Targeted Derepression of the Human Immunodeficiency Virus Type 1 Long Terminal Repeat by Pyrrole-Imidazole Polyamides

The host factor LSF represses the human immunodeficiency virus type 1 long terminal repeat (LTR) by mediating recruitment of histone deacetylase. We show that pyrrole-imidazole polyamides targeted to the LTR can specifically block LSF binding both in vitro and within cells via direct access to chromatin, resulting in increased LTR expression

Measurement error caused by spatial misalignment in environmental epidemiology

Copyright @ 2009 Gryparis et al - Published by Oxford University Press.In many environmental epidemiology studies, the locations and/or times of exposure measurements and health assessments do not match. In such settings, health effects analyses often use the predictions from an exposure model as a covariate in a regression model. Such exposure predictions contain some measurement error as the predicted values do not equal the true exposures. We provide a framework for spatial measurement error modeling, showing that smoothing induces a Berkson-type measurement error with nondiagonal error structure. From this viewpoint, we review the existing approaches to estimation in a linear regression health model, including direct use of the spatial predictions and exposure simulation, and explore some modified approaches, including Bayesian models and out-of-sample regression calibration, motivated by measurement error principles. We then extend this work to the generalized linear model framework for health outcomes. Based on analytical considerations and simulation results, we compare the performance of all these approaches under several spatial models for exposure. Our comparisons underscore several important points. First, exposure simulation can perform very poorly under certain realistic scenarios. Second, the relative performance of the different methods depends on the nature of the underlying exposure surface. Third, traditional measurement error concepts can help to explain the relative practical performance of the different methods. We apply the methods to data on the association between levels of particulate matter and birth weight in the greater Boston area.This research was supported by NIEHS grants ES012044 (AG, BAC), ES009825 (JS, BAC), ES007142 (CJP), and ES000002 (CJP), and EPA grant R-832416 (JS, BAC)

Integrated measures of lead and manganese exposure improve estimation of their joint effects on cognition in Italian school-age children

Every day humans are exposed to mixtures of chemicals, such as lead (Pb) and manganese (Mn). An underappreciated aspect of studying the health effects of mixtures is the role that the exposure biomarker media (blood, hair, etc.) may play in estimating the effects of the mixture. Different biomarker media represent different aspects of each chemical's toxicokinetics, thus no single medium can fully capture the toxicokinetic profile for all the chemicals in a mixture. A potential solution to this problem is to combine exposure data across different media to derive integrated estimates of each chemical's internal concentration. This concept, formalized as a multi-media biomarker (MMB) has proven effective for estimating the health impacts of Pb exposure, but may also be useful to estimate mixture effects, such as the joint effects of metals like Pb and Mn, while factoring in how the association changes based upon the biomarker media. Levels of Pb and Mn were quantified in five media: blood, hair, nails, urine, and saliva in the Public Health Impact of Metals Exposure (PHIME) project, a study of Italian adolescents aged 10–14 years. MMBs were derived for both metals using weighted quantile sum (WQS) regression across the five media. Age-adjusted Wechsler Intelligence Scale for Children (WISC) IQ scores, measured at the same time as the exposure measures, were the primary outcome and models were adjusted for sex and socioeconomic status. The levels Pb and Mn were relatively low, with median blood Pb of 1.27 (IQR: 0.84) μg/dL and median blood Mn of 1.09 (IQR: 0.45) μg/dL. Quartile increases in a Pb-Mn combination predicted decreased Full Scale IQ of 1.9 points (95% CI: 0.3, 3.5) when Pb and Mn exposure levels were estimated using MMBs, while individual regressions for each metal were not associated with Full Scale IQ. Additionally, a quartile increase in the WQS index of Pb and Mn, measured using MMBs, were associated with reductions in Verbal IQ by 2.8 points (1.0, 4.5). Weights that determine the contributions of the metals to the joint effect highlighted that the contribution of the Pb-Mn was 72–28% for Full Scale IQ and 42–58% for Verbal IQ. We found that the joint effects of Pb and Mn are strongly affected by the medium used to measure exposure and that the joint effects of the Pb and Mn MMBs on cognition were the stronger than any individual biomarker. Thus, increase power and accuracy for measuring mixture effects compared to individual biomarkers. As the number of chemicals in mixtures increases, appropriate biomarker selection will become increasingly important and MMBs are a natural way to reduce bias in such analyses

Salinity drives meiofaunal community structure dynamics across the Baltic ecosystem

