A comparison of two approaches to implementing propensity score methods following multiple imputation

Background. In observational research on causal effects, missing data and confounding are very common problems. Multiple imputation and propensity score methods have gained increasing interest as methods to deal with these, but despite their popularity methodologists have mainly focused on how they perform in isolation.   Methods. We studied two approaches to implementing propensity score methods following multiple imputation, both of which have been used in applied research, and compared their performance by way of Monte Carlo simulation for a continuous outcome and partially unobserved covariate, treatment or outcome data. In the first, so-called Within, approach, propensity score analysis is performed within each of m imputed datasets, and the resulting m effect estimates are averaged. In the Across approach, for each subject the m estimated propensity scores are averaged first, after which the propensity score method is implemented based on each subject’s average propensity score. Because of its common use, complete case analysis was also implemented. Five propensity score estimators were studied, including regression, matching, and inverse probability weighting.   Results. The Within approach was found to be superior to the Across approach in terms of bias as well as variance in settings with missing covariate data, when missing data were missing at random as well as when they were missing completely at random. In settings with incomplete treatment or outcome values only, the Within and Across approaches yielded similar results. Complete case analysis was generally least efficient and unbiased only in scenarios where missing data were missing completely at random.   Conclusion. We advise researchers not to use the Across approach as the default method, because even when data are missing completely at random, this may yield biased effect estimates. Instead, the Within is the preferred approach when implementing propensity score methods following multiple imputation

Chimpanzees (Pan troglodytes) Fail a What-Where-When Task but Find Rewards by Using a Location-Based Association Strategy

Recollecting the what-where-when of an episode, or episodic-like memory, has been established in corvids and rodents. In humans, a linkage between remembering the past and imagining the future has been recognised. While chimpanzees can plan for the future, their episodic-like memory has hardly been investigated. We tested chimpanzees (Pan troglodytes) with an adapted food-caching paradigm. They observed the baiting of two locations amongst four and chose one after a given delay (15 min, 1 h or 5 h). We used two combinations of food types, a preferred and a less preferred food that disappeared at different rates. The subjects had to base their choices on the time elapsed since baiting, and on their memory of which food was where. They could recover either their preferred food or the one that remained present. All animals failed to obtain the preferred or present foods above chance levels. They were like-wise unsuccessful at choosing baited cups above chance levels. The subjects, thus, failed to use any feature of the baiting events to guide their choices. Nonetheless, their choices were not random, but the result of a developed location-based association strategy. Choices in the second half of the study correlated with the rewards obtained at each location in the first half of the study, independent from the choices made for each location in the first half of the study. This simple location-based strategy yielded a fair amount of food. The animals' failure to remember the what-where-when in the presented set-up may be due to the complexity of the task, rather than an inability to form episodic-like memories, as they even failed to remember what was where after 15 minutes

Melanoma incidence and mortality in Scotland 1979–2003

We studied 12 450 cases of invasive melanoma diagnosed in Scotland in 1979–2003, by thickness, pathological type, and body site at ages under 40, 40–59, and 60 years and over. Melanoma incidence trebled in males from 3.57 to 10.93/105 per year, and increased 2.3-fold in females from 5.60 to 12.96/105 per year. The rate of increase fell in each successive 5-year period. The greatest increase was in males aged 60 years and over at diagnosis. Significant incidence increases were seen in melanomas <1 mm in all three age groups, but those >4 mm only increased significantly at ages 60 years and over. All histological types increased significantly at ages 60 years and over, and in this age group the greatest increase was seen on the head and neck. Five-year disease-free survival improved steadily. Survival figures for 1994–1998 ranged from 93.6% for males and 95.8% for females with tumours <1 mm, to 52.4 and 48.3%, respectively, for those with tumours >4 mm. Over the 25 years, melanoma mortality doubled in males from 1.1 to 2.4/105 per year, but was unchanged in females at 1.5/105 per year. Public education on melanoma is required both for primary prevention and earlier diagnosis, particularly for older males

RNA-sequencing reveals the complexities of the transcriptional response to lignocellulosic biofuel substrates in Aspergillus niger

