An alternative hypothesis testing strategy for secondary phenotype data in case-control genetic association studies

Motivated by the challenges associated with accounting for the ascertainment when analyzing secondary phenotypes that are correlated with case-control status, Lin and Zeng have proposed a method that properly reflects the case-control sampling (Lin and Zeng, 2009). The Lin and Zeng method has the advantage of accurately estimating effect sizes for secondary phenotypes that are normally distributed or dichotomous. This method can be computationally intensive in practice under the null hypothesis when the likelihood surface that needs to be maximized can be relatively flat. We propose an extension of the Lin and Zeng method for hypothesis testing that uses proportional odds logistic regression to circumvent these computational issues. Through simulation studies, we compare the power and type-1 error rate of our method to standard approaches and Lin and Zeng's approach

When Policy Meets Practice: The Dilemma for Guidance on Risk Assessment Under the Cartagena Protocol on Biosafety

The Conference of the Parties serving as the meeting of the Parties (COP-MOP) to the Cartagena Protocol on Biosafety to the Convention on Biological Diversity decided years ago to undertake the development of guidance on risk assessment of living modified organisms (LMOs) resulting from modern biotechnology, in order to assist the Parties to the protocol to conduct risk assessments in line with the principles and methodology described therein. After many years of working through ad hoc technical expert groups (AHTEG) and open-ended online forum discussions, including an extensive process to test and revise the guidance document, the COP-MOP did not decide to endorse the last version of the document when it was finally presented to them. A failure to achieve consensus that the guidance, as it had evolved, is relevant and useful is seen as a potential setback for many Parties to the protocol with little to no experience with risk assessment. There are a number of reasons for the lack of success in this attempt to develop useful guidance on risk assessment, including a poorly defined and shifting purpose, misplaced expertise, and a misguided testing process, mostly perpetuated by the constraints of using processes of the Convention. These problems with the development of the Guidance on Risk Assessment of LMOs are explored here in an effort to elucidate the missteps that should be avoided and the lessons that can be learned. Most prominent is a need to rely upon the expanding past and present experiences with actual cases of risk assessments of LMOs, if there is to be any further attempt to develop guidance on risk assessment under the Convention and its protocol

Caloric Expenditure of Normal and Lower Body Positive Pressure Treadmill Running

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Perceived Exertion and Affective Responses During Normal and Lower Body Positive Pressure Treadmill Running

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Epidemiology, genetics, and subtyping of preserved ratio impaired spirometry (PRISm) in COPDGene.

BackgroundPreserved Ratio Impaired Spirometry (PRISm), defined as a reduced FEV1 in the setting of a preserved FEV1/FVC ratio, is highly prevalent and is associated with increased respiratory symptoms, systemic inflammation, and mortality. Studies investigating quantitative chest tomographic features, genetic associations, and subtypes in PRISm subjects have not been reported.MethodsData from current and former smokers enrolled in COPDGene (n = 10,192), an observational, cross-sectional study which recruited subjects aged 45-80 with ≥10 pack years of smoking, were analyzed. To identify epidemiological and radiographic predictors of PRISm, we performed univariate and multivariate analyses comparing PRISm subjects both to control subjects with normal spirometry and to subjects with COPD. To investigate common genetic predictors of PRISm, we performed a genome-wide association study (GWAS). To explore potential subgroups within PRISm, we performed unsupervised k-means clustering.ResultsThe prevalence of PRISm in COPDGene is 12.3%. Increased dyspnea, reduced 6-minute walk distance, increased percent emphysema and decreased total lung capacity, as well as increased segmental bronchial wall area percentage were significant predictors (p-value <0.05) of PRISm status when compared to control subjects in multivariate models. Although no common genetic variants were identified on GWAS testing, a significant association with Klinefelter's syndrome (47XXY) was observed (p-value < 0.001). Subgroups identified through k-means clustering include a putative "COPD-subtype", "Restrictive-subtype", and a highly symptomatic "Metabolic-subtype".ConclusionsPRISm subjects are clinically and genetically heterogeneous. Future investigations into the pathophysiological mechanisms behind and potential treatment options for subgroups within PRISm are warranted.Trial registrationClinicaltrials.gov Identifier: NCT000608764

Limb-state information encoded by peripheral and central somatosensory neurons:Implications for an afferent interface

A major issue to be addressed in the development of neural interfaces for prosthetic control is the need for somatosensory feedback. Here, we investigate two possible strategies: electrical stimulation of either dorsal root ganglia (DRG) or primary somatosensory cortex (S1). In each approach, we must determine a model that reflects the representation of limb state in terms of neural discharge. This model can then be used to design stimuli that artificially activate the nervous system to convey information about limb state to the subject. Electrically activating DRG neurons using naturalistic stimulus patterns, modeled on recordings made during passive limb movement, evoked activity in S1 that was similar to that of the original movement. We also found that S1 neural populations could accurately discriminate different patterns of DRG stimulation across a wide range of stimulus pulse-rates. In studying the neural coding in S1, we also decoded the kinematics of active limb movement using multi-electrode recordings in the monkey. Neurons having both proprioceptive and cutaneous receptive fields contributed equally to this decoding. Some neurons were most informative of limb state in the recent past, but many others appeared to signal upcoming movements suggesting that they also were modulated by an efference copy signal. Finally, we show that a monkey was able to detect stimulation through a large percentage of electrodes implanted in area 2. We discuss the design of appropriate stimulus paradigms for conveying time-varying limb state information, and the relative merits and limitations of central and peripheral approaches