Coastal benthic biodiversity is under increased pressure from climate change, eutrophication, hypoxia, and changes in salinity due to increase in river runoff. The Baltic Sea is a large brackish system characterized by steep environmental gradients that experiences all of the mentioned stressors. As such it provides an ideal model system for studying the impact of on‐going and future climate change on biodiversity and function of benthic ecosystems. Meiofauna (animals < 1 mm) are abundant in sediment and are still largely unexplored even though they are known to regulate organic matter degradation and nutrient cycling. In this study, benthic meiofaunal community structure was analysed along a salinity gradient in the Baltic Sea proper using high‐throughput sequencing. Our results demonstrate that areas with higher salinity have a higher biodiversity, and salinity is probably the main driver influencing meiofauna diversity and community composition. Furthermore, in the more diverse and saline environments a larger amount of nematode genera classified as predators prevailed, and meiofauna‐macrofauna associations were more prominent. These findings show that in the Baltic Sea, a decrease in salinity resulting from accelerated climate change will probably lead to decreased benthic biodiversity, and cause profound changes in benthic communities, with potential consequences for ecosystem stability, functions and services

Ready ... Go: Amplitude of the fMRI Signal Encodes Expectation of Cue Arrival Time

What happens when the brain awaits a signal of uncertain arrival time, as when a sprinter waits for the starting pistol? And what happens just after the starting pistol fires? Using functional magnetic resonance imaging (fMRI), we have discovered a novel correlate of temporal expectations in several brain regions, most prominently in the supplementary motor area (SMA). Contrary to expectations, we found little fMRI activity during the waiting period; however, a large signal appears after the “go” signal, the amplitude of which reflects learned expectations about the distribution of possible waiting times. Specifically, the amplitude of the fMRI signal appears to encode a cumulative conditional probability, also known as the cumulative hazard function. The fMRI signal loses its dependence on waiting time in a “countdown” condition in which the arrival time of the go cue is known in advance, suggesting that the signal encodes temporal probabilities rather than simply elapsed time. The dependence of the signal on temporal expectation is present in “no-go” conditions, demonstrating that the effect is not a consequence of motor output. Finally, the encoding is not dependent on modality, operating in the same manner with auditory or visual signals. This finding extends our understanding of the relationship between temporal expectancy and measurable neural signals

Associations of a metal mixture measured in multiple biomarkers with IQ: Evidence from italian adolescents living near ferroalloy industry

BACKGROUND: Research on the health effects of chemical mixtures has focused mainly on early life rather than adolescence, a potentially important developmental life stage. OBJECTIVES: We examined associations of a metal mixture with general cognition in a cross-sectional study of adolescents residing near ferromanga-nese industry, a source of airborne metals emissions. METHODS: We measured manganese (Mn), lead (Pb), copper (Cu), and chromium (Cr) in hair, blood, urine, nails, and saliva from 635 Italian adolescents 10–14 years of age. Full-scale, verbal, and performance intelligence quotient (FSIQ, VIQ, PIQ) scores were assessed using the Wechsler Intelligence Scale for Children-III. Multivariable linear regression and Bayesian kernel machine regression (BKMR) were used to estimate associations of the metal mixture with IQ. In secondary analyses, we used BKMR’s hierarchical variable selection option to inform biomarker selection for Mn, Cu, and Cr. RESULTS: Median metal concentrations were as follows: hair Mn, 0:08 lg=g; hair Cu, 9:6 lg=g; hair Cr, 0:05 lg=g; and blood Pb, 1:3 lg=dL. Adjusted models revealed an inverted U-shaped association between hair Cu and VIQ, consistent with Cu as an essential nutrient that is neurotoxic in excess. At low levels of hair Cu (10th percentile, 5:4 lg=g), higher concentrations (90th percentiles) of the mixture of Mn, Pb, and Cr (0:3 lg=g, 2:6 lg=dL, and 0:1 lg=g, respectively) were associated with a 2.9 (95% CI: −5:2, −0:5)–point decrease in VIQ score, compared with median concentrations of the mixture. There was suggestive evidence of interaction between Mn and Cu. In secondary analyses, saliva Mn, hair Cu, and saliva Cr were selected as the biomarkers most strongly associated with VIQ score. DISCUSSION: Higher adolescent levels of Mn, Pb, and Cr were associated with lower IQ scores, especially at low Cu levels. Findings also support fur-ther investigation into Cu as both beneficial and toxic for neurobehavioral outcomes