Background: Saprobic fungi are the predominant industrial sources of Carbohydrate Active enZymes (CAZymes) used for the saccharification of lignocellulose during the production of second generation biofuels. The production of more effective enzyme cocktails is a key objective for efficient biofuel production. To achieve this objective, it is crucial to understand the response of fungi to lignocellulose substrates. Our previous study used RNA-seq to identify the genes induced in Aspergillus niger in response to wheat straw, a biofuel feedstock, and showed that the range of genes induced was greater than previously seen with simple inducers. Results: In this work we used RNA-seq to identify the genes induced in A. niger in response to short rotation coppice willow and compared this with the response to wheat straw from our previous study, at the same time-point. The response to willow showed a large increase in expression of genes encoding CAZymes. Genes encoding the major activities required to saccharify lignocellulose were induced on willow such as endoglucanases, cellobiohydrolases and xylanases. The transcriptome response to willow had many similarities with the response to straw with some significant differences in the expression levels of individual genes which are discussed in relation to differences in substrate composition or other factors. Differences in transcript levels include higher levels on wheat straw from genes encoding enzymes classified as members of GH62 (an arabinofuranosidase) and CE1 (a feruloyl esterase) CAZy families whereas two genes encoding endoglucanases classified as members of the GH5 family had higher transcript levels when exposed to willow. There were changes in the cocktail of enzymes secreted by A. niger when cultured with willow or straw. Assays for particular enzymes as well as saccharification assays were used to compare the enzyme activities of the cocktails. Wheat straw induced an enzyme cocktail that saccharified wheat straw to a greater extent than willow. Genes not encoding CAZymes were also induced on willow such as hydrophobins as well as genes of unknown function. Several genes were identified as promising targets for future study. Conclusions: By comparing this first study of the global transcriptional response of a fungus to willow with the response to straw, we have shown that the inducing lignocellulosic substrate has a marked effect upon the range of transcripts and enzymes expressed by A. niger. The use by industry of complex substrates such as wheat straw or willow could benefit efficient biofuel production

Difference in balance measures between patients with chronic ankle instability and patients after an acute ankle inversion trauma

Neuromuscular control of the ankle is disturbed in patients with chronic ankle instability due to an initial ankle inversion trauma. Static balance is assumed to be a measure for this disturbance. Functional (ankle) scores are another way to evaluate ankle impairment. The hypothesis was that there is a difference in static balance measures between small groups of healthy subjects, patients after an acute ankle inversion trauma and patients with chronic ankle instability and that static balance measures correlate well with functional scores. Static balance in healthy subjects (N = 15), patients after a primary ankle inversion injury (N = 14) and patients with chronic ankle instability (N = 23) was tested with a single leg test on a force plate (Postural Sway test) and on a compliant floor (Simple Balance test). Functional impairment was evaluated with the Karlsson, AOFAS and SF-36 (ankle) scores. There was a statistically significant and clinically relevant difference in functional (ankle) scores, but not a statistically significant difference in balance measures between the groups. Balance measures did not correlate to the functional scores. It was concluded that, despite a clinically relevant difference in functional outcome measures between the groups, static balance measures do not appear to be useful for clinical application in the individual patient

Fungal enzyme sets for plant polysaccharide degradation

Enzymatic degradation of plant polysaccharides has many industrial applications, such as within the paper, food, and feed industry and for sustainable production of fuels and chemicals. Cellulose, hemicelluloses, and pectins are the main components of plant cell wall polysaccharides. These polysaccharides are often tightly packed, contain many different sugar residues, and are branched with a diversity of structures. To enable efficient degradation of these polysaccharides, fungi produce an extensive set of carbohydrate-active enzymes. The variety of the enzyme set differs between fungi and often corresponds to the requirements of its habitat. Carbohydrate-active enzymes can be organized in different families based on the amino acid sequence of the structurally related catalytic modules. Fungal enzymes involved in plant polysaccharide degradation are assigned to at least 35 glycoside hydrolase families, three carbohydrate esterase families and six polysaccharide lyase families. This mini-review will discuss the enzymes needed for complete degradation of plant polysaccharides and will give an overview of the latest developments concerning fungal carbohydrate-active enzymes and their corresponding families

Evaluation of a Dutch school-based depression prevention program for youths in highrisk neighborhoods: study protocol of a two-armed randomized controlled trial

