Clinical Service Delivery of Noninvasive Prenatal Diagnosis by Relative Haplotype Dosage for Single-Gene Disorders.

A relative haplotype dosage (RHDO)-based method was developed and implemented into routine clinical practice for noninvasive prenatal diagnosis (NIPD) of multiple single-gene disorders: spinal muscular atrophy, Duchenne and Becker muscular dystrophies, and cystic fibrosis. This article describes the experiences of the first 152 pregnancies to have NIPD by RHDO as part of a routine clinical service. Provision of results within a clinically useful time frame (mean, 11 calendar days) was shown to be possible, with a very low failure rate (4%), none being due to a technical failure. Where follow-up confirmatory testing was performed for audit purposes, 100% concordance was seen with the NIPD result, and no discrepancies have been reported. The robust performance of the assay, together with high sensitivity and specificity, demonstrates that NIPD by RHDO is feasible for use in a clinical setting.

An Integrated Assessment Model for Valuing Water Quality Changes in the U.S.

The US Environmental Protection Agency (EPA) often requires expertise from environmental assessors, hydrologists, economists, and others to analyze the benefits of regional and national policy decisions related to changes in water quality. This led EPA to develop two models to form an Integrated Assessment Model (IAM): HAWQS is a web-based water quantity and quality modeling systems and BenSPLASH is a modeling platform for quantifying the economic benefits of changes in water quality. This paper discusses the development of the component models and applies HAWQS and BenSPLASH to a case study in the Republican River Basin.

Indicators of Readiness and Capacity for Implementation of Healthy Eating Strategies in Child Care Settings Serving Low-Income Children.

OBJECTIVE: Identify factors perceived to influence implementation of healthy eating policy, systems, and environmental strategies (PSEs) in child care settings serving low-income children. DESIGN: This mixed-methods study, conducted in 2015-2016, used semi-structured interviews (n = 18), focus groups (n = 23), and an expert panel. PARTICIPANTS: Public health (n = 11) and Supplemental Nutrition Assistance Program-Education practitioners (n = 9) and community residents (n = 174) from 9 counties in Ohio. Expert panelists (n = 10) had experience implementing PSEs in child care settings. PHENOMENON OF INTEREST: Implementation factors influencing healthy eating PSEs in child care settings. ANALYSIS: Qualitative thematic analysis of 41 transcripts using a grounded theory approach. Indicators for each theme were operationalized. Consensus feedback from an expert panel weighted themes and indicators based on perceived importance for implementation. RESULTS: Identified themes relevant to implementation of PSEs included (1) organizational and practitioner capacity, (2) child care capacity, (3) networks and relationships, and (4) community resources and motivations. Nineteen indicators related to the 4 themes were identified and weighted. CONCLUSIONS AND IMPLICATIONS: Findings highlighted key factors within domains of influence and informed the operationalization of the indicators and the development of an assessment tool. The assessment tool is designed to tailor PSE implementation to the realities of different child care settings.

Using structural restrictions to achieve theoretical consistency in benefit transfers.

Analysts often extrapolate estimates of the value of environmental improvements reported in prior studies to evaluate new policy proposals, a practice sometimes referred to as "benefit transfer." Benefit transfer functions are frequently specified based on statistical considerations alone. However, such a purely statistical approach can lead to willingness-to-pay functions that fail to satisfy some aspects of theoretical consistency that may be especially important for policy evaluations. In this paper, we examine several previous meta-analyses of nonmarket valuation studies in light of the adding-up condition, which is one important aspect of theoretical validity. We then use meta-regression to estimate a new willingness-to-pay function for surface water quality improvements intended to be used for benefit transfers. We estimate the meta-regression model using summary results from 51 previously published stated preference studies. An important feature of our approach is that we develop the meta-regression estimating equation to ensure that the resulting benefit transfer function will necessarily comply with the adding-up condition. This is achieved by first specifying a marginal willingness-to-pay function and then deriving an expression for total willingness-to-pay. This leads to a non-linear estimating equation, so we estimate the parameters of the model using non-linear least squares. We discuss the advantages and disadvantages of our approach relative to other structural approaches, and we compare our empirical results to a more traditional nonstructural meta-regression model. Finally, we examine the quantitative importance of imposing the adding-up condition in our case study by performing some illustrative calculations of willingness-to-pay for hypothetical water quality improvements using both structural and non-structural models.