An overview of methods to address distinct research questions on environmental mixtures: an application to persistent organic pollutants and leukocyte telomere length

Background Numerous methods exist to analyze complex environmental mixtures in health studies. As an illustration of the different uses of mixture methods, we employed methods geared toward distinct research questions concerning persistent organic chemicals (POPs) as a mixture and leukocyte telomere length (LTL) as an outcome. Methods With information on 18 POPs and LTL among 1,003 U.S. adults (NHANES, 2001-2002), we used unsupervised methods including clustering to identify profiles of similarly exposed participants, and Principal Component Analysis (PCA) and Exploratory Factor Analysis (EFA) to identify common exposure patterns. We also employed supervised learning techniques, including penalized, weighted quantile sum (WQS), and Bayesian kernel machine (BKMR) regressions, to identify potentially toxic agents, and characterize nonlinear associations, interactions, and the overall mixture effect. Results Clustering separated participants into high, medium, and low POP exposure groups; longer log-LTL was found among those with high exposure. The first PCA component represented overall POP exposure and was positively associated with log-LTL. Two EFA factors, one representing furans and the other PCBs 126 and 118, were positively associated with log-LTL. Penalized regression methods selected three congeners in common (PCB 126, PCB 118, and furan 2,3,4,7,8-pncdf) as potentially toxic agents. WQS found a positive overall effect of the POP mixture and identified six POPs as potentially toxic agents (furans 1,2,3,4,6,7,8-hxcdf, 2,3,4,7,8-pncdf, and 1,2,3,6,7,8-hxcdf, and PCBs 99, 126, 169). BKMR found a positive linear association with furan 2,3,4,7,8-pncdf, suggestive evidence of linear associations with PCBs 126 and 169, and a positive overall effect of the mixture, but no interactions among congeners. Conclusions Using different methods, we identified patterns of POP exposure, potentially toxic agents, the absence of interaction, and estimated the overall mixture effect. These applications and results may serve as a guide for mixture method selection based on specific research questions

Do experts see it in slow motion? Altered timing of action simulation uncovers domain-specific perceptual processing in expert athletes

Accurate encoding of the spatio-temporal properties of others' actions is essential for the successful implementation of daily activities and, even more, for successful sportive performance, given its role in movement coordination and action anticipation. Here we investigated whether athletes are provided with special perceptual processing of spatio-temporal properties of familiar sportive actions. Basketball and volleyball players and novices were presented with short video-clips of free basketball throws that were partially occluded ahead of realization and were asked to judge whether a subsequently presented pose was either taken from the same throw depicted in the occluded video (action identification task) or temporally congruent with the expected course of the action during the occlusion period (explicit timing task). Results showed that basketball players outperformed the other groups in detecting action compatibility when the pose depicted earlier or synchronous, but not later phases of the movement as compared to the natural course of the action during occlusion. No difference was obtained for explicit estimations of timing compatibility. This leads us to argue that the timing of simulated actions in the experts might be slower than that of perceived actions ("slow-motion" bias), allowing for more detailed representation of ongoing actions and refined prediction abilities

Motor activity improves temporal expectancy

Certain brain areas involved in interval timing are also important in motor activity. This raises the possibility that motor activity might influence interval timing. To test this hypothesis, we assessed interval timing in healthy adults following different types of training. The pre- and post-training tasks consisted of a button press in response to the presentation of a rhythmic visual stimulus. Alterations in temporal expectancy were evaluated by measuring response times. Training consisted of responding to the visual presentation of regularly appearing stimuli by either: (1) pointing with a whole-body movement, (2) pointing only with the arm, (3) imagining pointing with a whole-body movement, (4) simply watching the stimulus presentation, (5) pointing with a whole-body movement in response to a target that appeared at irregular intervals (6) reading a newspaper. Participants performing a motor activity in response to the regular target showed significant improvements in judgment times compared to individuals with no associated motor activity. Individuals who only imagined pointing with a whole-body movement also showed significant improvements. No improvements were observed in the group that trained with a motor response to an irregular stimulus, hence eliminating the explanation that the improved temporal expectations of the other motor training groups was purely due to an improved motor capacity to press the response button. All groups performed a secondary task equally well, hence indicating that our results could not simply be attributed to differences in attention between the groups. Our results show that motor activity, even when it does not play a causal or corrective role, can lead to improved interval timing judgments