Contains fulltext : 102517.pdf (publisher's version ) (Open Access)Background Research has indicated that depression prevention programs attenuate the development of symptoms of depression in adolescents. To implement these programs on a large scale, implementation in a school setting with teachers providing the programs is needed. In the present study, the effectiveness of the Dutch depression prevention program Op Volle Kracht (OVK) provided by school teachers during school hours with adolescents from high risk neighborhoods will be tested. The mediating effects of cognitive distortions and alexithymia will be evaluated as well. We hypothesize that the OVK program will prevent or decrease reported depressive symptoms, and that this association will be mediated by cognitive distortions and alexithymia. Methods/Design Schools with at least 30% of their pupils living in low income areas in the Netherlands are invited to participate in the study. Classes from vocational training up to pre-university level are eligible and 1324 adolescents (11-14 years) will be participating in the study. Randomisation will be done at class level, randomly assigning participants to an intervention group (OVK) and a control group (care as usual), stratifying by school level (high versus low). Trained school teachers will be delivering the program, which covers cognitive-behavioral and social problem-solving skills. Longitudinal data will be collected with self-report measurements administered in the school setting at baseline, post intervention and at two follow ups (at 6 and 12 months). Primary outcome is the level of depressive symptoms, and secondary outcomes include: cognitive errors, response style, attributional style, alexithymia, stressful life events, substance use, happiness, and school grades. Discussion If the OVK program proves to be effective when it is provided by school teachers, a structural implementation of the program in the school curriculum will enhance the quality of the lives of adolescents and their families and will reduce costs in health care. In addition, the results of the study advances current knowledge on the underlying mechanisms of the development of depression and may aid the improvement of depression prevention programs in general.7 p

A randomized controlled trial testing the effectiveness of a universal school-based depression prevention program 'Op Volle Kracht' in the Netherlands

Contains fulltext : 102521.pdf (publisher's version ) (Open Access)Background: The incidence of depressive symptoms increases during adolescence, from 10.0% to 24.5% at age 11 to 15, respectively. Experiencing elevated levels of depressive symptoms increases the risk of a depressive disorder in adulthood. A universal school-based depression prevention program Op Volle Kracht (OVK) was developed, based on the Penn Resiliency Program, aimed at preventing the increase of depressive symptoms during adolescence and enhancing positive development. In this study the effectiveness of OVK will be tested and possible mediators of program effects will be focus of study as well. Method: The effectiveness of OVK will be tested in a randomized controlled trial with two conditions, intervention (OVK) and control condition (care as usual). Schools are randomly assigned to research conditions. OVK will be incorporated in the school curriculum, maximizing program attendance. OVK consists of 16 lessons of 50 min, given by trained psychologists to groups of 11-15 students. OVK contains Cognitive Behavioral Therapy, social skills training, problem solving and decision making. Outcomes are measured at 6, 12, 18 and 24 months follow up, to monitor long term program effects. Primary outcome is level of depressive symptoms, secondary outcomes are: anxiety, hopelessness, cognitive bias, substance use, truancy, life satisfaction, coping, self-efficacy, optimism, happiness, friendship, school performance and school attitude. The questionnaires for students will be administered in the school setting. Parents will complete a questionnaire at baseline only. Discussion: In this paper the study into the effectiveness of the depression prevention program OVK was described. It is expected that OVK will prevent the increase in depressive symptoms during adolescence and enhance positive development in the intervention condition, compared to the control condition. If OVK will be effective, it can be implemented in the school context by which numerous adolescents can be reached.9 p

Enzyme-linked immunoassay for dengue virus IgM and IgG antibodies in serum and filter paper blood

BACKGROUND: The reproducibilty of dengue IgM and IgG ELISA was studied in serum and filter paper blood spots from Vietnamese febrile patients. METHODS: 781 pairs of acute (t0) and convalescent sera, obtained after three weeks (t3) and 161 corresponding pairs of filter paper blood spots were tested with ELISA for dengue IgG and IgM. 74 serum pairs were tested again in another laboratory with similar methods, after a mean of 252 days. RESULTS: Cases were classified as no dengue (10 %), past dengue (55%) acute primary (7%) or secondary (28%) dengue. Significant differences between the two laboratories' results were found leading to different diagnostic classification (kappa 0.46, p < 0.001). Filter paper results correlated poorly to serum values, being more variable and lower with a mean (95% CI) difference of 0.82 (0.36 to 1.28) for IgMt3, 0.94 (0.51 to 1.37) for IgGt0 and 0.26 (-0.20 to 0.71) for IgGt3. This also led to differences in diagnostic classification (kappa value 0.44, p < 0.001) The duration of storage of frozen serum and dried filter papers, sealed in nylon bags in an air-conditioned room, had no significant effect on the ELISA results. CONCLUSION: Dengue virus IgG antibodies in serum and filter papers was not affected by duration of storage, but was subject to inter-laboratory variability. Dengue virus IgM antibodies measured in serum reconstituted from blood spots on filter papers were lower than in serum, in particular in the acute phase of disease. Therefore this method limits its value for diagnostic confirmation of individual patients with dengue virus infections. However the detection of dengue virus IgG antibodies eluted from filter paper can be used for sero-prevalence cross sectional studies