Feature-level exploration of a published Affymetrix GeneChip control dataset

A comment on Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset by SE Choe, M Boutros, AM Michelson, GM Church and MS Halfon. Genome Biology 2005, 6:R16.     

Punishment and cooperation in nature

Humans use punishment to promote cooperation in laboratory experiments but evidence that punishment plays a similar role in non-human animals is comparatively rare. In this article, we examine why this may be the case by reviewing evidence from both laboratory experiments on humans and ecologically relevant studies on non-human animals. Generally, punishment appears to be most probable if players differ in strength or strategic options. Although these conditions are common in nature, punishment (unlike other forms of aggression) involves immediate payoff reductions to both punisher and target, with net benefits to punishers contingent on cheats behaving more cooperatively in future interactions. In many cases, aggression yielding immediate benefits may suffice to deter cheats and might explain the relative scarcity of punishment in nature.     

Male cleaner wrasses adjust punishment of female partners according to the stakes

Punishment is an important deterrent against cheating in cooperative interactions. In humans, the severity of cheating affects the strength of punishment which, in turn, affects the punished individual's future behaviour. Here, we show such flexible adjustments for the first time in a non-human species, the cleaner wrasse (Labroides dimidiatus), where males are known to punish female partners. We exposed pairs of cleaners to a model client offering two types of food, preferred 'prawn' items and less-preferred 'flake' items. Analogous to interactions with real clients, eating a preferred prawn item ('cheating') led to model client removal. We varied the extent to which female cheating caused pay-off reduction to the male and measured the corresponding severity of male punishment. Males punished females more severely when females cheated during interactions with high value, rather than low value, model clients; and when females were similar in size to the male. This pattern may arise because, in this protogynous hermaphrodite, cheating by similar-sized females may reduce size differences to the extent that females change sex and become reproductive competitors. In response to more severe punishment from males, females behaved more cooperatively. Our results show that punishment can be adjusted to circumstances and that such subtleties can have an important bearing on the outcome of cooperative interactions.     

Efficacy of once-daily indacaterol 75 mug relative to alternative bronchodilators in COPD: A study level and a patient level network meta-analysis

ABSTRACT: BACKGROUND: The objective of this study was to evaluate the comparative efficacy of indacaterol 75 mug once daily (OD), tiotropium 18 mug OD, salmeterol 50 mug twice daily (BID), formoterol 12 mug BID, and placebo for the treatment of chronic obstructive pulmonary disease (COPD) based on individual patient data (IPD) from randomized controlled trials (RCTs) from the indacaterol trial program and aggregate data (AD) identified from a systematic review of RCTs. METHODS: 21 RCTs were included in the AD analysis that evaluated: indacaterol 75 mug (n = 2 studies), indacaterol 150 mug (n = 3), indacaterol 300 mug (n = 2), tiotropium 18 mug (n = 10), salmeterol 50 mug (n = 6), and formoterol 12 mug (n = 4). All of the studies except for one head-to-head comparison (tiotropium vs. salmeterol) were placebo controlled. Outcomes of interest were trough forced expiratory volume in 1 s (FEV1) and St. George's Respiratory Questionnaire (SGRQ) total score at week 12. The AD from all trials was analysed simultaneously using a Bayesian network meta-analysis (NMA) and relative treatment effects between all regimens were obtained. In a separate analysis, the IPD available from the 6 indacaterol RCTs was analysed in a NMA. Treatment-by-covariate interactions were included in both analyses to improve similarity of the trials. RESULTS: All interventions compared were more efficacious than placebo regarding FEV1 at 12 weeks. Indacaterol 75 mug is expected to result in a comparable FEV1 at 12 weeks to tiotropium and salmeterol based on both IPD and AD analyses. In comparison to formoterol, the IPD and AD results indicate indacaterol 75 mug is more efficacious (IPD = 0.07 L difference; 95%Credible Interval (CrI) 0.02 to 0.11; AD = 0.05 L difference; 95%CrI 0.01; 0.09). In terms of SGRQ total score at 12 weeks, indacaterol 75 mug and formoterol were more efficacious than placebo, whereas for tiotropium and salmeterol the credible intervals included zero for the AD results only (tiotropium: -2.99 points improvement versus placebo; 95%CrI 6.48 to 0.43; salmeterol:-2.52; 95%CrI: -5.34; 0.44). Both IPD and AD results suggest that indacaterol 75 mug is expected to be comparable to all active treatments. CONCLUSIONS: Based on a synthesis of currently available AD RCT evidence as well as an IPD network meta-analysis of six RCTs, indacaterol 75 mug is expected to be at least as efficacious as formoterol and comparable to tiotropium and salmeterol regarding FEV1. Furthermore, indacaterol 75 mug shows comparable level of improvement in health-related quality of life to tiotropium, salmeterol, and formoterol, as measured by the SGRQ.     

The Effects of Juvenile Stress on Anxiety,Cognitive Bias and Decision Making in Adulthood: A Rat Model

Stress experienced in childhood is associated with an increased risk of developing psychiatric disorders in adulthood. These disorders are particularly characterized by disturbances to emotional and cognitive processes, which are not currently fully modeled in animals. Assays of cognitive bias have recently been used with animals to give an indication of their emotional/cognitive state. We used a cognitive bias test, alongside a traditional measure of anxiety (elevated plus maze), to investigate the effects of juvenile stress (JS) on adulthood behaviour using a rodent model. During the cognitive bias test, animals were trained to discriminate between two reward bowls based on a stimulus (rough/smooth sandpaper) encountered before they reached the bowls. One stimulus (e.g. rough) was associated with a lower value reward than the other (e.g. smooth). Once rats were trained, their cognitive bias was explored through the presentation of an ambiguous stimulus (intermediate grade sandpaper): a rat was classed as optimistic if it chose the bowl ordinarily associated with the high value reward. JS animals were lighter than controls, exhibited increased anxiety-like behaviour in the elevated plus maze and were more optimistic in the cognitive bias test. This increased optimism may represent an optimal foraging strategy for these underweight animals. JS animals were also faster than controls to make a decision when presented with an ambiguous stimulus, suggesting altered decision making. These results demonstrate that stress in the juvenile phase can increase anxiety-like behaviour and alter cognitive bias and decision making in adulthood in a rat model.     

