</p> <p>Methods and design</p> <p>The Lawrence Latino Diabetes Prevention Project (LLDPP) is a community-based translational research study which aims to reduce the risk of diabetes among Latinos who have a ≥ 30% probability of developing diabetes in the next 7.5 years per a predictive equation. The project was conducted in Lawrence, Massachusetts, a predominantly Caribbean-origin urban Latino community. Individuals were identified primarily from a community health center's patient panel, screened for study eligibility, randomized to either a usual care or a lifestyle intervention condition, and followed for one year. Like the efficacious Diabetes Prevention Program (DPP), the LLDPP intervention targeted weight loss through dietary change and increased physical activity. However, unlike the DPP, the LLDPP intervention was less intensive, tailored to literacy needs and cultural preferences, and delivered in Spanish. The group format of the intervention (13 group sessions over 1 year) was complemented by 3 individual home visits and was implemented by individuals from the community with training and supervision by a clinical research nutritionist and a behavioral psychologist. Study measures included demographics, Stern predictive equation components (age, gender, ethnicity, fasting glucose, systolic blood pressure, HDL-cholesterol, body mass index, and family history of diabetes), glycosylated hemoglobin, dietary intake, physical activity, depressive symptoms, social support, quality of life, and medication use. Body weight was measured at baseline, 6-months, and one-year; all other measures were assessed at baseline and one-year. All surveys were orally administered in Spanish.</p> <p>Results</p> <p>A community-academic partnership enabled the successful recruitment, intervention, and assessment of Latinos at risk of diabetes with a one-year study retention rate of 93%.</p> <p>Trial registration</p> <p>NCT00810290</p

Halogens as tracers of protosolar nebula material in comet 67P/Churyumov–Gerasimenko

We report the first in situ detection of halogens in a cometary coma, that of 67P/ChuryumovGerasimenko. Neutral gas mass spectra collected by the European Space Agency’s Rosetta spacecraft during four periods of interest from the first comet encounter up to perihelion indicate that the main halogen-bearing compounds are HF, HCl and HBr. The bulk elemental abundances relative to oxygen are ~8.9 × 10⁻⁵ for F/O, ~1.2 × 10⁻⁴ for Cl/O and ~2.5 × 10⁻⁶ for Br/O, for the volatile fraction of the comet. The cometary isotopic ratios for ³⁷Cl/³⁵Cl and ⁸¹Br/⁷⁹Br match the Solar system values within the error margins. The observations point to an origin of the hydrogen halides in molecular cloud chemistry, with frozen hydrogen halides on dust grains, and a subsequent incorporation into comets as the cloud condensed and the Solar system formed

Association between LRP5 polymorphism and bone mineral density: a Bayesian meta-analysis

<p>Abstract</p> <p>Background</p> <p>The low-density lipoprotein receptor-related protein 5 gene (LRP5) was identified to be linked to the variation in BMD in high bone mass pedigrees. Subsequent population-based studies of the association between the LRP5 gene and BMD have yielded conflicting results. The present study was aimed at examining the association between LRP5 gene and BMD by using meta-analysis.</p> <p>Methods</p> <p>A systematic electronic search of literature was conducted to identify all published studies in English on the association between LRP5 gene and osteoporosis-related phenotypes, including bone mineral density and fracture. BMD data were summarized from individual studies by LRP5 genotype, and a synthesis of data was performed with random-effects meta-analyses. After excluding studies on animal and review papers, there were 19 studies for the synthesis. Among these studies, 10 studies used the rs3736228 (A1330V) polymorphism and reported BMD values.</p> <p>Results</p> <p>The 10 eligible studies comprised 16,705 individuals, with the majority being women (n = 8444), aged between 18 – 81 years. The overall distribution of genotype frequencies was: AA, 68%, AV and VV, 32%. However, the genotype frequency varied significantly within as well as between ethnic populations. On random-effects meta-analysis, lumbar spine BMD among individuals with the AA genotype was on average 0.018 (95% confidence interval [CI]: 0.012 to 0.023) g/cm²higher than those with either AV or VV genotype. Similarly, femoral neck BMD among carriers of the AA genotype was 0.011 (95%CI: 0.004 to 0.017) g/cm²higher than those without the genotype. While there was no significant heterogeneity in the association between the A1330V polymorphism and lumbar spine BMD (p = 0.55), the association was heterogeneous for femoral neck BMD (p = 0.05). The probability that the difference is greater than one standard deviation was 0.34 for femoral neck BMD and 0.54 for lumbar spine BMD.</p> <p>Conclusion</p> <p>These results suggest that there is a modest effect of the A1330V polymorphism on BMD in the general population, and that the modest association may limit its clinical use.</p

Improving management of type 1 diabetes in the UK: the Dose Adjustment For Normal Eating (DAFNE) programme as a research test-bed. A mixed-method analysis of the barriers to and facilitators of successful diabetes self-management, a health economic analysis, a cluster randomised controlled trial of different models of delivery of an educational intervention and the potential of insulin pumps and additional educator input to improve outcomes

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