Causal analysis of case-control data

In a series of papers, Robins and colleagues describe inverse probability of treatment weighted (IPTW) estimation in marginal structural models (MSMs), a method of causal analysis of longitudinal data based on counterfactual principles. This family of statistical techniques is similar in concept to weighting of survey data, except that the weights are estimated using study data rather than defined so as to reflect sampling design and post-stratification to an external population. Several decades ago Miettinen described an elementary method of causal analysis of case-control data based on indirect standardization. In this paper we extend the Miettinen approach using ideas closely related to IPTW estimation in MSMs. The technique is illustrated using data from a case-control study of oral contraceptives and myocardial infarction

Variability in spawning frequency and reproductive development of the narrow-barred Spanish mackerel (Scomberomorus commerson) along the west coast of Australia

The narrow-barred Spanish mackerel (Scomberomorus commerson) is widespread throughout the Indo-West Pacific region. This study describes the reproductive biology of S. commerson along the west coast of Australia, where it is targeted for food consumption and sports fishing. Development of testes occurred at a smaller body size than for ovaries, and more than 90% of males were sexually mature by the minimum legal length of 900 mm TL compared to 50% of females. Females dominated overall catches although sex ratios within daily catches vary considerably and females were rarely caught when spaw n ing. Scomberomorus commerson are seasonally abundant in coastal waters and most of the commercial catch is taken prior to the reproductive season. Spawning occurs between about August and November in the Kimberley region and between October and January in the Pilbara region. No spawning activity was recorded in the more southerly West Coast region, and only in the north Kimberley region were large numbers of fish with spawning gonads collected. Catches dropped to a minimum when spawning began in the Pilbara region, when fish became less abundant in inshore waters and inclement weather conditions limited fishing on still productive offshore reefs. Final maturation and ovulation of oocytes took place within a 24-hour period, and females spawned in the afternoon-evening every three days. A third of these spawning females released batches of eggs on consecutive days. Relationships between length, weight, and batch fecundity are presented

Biological characteristics and mortality of western butterfish (Pentapodus vitta), an abundant bycatch species of prawn trawling and recreational fishing in a large subtropical embayment

The western butterfish (Pentapodus vitta) is numerous in the bycatch of prawn trawling and recreational fishing in Shark Bay, Western Australia. We have thus determined crucial aspects of its biological characteristics and the potential impact of fishing on its abundance within this large subtropical marine embayment. Although both sexes attained a maximum age of 8 years, males grow more rapidly and to a larger size. Maturity is attained at the end of the first year of life and spawning occurs between October and January. The use of a Bayesian approach to combine independent estimates for total mortality, Z, and natural mortality, M, yielded slightly higher point estimates for Z than M. This result indicates that P. vitta is lightly impacted by fishing. It is relevant that, potentially, the individuals can spawn twice before recruitment into the fishery and that 73% of recreationally caught individuals are returned live to the water

Extended Photometry for the DEEP2 Galaxy Redshift Survey: A Testbed for Photometric Redshift Experiments

This paper describes a new catalog that supplements the existing DEEP2 Galaxy Redshift Survey photometric and spectroscopic catalogs with ugriz photometry from two other surveys; the Canada-France-Hawaii Legacy Survey (CFHTLS) and the Sloan Digital Sky Survey (SDSS). Each catalog is cross-matched by position on the sky in order to assign ugriz photometry to objects in the DEEP2 catalogs. We have recalibrated the CFHTLS photometry where it overlaps DEEP2 in order to provide a more uniform dataset. We have also used this improved photometry to predict DEEP2 BRI photometry in regions where only poorer measurements were available previously. In addition, we have included improved astrometry tied to SDSS rather than USNO-A2.0 for all DEEP2 objects. In total this catalog contains ~27,000 objects with full ugriz photometry as well as robust spectroscopic redshift measurements, 64% of which have r > 23. By combining the secure and accurate redshifts of the DEEP2 Galaxy Redshift Survey with ugriz photometry, we have created a catalog that can be used as an excellent testbed for future photo-z studies, including tests of algorithms for surveys such as LSST and DES.Comment: 12 pages, 6 figures and 5 tables. Accepted to The Astrophysical Journal Supplement. Catalogs are publicly available at http://deep.ps.uci.edu/DR4/photo.extended.htm