Breast cancer risk and 6q22.33: combined results from Breast Cancer Association Consortium and Consortium of Investigators on Modifiers of BRCA1/2

Recently, a locus on chromosome 6q22.33 (rs2180341) was reported to be associated with increased breast cancer risk in the Ashkenazi Jewish (AJ) population, and this association was also observed in populations of non-AJ European ancestry. In the present study, we performed a large replication analysis of rs2180341 using data from 31,428 invasive breast cancer cases and 34,700 controls collected from 25 studies in the Breast Cancer Association Consortium (BCAC). In addition, we evaluated whether rs2180341 modifies breast cancer risk in 3,361 BRCA1 and 2,020 BRCA2 carriers from 11 centers in the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). Based on the BCAC data from women of European ancestry, we found evidence for a weak association with breast cancer risk for rs2180341 (per-allele odds ratio (OR)?=?1.03, 95% CI 1.00-1.06, p?=?0.023). There was evidence for heterogeneity in the ORs among studies (I(2)?=?49.3%; p?=?<0.004). In CIMBA, we observed an inverse association with the minor allele of rs2180341 and breast cancer risk in BRCA1 mutation carriers (per-allele OR?=?0.89, 95%CI 0.80-1.00, p?=?0.048), indicating a potential protective effect of this allele. These data suggest that that 6q22.33 confers a weak effect on breast cancer risk.     

Juvenile Female Aggression in Cooperatively Breeding Pied Babblers: Causes and Contexts

Sex biases in adult aggression have been well studied and commonly arise when resources which affect survival or lifetime reproductive success are less abundant or more valuable for individuals of one sex. Despite the prevalence of sex biases in adult aggression, evidence for sex biases in juvenile aggression is scant. Here, we present evidence for female‐biased juvenile aggression in cooperatively breeding pied babblers (Turdoides bicolor). Unlike most cases of non‐lethal sibling aggression, juvenile aggression in pied babblers does not seem to be determined by food availability. Instead, we found that juvenile aggression was related to adult dispersal patterns. This study shows that females that were more aggressive as juveniles attempted dispersal earlier than less aggressive females. Potential explanations for the association between juvenile aggression and adult dispersal patterns are discussed.     

Competitive interactions between two successful molluscan invaders of freshwaters: an experimental study

The New Zealand mud snail Potamopyrgus antipodarum (Hydrobiidae) and the pulmonate Physella acuta (Physidae) have invaded freshwaters in many parts of the world and become established. They co-exist in many streams, lakes and ponds in New Zealand, often at high densities. In the present study the effects of intraspecific- and interspecific interactions between the two species on growth and reproductive output were examined in laboratory mesocosms. In 30-day experiments, growth of Potamopyrgus antipodarum was lower in high density treatments than controls providing evidence for competition at higher densities of both snail species. No competitive effect was obtained for Physella acuta when controls were compared with high-density treatments, but growth was reduced at high densities of conspecifics. Numbers of juveniles released by Potamopyrgus antipodarum in 40 day trials declined at high snail densities and were lowest at high densities of conspecifics. Egg production by Physella acuta was also reduced at high snail densities. However, when the two species were kept together at equal densities (total snail density twice that of controls), egg production by Physella acuta was significantly higher than in all other treatments, suggesting facilitation by the congenor. Lastly, in a 10-day experiment, Physella acuta grew faster in water conditioned by Potamopyrgus antipodarum than in Physa-conditioned water, whereas Potamopyrgus antipodarum showed no growth response to Physella-conditioned water. Overall, our results indicate that growth and reproductive output of both snail species are influenced more by the density of conspecifics than the presence and density of the other species. The successful co-existence of the two species in New Zealand freshwaters therefore may be a reflection, at least in part, of few competitive interactions between them.     

The impact of mechanical impedance on the emergence of carrot and onion seedlings

The development of a method using wax layers to simulate the effect of strong soil crusts on seedling emergence is described. Wax layers of different strengths were prepared by melting together white soft paraffin and paraffin wax in different proportions. The wax discs were placed above seeds planted in wet, but well-aerated sand in controlled environments. The effect of adding charcoal to the wax discs to prevent transmission of light was also tested. When wax layer penetrometer pressure was 0.2–0.25 MPa, light transmission greatly decreased the final emergence of carrot, but not onion seedlings. Penetrometer pressures above 0.25 MPa greatly decreased emergence through black wax layers in both carrot and onion. The presence of 2–4 mm stones immediately below wax layers (to simulate aggregates) decreased the emergence of onion shoots through wax layers with penetrometer pressures of 0.25 MPa and above. The emergence of carrot and onion seedlings from wax layers was compared to emergence in the field from different soil types and aggregate sizes. In both laboratory and field experiments, carrot gave better emergence than onion when emergence was relatively poor. Results were consistent with the hypothesis that mechanical impedance is a major factor in poor crop emergence in temperate conditions.