Non-invasive prenatal diagnosis of spinal muscular atrophy by relative haplotype dosage.

Although technically possible, few clinical laboratories across the world have implemented non-invasive prenatal diagnosis (NIPD) for selected single-gene disorders, mostly owing to the elevated costs incurred. Having previously proven that NIPD for X-linked disorders can be feasibly implemented in clinical practice, we have now developed a test for the NIPD of an autosomal-recessive disorder, spinal muscular atrophy (SMA). Cell-free DNA was extracted from maternal blood and prepared for massively parallel sequencing on an Illumina MiSeq by targeted capture enrichment of single-nucleotide polymorphisms across a 6 Mb genomic window on chromosome 5 containing the SMN1 gene. Maternal, paternal and proband DNA samples were also tested for haplotyping purposes. Sequencing data was analysed by relative haplotype dosage (RHDO). Six pregnant SMA carriers and 10 healthy pregnant donors were recruited through the NIPSIGEN study. Inheritance of the maternally and paternally derived alleles of the affected SMN1 gene was determined in the foetus by RHDO analysis for autosomal-recessive disorders. DNA from the proband (for SMA carriers) or an invasively obtained foetal sample (for healthy pregnant donors) was used to identify the maternal and paternal reference haplotypes associated with the affected SMN1 gene. Results for all patients correlated with known outcomes and showed a testing specificity and sensitivity of 100%. On top of showing high accuracy and reliability throughout the stages of validation, our novel test for NIPD of SMA is also affordable and viable for implementation into clinical service.

A framework to quantify the strength of ecological links between an environmental stressor and final ecosystem services.

Anthropogenic stressors such as climate change, increased fire frequency, and pollution drive shifts in ecosystem function and resilience. Scientists generally rely on biological indicators of these stressors to signal that ecosystem conditions have been altered. However, these biological indicators are not always capable of being directly related to ecosystem components that provide benefits to humans and/or can be used to evaluate the cost-benefit of a change in health of the component (ecosystem services). Therefore, we developed the STEPS (STressor - Ecological Production function - final ecosystem Services) Framework to link changes in a biological indicator of a stressor to final ecosystem services. The STEPS framework produces "chains" of ecological components that explore the breadth of impacts resulting from the change of a stressor. Chains are comprised of the biological indicator, the ecological production function (EPF; which uses ecological components to link the biological indicator to a final ecosystem service), and the user group who directly uses, appreciates, or values the component. The framework uses a qualitative score (High, Medium, Low) to describe the Strength of Science (SOS) for the relationship between each component in the EPF. We tested the STEPS Framework within a workshop setting using the exceedance of critical loads of air pollution as a model stressor and the Final Ecosystem Goods and Services Classification System (FEGS-CS) to describe final ecosystem services. We identified chains for four modes of ecological response to deposition: aquatic acidification, aquatic eutrophication, terrestrial acidification, and terrestrial eutrophication. The workshop participants identified 183 unique EPFs linking a change in a biological indicator to a FEGS; and when accounting for the multiple beneficiaries, we ended with 1104 chains. The SOS scores were effective in identifying chains with the highest confidence ranking as well as those where more research is needed. The STEPS framework could be adapted to any system in which a stressor is modifying a biological component. The results of the analysis can be used by the social science community to apply valuation measures to multiple or selected chains, providing a comprehensive analysis of the effects of anthropogenic stressors on measures of human well-being.