Female teat size is a reliable indicator of annual breeding success in European badgers: Genetic validation

Assessing which females have bred successfully is a central requirement in many ecological field studies, providing an estimate of the effective female population size. Researchers have applied teat measurements previously to assess whether females, in a variety of mammalian species, have bred; however, this technique has not been validated genetically. Furthermore, several analytical techniques are available to classify individuals, but their misclassification rates have not been compared. We used 22 microsatellite loci to assign maternity, with 95% confidence, within a high-density population of European badgers Meles meles, as plural and subterranean breeding means that maternity cannot be inferred from behavioural observations. The teat lengths and diameters of 136 females, measured May–July 1994–2005, from social groups in which all offspring were assigned a mother, were reliable indicators of recent breeding success. A Generalised Linear Mixed Model (GLMM) classified both breeding and non-breeding females with lower error rates than discriminant analyses and crude teat-size criteria. The GLMM model logit probability = −20 + 1.8 month + 1.6 mean teat length + 1.0 mean teat diameter can be applied quickly in the field to assess the probability with which a female badger should be assigned maternity. This is a low-cost measure which, after validation, could be used in other badger or mammalian populations to assess the breeding success of females. This may be a particularly useful welfare tool for veterinary practitioners, especially during badger culls

Best Practices for Tourism Center Development Along the Red Sea Coast

The spectacular coastlines along Egypt\u27s Red Sea and Gulf of Aqaba are the focus for one of the fastest growing tourism economies in the world. In order to accomplish national objectives for growth in permanent, well-paying jobs and in foreign exchange earnings, the Tourism Development Authority (TDA) has launched an initiative to make land available to investors for resort development along these coastlines. As of December, 1997, 6,000 hotel rooms are under construction in the Red Sea region and the TDA has proposals for at least 240 major resorts to be built by the year 2020. While this program has begun to yield impressive results in terms of new hotel construction, tourism jobs and tourist visitations, TDA has recognized that priority must be given to guiding private development in ways that protect Egypt\u27s natural heritage and insure that tourism can be sustained far into the future. It is clear from experience to date that such rapid growth, if not carefully planned and managed, threatens the very attractions that bring visitors here. In the best practices described here, TDA defines well planned and managed -- as distinct from haphazard and destructive -- tourism development for the Red Sea coastal environment. We look to lessons gained from several case studies of tourism center sites being jointly planned by TDA and development companies and from studies of successful established tourism centers in Egypt and from other parts of the world. We also draw upon technical literature from a variety of related fields, including marine biology, landscape architecture, engineering, tourism marketing, environmental planning, and others. These lessons and research are distilled into best practices for the planning and siting of new tourism centers and for the use and protection of environmental assets adjacent to the centers including the coral reef ecosystems, the beaches and headlands, the setback areas along coastal waters, and the surrounding desert landscape. This Best Practices Handbook is designed to be practical, well-illustrated and easily understood. It covers aspects of tourism center development that will: assist the development community to achieve environmentally sound, aesthetically pleasing and market-sensitive tourism centers, and assist the TDA and other public agencies by providing benchmarks on which to set environmental policies, guide the location of tourism centers and the subdivision of public lands, judge development plans and proposals, and base environmental management regulations. In the first section, Best Practices focuses on the framework for tourism development and environmental protection: the roles and responsibilities of key groups and the development process. The subsequent section describes the unique physical and environmental context in which tourism development is occurring and the special measures needed to respect these development shaping features. The subsequent sections address the best practices to accomplish sustainable tourism development. The best practices are not presented as a rigid set of prescribed steps and procedures, but rather as guidance and assistance in designing successful tourism facilities and managing the environmental assets on which tourism depends. Furthermore, this should be seen as our first effort. We intend to build upon and refine these practices as wel gain continued experience. Your suggestions for improvement will be sincerely appreciated

