Counterfactuals and causal inference: Methods and principles for social research

"Most quantitative empirical analyses are motivated by the desire to estimate the causal effect of an independent variable on a dependent variable. Although the randomized experiment is the most powerful design for this task, in most social science research done outside of psychology, experimental designs are infeasible. (Winship & Morgan, 1999, p. 659)." This quote from earlier work by Winship and Morgan, which was instrumental in setting the groundwork for their book, captures the essence of our review of Morgan and Winship's book: It is about causality in nonexperimental settings.

Bacterial sensors: synthetic design and application principles

Bacterial reporters are live, genetically engineered cells with promising application in bioanalytics. They contain genetic circuitry to produce a cellular sensing element, which detects the target compound and relays the detection to specific synthesis of so-called reporter proteins (the presence or activity of which is easy to quantify). Bioassays with bacterial reporters are a useful complement to chemical analytics because they measure biological responses rather than total chemical concentrations. Simple bacterial reporter assays may also replace more costly chemical methods as a first line sample analysis technique. Recent promising developments integrate bacterial reporter cells with microsystems to produce bacterial biosensors. This lecture presents an in-depth treatment of the synthetic biological design principles of bacterial reporters, the engineering of which started as simple recombinant DNA puzzles, but has now become a more rational approach of choosing and combining sensing, controlling and reporting DNA 'parts'. Several examples of existing bacterial reporter designs and their genetic circuitry will be illustrated. Besides the design principles, the lecture also focuses on the application principles of bacterial reporter assays. A variety of assay formats will be illustrated, and principles of quantification will be dealt with. In addition to this discussion, substantial reference material is supplied in various Annexes.

New Avenues for Theoretical Contributions in Enterprise Architecture Principles - A Literature Review

Enterprise Architecture (EA), which has been approached by both academia and industry, is considered comprising not only architectural representations, but also principles guiding architecture's design and evolution. Even though the concept of EA principles has been defined as the integral part of EA, the number of publications on this subject is very limited and only a few organizations use EA principles to manage their EA endeavors. In order to critically assess the current state of research and identify research gaps in EA principles, we focus on four general aspects of theoretical contributions in IS. By applying these aspects to EA principles, we outline future research directions in EA principles nature, adoption, practices, and impact.

Simultaneous Mendelian and clonal genome transmission in a sexually reproducing, all-triploid vertebrate.

Meiosis in triploids faces the seemingly insuperable difficulty of dividing an odd number of chromosome sets by two. Triploid vertebrates usually circumvent this problem through either asexuality or some forms of hybridogenesis, including meiotic hybridogenesis that involve a reproductive community of different ploidy levels and genome composition. Batura toads (Bufo baturae; 3n = 33 chromosomes), however, present an all-triploid sexual reproduction. This hybrid species has two genome copies carrying a nucleolus-organizing region (NOR+) on chromosome 6, and a third copy without it (NOR-). Males only produce haploid NOR+ sperm, while ova are diploid, containing one NOR+ and one NOR- set. Here, we conduct sibship analyses with co-dominant microsatellite markers so as (i) to confirm the purely clonal and maternal transmission of the NOR- set, and (ii) to demonstrate Mendelian segregation and recombination of the NOR+ sets in both sexes. This new reproductive mode in vertebrates ('pre-equalizing hybrid meiosis') offers an ideal opportunity to study the evolution of non-recombining genomes. Elucidating the mechanisms that allow simultaneous transmission of two genomes, one of Mendelian, the other of clonal inheritance, might shed light on the general processes that regulate meiosis in vertebrates.

A comparison of three methods of Mendelian randomization when the genetic instrument, the risk factor and the outcome are all binary.

The method of instrumental variable (referred to as Mendelian randomization when the instrument is a genetic variant) has been initially developed to infer on a causal effect of a risk factor on some outcome of interest in a linear model. Adapting this method to nonlinear models, however, is known to be problematic. In this paper, we consider the simple case when the genetic instrument, the risk factor, and the outcome are all binary. We compare via simulations the usual two-stages estimate of a causal odds-ratio and its adjusted version with a recently proposed estimate in the context of a clinical trial with noncompliance. In contrast to the former two, we confirm that the latter is (under some conditions) a valid estimate of a causal odds-ratio defined in the subpopulation of compliers, and we propose its use in the context of Mendelian randomization. By analogy with a clinical trial with noncompliance, compliers are those individuals for whom the presence/absence of the risk factor X is determined by the presence/absence of the genetic variant Z (i.e., for whom we would observe X = Z whatever the alleles randomly received at conception). We also recall and illustrate the huge variability of instrumental variable estimates when the instrument is weak (i.e., with a low percentage of compliers, as is typically the case with genetic instruments for which this proportion is frequently smaller than 10%) where the inter-quartile range of our simulated estimates was up to 18 times higher compared to a conventional (e.g., intention-to-treat) approach. We thus conclude that the need to find stronger instruments is probably as important as the need to develop a methodology allowing to consistently estimate a causal odds-ratio.