Non-invasive prenatal diagnosis of Duchenne and Becker muscular dystrophies by relative haplotype dosage.

OBJECTIVE: Development of an accurate and affordable test for the non-invasive prenatal diagnosis of Duchenne and Becker muscular dystrophies (DMD/BMD) to implement in clinical practice. METHOD: Cell-free DNA was extracted from maternal blood and prepared for massively parallel sequencing on an Illumina MiSeq by targeted capture enrichment of single nucleotide polymorphisms (SNPs) across the dystrophin gene on chromosome X. Sequencing data were analysed by relative haplotype dosage. RESULTS: Seven healthy pregnant donors and two pregnant DMD carriers all bearing a male fetus were recruited through the non-invasive prenatal diagnosis for single gene disorders study. Non-invasive prenatal diagnosis testing was conducted by relative haplotype dosage analysis for X-linked disorders where the genomic DNA from the chorionic villus sampling (for healthy pregnant donors) or from the proband (for pregnant DMD carriers) was used to identify the reference haplotype. Results for all patients showed a test accuracy of 100%, when the calculated fetal fraction was >4% and correlated with known outcomes. A recombination event was also detected in a DMD patient. CONCLUSION: Our new test for NIPD of DMD/BMD has been shown to be accurate and reliable during initial stages of validation. It is also feasible for implementation into clinical service.

Molecular tools for bathing water assessment in Europe: Balancing social science research with a rapidly developing environmental science evidence-base.

The use of molecular tools, principally qPCR, versus traditional culture-based methods for quantifying microbial parameters (e.g., Fecal Indicator Organisms) in bathing waters generates considerable ongoing debate at the science-policy interface. Advances in science have allowed the development and application of molecular biological methods for rapid (~2 h) quantification of microbial pollution in bathing and recreational waters. In contrast, culture-based methods can take between 18 and 96 h for sample processing. Thus, molecular tools offer an opportunity to provide a more meaningful statement of microbial risk to water-users by providing near-real-time information enabling potentially more informed decision-making with regard to water-based activities. However, complementary studies concerning the potential costs and benefits of adopting rapid methods as a regulatory tool are in short supply. We report on findings from an international Working Group that examined the breadth of social impacts, challenges, and research opportunities associated with the application of molecular tools to bathing water regulations.

Postnatal loss of brainstem serotonin neurones compromises the ability of neonatal rats to survive episodic severe hypoxia.

Pet-1(-/-) mice with a prenatal, genetically induced loss of 5-hydroxytryptamine (5-HT, serotonin) neurones are compromised in their ability to withstand episodic environmental anoxia via autoresuscitation. Given the prenatal role of 5-HT neurones in the development of neural networks, here we ask if a postnatal loss of 5-HT neurones also compromises autoresuscitation. We treated neonatal rat pups at postnatal day (P)2-3 with an intra-cisternal injection of 5,7-dihydroxytryptamine (5,7-DHT; ~40 µg; n = 8) to pharmacologically lesion the 5-HT system, or vehicle (control; n = 14). At P7-10 we exposed unanaesthetized treated and control pups to 15 episodes of environmental anoxia (97% N(2), 3% CO(2)). Medullary 5-HT content was reduced 80% by 5,7-DHT treatment (P < 0.001). Baseline ventilation (V(E)), metabolic rate (V(O(2))), ventilatory equivalent (V(E)/V(O(2))), heart rate (HR), heart rate variability (HRV) and arterial haemoglobin saturation (S(aO(2))) were no different in 5-HT-deficient pups compared to controls. However, only 25% of 5-HT-deficient pups survived all 15 episodes of environmental anoxia, compared to 79% of control littermates (P = 0.007). High mortality of 5,7-DHT-treated pups was associated with delayed onset of gasping (P < 0.001), delayed recovery of HR from hypoxic-induced bradycardia (P < 0.001), and delayed recovery of eupnoea from hypoxic-induced apnoea (P < 0.001). Treatment with 5,7-DHT affected neither the gasping pattern once initiated, nor HR, V(E)/V(O(2)) or S(aO(2)) during the intervening episodes of room air. A significant increase in HRV occurred in all animals with repeated exposure, and in 5-HT-deficient pups this increase occurred immediately prior to death. We conclude that a postnatal loss of brainstem 5-HT content compromises autoresuscitation in response to environmental anoxia. This report provides new evidence in rat pups that 5-HT neurones serve a physiological role in autoresuscitation. Our data may be relevant to understanding the aetiology of the sudden infant death syndrome (SIDS), in which there is medullary 5-HT deficiency and in some cases evidence of severe hypoxia and failed autoresuscitation.