Leaf litter mixtures alter microbial community development: Mechanisms for non-additive effects in litter decomposition

To what extent microbial community composition can explain variability in ecosystem processes remains an open question in ecology. Microbial decomposer communities can change during litter decomposition due to biotic interactions and shifting substrate availability. Though relative abundance of decomposers may change due to mixing leaf litter, linking these shifts to the non-additive patterns often recorded in mixed species litter decomposition rates has been elusive, and links community composition to ecosystem function. We extracted phospholipid fatty acids (PLFAs) from single species and mixed species leaf litterbags after 10 and 27 months of decomposition in a mixed conifer forest. Total PLFA concentrations were 70% higher on litter mixtures than single litter types after 10 months, but were only 20% higher after 27 months. Similarly, fungal-to-bacterial ratios differed between mixed and single litter types after 10 months of decomposition, but equalized over time. Microbial community composition, as indicated by principal components analyses, differed due to both litter mixing and stage of litter decomposition. PLFA biomarkers a15∶0 and cy17∶0, which indicate gram-positive and gram-negative bacteria respectively, in particular drove these shifts. Total PLFA correlated significantly with single litter mass loss early in decomposition but not at later stages. We conclude that litter mixing alters microbial community development, which can contribute to synergisms in litter decomposition. These findings advance our understanding of how changing forest biodiversity can alter microbial communities and the ecosystem processes they mediate

The extracellular matrix, p53 and estrogen compete to regulate cell-surface Fas/Apo-1 suicide receptor expression in proliferating embryonic cerebral cortical precursors, and reciprocally, Fas-ligand modifies estrogen control of cell-cycle proteins

BACKGROUND: Apoptosis is important for normal cerebral cortical development. We previously showed that the Fas suicide receptor was expressed within the developing cerebral cortex, and that in vitro Fas activation resulted in caspase-dependent death. Alterations in cell-surface Fas expression may significantly influence cortical development. Therefore, in the following studies, we sought to identify developmentally relevant cell biological processes that regulate cell-surface Fas expression and reciprocal consequences of Fas receptor activation. RESULTS: Flow-cytometric analyses identified two distinct neural sub-populations that expressed Fas on their cell surface at high (Fas(Hi)) or moderate (Fas(Mod)) levels. The anti-apoptotic protein FLIP further delineated a subset of Fas-expressing cells with potential apoptosis-resistance. Fas(Mod )precursors were mainly in G0, while Fas(Hi )precursors were largely apoptotic. However, birth-date analysis indicated that neuroblasts express the highest levels of cell-surface Fas at the end of S-phase, or after their final round of mitosis, suggesting that Fas expression is induced at cell cycle checkpoints or during interkinetic nuclear movements. Fas(Hi )expression was associated with loss of cell-matrix adhesion and anoikis. Activation of the transcription factor p53 was associated with induction of Fas expression, while the gonadal hormone estrogen antagonistically suppressed cell-surface Fas expression. Estrogen also induced entry into S-phase and decreased the number of Fas-expressing neuroblasts that were apoptotic. Concurrent exposure to estrogen and to soluble Fas-ligand (sFasL) suppressed p21/waf-1 and PCNA. In contrast, estrogen and sFasL, individually and together, induced cyclin-A expression, suggesting activation of compensatory survival mechanisms. CONCLUSIONS: Embryonic cortical neuronal precursors are intrinsically heterogeneous with respect to Fas suicide-sensitivity. Competing intrinsic (p53, cell cycle, FLIP expression), proximal (extra-cellular matrix) and extrinsic factors (gonadal hormones) collectively regulate Fas suicide-sensitivity either during neurogenesis, or possibly during neuronal migration, and may ultimately determine which neuroblasts successfully contribute neurons to the differentiating cortical plate