Dermatite atopique de l'enfant: principes généraux de la prise en charge [Atopic dermatitis in children: general principles of management].

Atopic dermatitis is the most frequent dermatosis in childhood. Numerous studies underscored the central role of skin barrier alterations in the pathogenesis of the inflammatory skin lesions. The management of atopic dermatitis has to be multidimensional. It combines among others some daily local care and a sporadic topical anti-inflammatory treatment during the acute flare-ups. The objective of this article is to summarize, in light of the recent European guidelines, the general principles of management of atopic dermatitis, for the general practitioner.

France's Charter for the Environment : of Presidents, Principles and Environmental Protection

France amended its constitution in 2005 to include a Charter for the Environment. The Charter lays out France's commitment to supporting the right to a 'balanced environment'. This article first traces the Charter's origins to a legacy-building presidential initiative. Jacques Chirac decided to invest in a neglected policy domain in which his own majority had shown little interest. He was obliged to intervene repeatedly in order to bring this project to a successful conclusion. In doing so, he staked out environmental affairs as an area of potential presidential supremacy. Next, the content of the Charter is examined. In this document, French traditions of universalism come together with an international movement for anticipatory environmental protection. This is reflected in the constitutionalisation of the precautionary principle, which emerged as the most controversial part of the Charter. The debates this provoked tended to caricature a risk-management principle whose meaning has been carefully refined to forestall objections. Finally, the Charter's potential efficacy is analysed. The post-Charter record of legislative and judicial activity concerning the environment is meagre, but not wholly inauspicious.

Plasmid electrotransfer of eye ciliary muscle: principles and therapeutic efficacy using hTNF-alpha soluble receptor in uveitis.

Due to its small size and particular isolating barriers, the eye is an ideal target for local therapy. Recombinant protein ocular delivery requires invasive and painful repeated injections. Alternatively, a transfected tissue might be used as a local producer of transgene-encoded therapeutic protein. We have developed a nondamaging electrically mediated plasmid delivery technique (electrotransfer) targeted to the ciliary muscle, which is used as a reservoir tissue for the long-lasting expression and secretion of therapeutic proteins. High and long-lasting reporter gene expression was observed, which was restricted to the ciliary muscle. Chimeric TNF-alpha soluble receptor (hTNFR-Is) electrotransfer led to elevated protein secretion in aqueous humor and to drastic inhibition of clinical and histological inflammation scores in rats with endotoxin-induced uveitis. No hTNFR-Is was detected in the serum, demonstrating the local delivery of proteins using this method. Plasmid electrotransfer to the ciliary muscle, as performed in this study, did not induce any ocular pathology or structural damage. Local and sustained therapeutic protein production through ciliary muscle electrotransfer is a promising alternative to repeated intraocular protein administration for a large number of inflammatory, degenerative, or angiogenic diseases.

Oxidation of proteins: Basic principles and perspectives for blood proteomics.

Protein oxidation mechanisms result in a wide array of modifications, from backbone cleavage or protein crosslinking to more subtle modifications such as side chain oxidations. Protein oxidation occurs as part of normal regulatory processes, as a defence mechanism against oxidative stress, or as a deleterious processes when antioxidant defences are overcome. Because blood is continually exposed to reactive oxygen and nitrogen species, blood proteomics should inherently adopt redox proteomic strategies. In this review, we recall the biochemical basis of protein oxidation, review the proteomic methodologies applied to analyse redox modifications, and highlight some physiological and in vitro responses to oxidative stress of various blood components.

The ciliary smooth muscle electrotransfer: basic principles and potential for sustained intraocular production of therapeutic proteins.