Failed heart rate recovery at a critical age in 5-HT-deficient mice exposed to episodic anoxia: implications for SIDS.

Mice deficient in the transcription factor Pet-1⁻/⁻ have a ∼70% deficiency of brainstem serotonin [5-hydroxytryptamine (5-HT)] neurons and exhibit spontaneous bradycardias in room air at postnatal day (P)5 and P12 and delayed gasping in response to a single episode of anoxia at P4.5 and P9.5 (Cummings KJ, Li A, Deneris ES, Nattie EE. Am J Physiol Regul Integr Comp Physiol 298: R1333-R1342, 2010; and Erickson JT, Sposato BC. J Appl Physiol 106: 1785-1792, 2009). We hypothesized that at a critical age Pet-1⁻/⁻ mice will fail to autoresuscitate during episodic anoxia, ultimately dying from a failure of gasping to restore heart rate (HR). We exposed P5, P8, and P12 Pet-1⁻/⁻ mice and wild-type littermates (WT) to four 30-s episodes of anoxia (97% N2-3% CO2), separated by 5 min of room air. We observed excess mortality in Pet-1⁻/⁻ only at P8: 43% of Pet-1⁻/⁻ animals survived past the third episode of anoxia while ∼95% of WT survived all four episodes (P = 0.004). No deaths occurred at P5 and at P12, and one of six Pet-1⁻/⁻ mice died after the fourth episode, while all WT animals survived. At P8, dying Pet-1⁻/⁻ animals had delayed gasping, recovery of HR, and eupnea after the first two episodes of anoxia (P < 0.001 for each); death ultimately occurred when gasping failed to restore HR. Both high- and low-frequency components of HR variability were abnormally elevated in dying Pet-1⁻/⁻ animals following the first episode of anoxia. Dying P8 Pet-1⁻/⁻ animals had significantly fewer 5-HT neurons in the raphe magnus than surviving animals (P < 0.001). Our data indicate a critical developmental window at which a brainstem 5-HT deficiency increases the risk of death during episodes of anoxia. They may apply to the sudden infant death syndrome, which occurs at a critical age and is associated with 5-HT deficiency.

Children prenatally exposed to cocaine: developmental outcomes and environmental risks at seven years of age.

Data are equivocal regarding the long-term consequences of prenatal exposure to cocaine on school-aged children. We compared 101 children exposed prenatally to cocaine with 130 unexposed children on measures of intelligence, visual motor, and motor abilities at age 7 years. Bivariate analyses revealed that cocaine-exposed children scored significantly lower than comparison children on the abbreviated Wechsler Intelligence Scale for Children-Third Edition Verbal and Full Scale IQ scores, the Visual Motor Integration and Motor Coordination standardized scores, and the Bruininks-Oseretsky Fine Motor Composite score. Regression analyses indicated that the biological mother's vocabulary and home environment assessed at the same 7-year visit were stronger predictors of developmental outcome than prenatal drug exposure. Level of cocaine exposure, however, predicted visual motor and motor skills. The results indicate that although prenatal cocaine exposure may confer some degree of developmental disadvantage in the visual motor domain, it frequently occurs in the context of an inadequate rearing environment, which may be a stronger determinant than prenatal cocaine exposure of children's outcome.