BACKGROUND: We have developed a nonviral gene therapy method based on the electrotransfer of plasmid in the ciliary muscle. These easily accessible smooth muscle cells could be turned into a biofactory for any therapeutic proteins to be secreted in a sustained manner in the ocular media. METHODS: Electrical conditions, design of electrodes, plasmid formulation, method and number of injections were optimized in vivo in the rat by localizing β-galactosidase expression and quantifying reporter (luciferase) and therapeutic (anti-tumor necrosis factor) proteins secretion in the ocular media. Anatomical measurements were performed via human magnetic resonance imaging to design a human eye-sized prototype that was tested in the rabbit. RESULTS: In the rat, transscleral injection of 30 µg of plasmid diluted in half saline (77 mM NaCl) followed by application of eight square-wave electrical pulses (15 V, 10 ms, 5.3 Hz) using two platinum/iridium electrodes, an internal wire and an external sheet, delivered plasmid efficiently to the ciliary muscle fibers. Gene transfer resulted in a long-lasting (at least 5 months) and plasmid dose-/injection number- dependent secretion of different molecular weight proteins mainly in the vitreous, without any systemic exposure. Because ciliary muscle anatomical measurements remained constant among ages in adult humans, an integrated device comprising needle-electrodes was designed and manufactured. Its usefulness was validated in the rabbit. CONCLUSIONS: Plasmid electrotransfer to the ciliary muscle with a suitable medical device represents a promising local and sustained protein delivery system for treating posterior segment diseases, avoiding repeated intraocular injections.

Does CRP Play a Causal Role in the Development of Coronary Heart Disease: Results of a Mendelian Randomisation Experiment Involving 128,935 People

Background: C-reactive protein (CRP) is associated with risk of coronary heart disease (CHD). Whether CRP is causally associated with CHD or merely a marker of underlying atherosclerosis is uncertain. Methods: We used a Mendelian randomisation design to investigate the causal relationship of CRP with CHD. We identified three genetic variants in the CRP locus (rs7553007, rs1130864 and rs1205) which influence CRP levels. We tested the three SNPs for association with CHD amongst 28,112 CHD cases and 100,823 controls. We then compared the observed relationship between the SNPs and CHD, with that predicted from the association of SNPs with CRP levels, and of CRP levels with CHD. Results: SNPs in the CRP locus were not associated with CHD: rs7553007, OR 0.98 (95% CI, 0.94-1.01); rs1130864, OR 1.00 (95% CI, 0.86-1.15); rs1205, OR 1.03 (95% CI, 0.99-1.07); combined OR for all three SNPs, 1.00 (95% CI, 0.97-1.02), per 20% lower CRP (figure). In contrast, the predicted OR for CHD from a 20% lower CRP level is 0.94 (95% CI, 0.94- 0.95), based on meta-analysis of observational studies. Conclusions: Though CRP variants are associated with CRP levels, and CRP levels with risk of CHD, we observed that CRP variants are not associated with CHD risk. Our Mendelian randomisation experiment strongly argues against a causal association of CRP with CHD.

Use of a Mendelian randomization approach to assess the causal relation of gamma-Glutamyltransferase with blood pressure and serum insulin levels.

Elevated levels of γ-glutamyltransferase (GGT) have been associated with elevated blood pressure (BP) and diabetes. However, the causality of these relations has not been addressed. The authors performed a cross-sectional analysis (2003-2006) among 4,360 participants from the population-based Cohorte Lausannoise (CoLaus) Study (Lausanne, Switzerland). The rs2017869 variant of the γ-glutamyltransferase 1 (GGT1) gene, which explained 1.6% of the variance in GGT levels, was used as an instrument for Mendelian randomization (MR). Sex-specific GGT quartiles were strongly associated with both systolic and diastolic BP (all P's < 0.0001). After multivariable adjustment, these relations were attenuated but remained significant. Using MR, the authors observed no positive association of GGT with BP (systolic: β -5.68, 95% confidence interval (CI): -11.51, 0.16 (P = 0.06); diastolic: β = -2.24, 95% CI: -5.98, 1.49 (P = 0.24)). The association of GGT with insulin was also attenuated after multivariable adjustment but persisted in the fully adjusted model (β = 0.07, 95% CI: 0.04, 0.09; P < 0.0001). Using MR, the authors also observed a positive association of GGT with insulin (β = 0.19, 95% CI: 0.01, 0.37; P = 0.04). In conclusion, the authors found evidence for a direct causal relation of GGT with fasting insulin but not with BP.