Algorithm of OMA for large-scale orthology inference

Since the publication of our article (Roth, Gonnet, and Dessimoz: BMC Bioinformatics 2008 9: 518), we have noticed several errors, which we correct in the following.     

Trends in overweight from 1980 through 2001 among preschool-aged children enrolled in a health maintenance organization

Objective: To examine overweight trends over a 22‐year period among preschool‐aged children from primarily middle‐income families enrolled in a health maintenance organization. Research Methods and Procedures: From well‐child care visits to a Massachusetts health maintenance organization, we randomly selected one visit per child per calendar year, yielding a study sample of 120,680 children seen at 366,109 visits from 1980 through 2001. Using multivariate logistic regression models accounting for repeated observations of individual children across years, we estimated trends in prevalence of overweight (weight‐for‐length/height ≥ 95th percentile) and at‐risk‐for‐overweight (85th to 95th percentile). Results: Over the 22‐year study period, the observed prevalence of overweight increased from 6.3% to 10.0% and at‐risk‐for‐overweight increased from 11.1% to 14.4%. These increases were evident among all groups of children including infants < 6 months of age. Overall, the adjusted odds ratios were 1.21 per decade (95% confidence interval, 1.17 to 1.25) for overweight and 1.06 per decade (95% confidence interval, 1.03 to 1.08) for at‐risk‐for‐overweight. Discussion: Rates of overweight are increasing in very young children, even infants, from primarily middle‐class families.     

Maternal corticotropin-releasing hormone levels during pregnancy and offspring adiposity

Objective: Animal models suggest that fetal exposure to glucocorticoids can program adiposity, especially central adiposity, later in life. We examined associations of maternal corticotropin‐releasing hormone (CRH) levels in the late 2nd trimester of pregnancy, a marker of fetal glucocorticoid exposure, with child adiposity at age 3 years. Research Methods and Procedures: We analyzed data from 199 participants in Project Viva, a prospective cohort study of pregnant women and their children, At age 3 years, the main outcomes were age‐sex‐specific BMI z score and the sum of subscapular (SS) and triceps (TR) skinfold thicknesses to represent overall adiposity, and ratio of SS to TR (SS:TR) to represent central adiposity. Results: Mean (standard deviation) maternal 2nd trimester log CRH was 4.94 (0.56) pg/mL. At age 3, mean (standard deviation) for BMI z score was 0.52 (1.02); for SS + TR, 16.51 (3.94) mm; and for SS:TR, 0.67 (0.17). Log CRH was mildly inversely correlated with birth weight (r = ?0.08), chiefly because of its association with length of gestation (r = ?0.21) rather than fetal growth (r = ?0.004). After adjustment for sociodemographic factors, maternal smoking, BMI, and gestational weight gain, fetal growth, length of gestation, breastfeeding duration, and (for SS:TR only) child's 3‐year BMI, each increment of 1 unit of log CRH was associated with a reduction in BMI z score [?0.43; 95% confidence interval (CI), ?0.73, ?0.14; p = 0.004] and possible reduction in SS + TR (?1.10; 95% CI, ?2.33, 0.14; p = 0.08). In contrast, log CRH was associated with higher SS:TR (0.07; 95% CI, 0.02, 0.13; p = 0.007). Discussion: Fetal exposure to glucocorticoids, although associated with an overall decrease in body size, may cause an increase in central adiposity.     

Web‐based Weight Loss in Primary Care: A Randomized Controlled Trial

Evidence is lacking regarding effective and sustainable weight loss approaches for use in the primary care setting. We conducted a 12-week randomized controlled trial to evaluate the short-term efficacy of a web-based weight loss intervention among 101 primary care patients with obesity and hypertension. Patients had access to a comprehensive website that used a moderate-intensity weight loss approach designed specifically for web-based implementation. Patients also participated in four (two in-person and two telephonic) counseling sessions with a health coach. Intent-to-treat analysis showed greater weight loss at 3 months (−2.56 kg; 95% CI −3.60, −1.53) among intervention participants (−2.28 ± 3.21 kg), relative to usual care (0.28 ± 1.87 kg). Similar findings were observed among intervention completers (−3.05 kg; 95% CI −4.24, −1.85). High rates of participant retention (84%) and website utilization were observed, with the greatest weight loss found among those with a high frequency of website logins (quartile 4 vs. 1: −4.16 kg; 95% CI −1.47, −6.84). The intervention's approach promoted moderate weight loss at 12 weeks, though greater weight loss was observed among those with higher levels of website utilization. Efficacious web-based weight loss interventions can be successfully offered in the primary care setting.     

Factors determining species richness of soil seed banks in lowland ancient woodlands

The demise of coppicing in UK ancient woodlands, combined with the planting of non-native, fast-growing conifers in the twentieth century, heightens the potential recharge value of ground flora seed banks. Soil cores from adjoining semi-natural and conifer-containing stands in four lowland ancient woods in central England were removed to establish seed bank species richness. During a fourteen-month germination trial soil from two depths yielded 6554 seedlings from 81 species, ten of which showed a strong affinity for ancient woodland conditions. Juncus effusus accounted for 80% of emergent seeds whilst 23 other species, including Lysimachia nummularia and Potentilla sterilis, were represented by only one individual. Species richness is described by a model that explains 40% of observed variance (P < 0.00001). The model has three significant variables: species richness increases as soil pH rises, and decreases with both depth and increasing time since the most recent planting/disturbance event. No difference was found in the density of seeds from species common to paired semi-natural and conifer-containing stands that were separated only by a woodland ride, suggesting prior management and environmental conditions have a greater influence on seed banks than current stand type. Sørensen similarity index values revealed poor congruence between above-ground vegetation and species in the seed bank. Taking pH measurements in conifer stands identified as younger in terms of planting/disturbance may help locate areas where greater numbers of species (including woodland specialists) are located. Caution is required, however, as these seed banks may also contain non-target, competitive species that may swamp the regeneration of woodland specialists.     

Correlates of Participation in a Pediatric Primary Care‐Based Obesity Prevention Intervention

The purpose of this study was to examine the correlates of participation in a childhood obesity prevention trial. We sampled parents of children recruited to participate in a randomized controlled trial. Eligible children were 2.0–6.9 years with BMI ≥95th percentile or 85th to <95th percentile if at least one parent was overweight. We attempted contact with parents of children who were potentially eligible. We recruited 475 parents via telephone following an introductory letter. We also interviewed 329 parents who refused participation. Parents who refused participation (n = 329) did not differ from those who participated (n = 475) by number of children at home (OR 0.94 per child; 95% CI: 0.77–1.15) or by child age (OR 1.07 per year; 95% CI: 0.95–1.20) or sex (OR 1.06 for females vs. males; 95% CI: 0.80–1.41). After multivariate adjustment, parents who were college graduates vs. <college graduates were less likely to participate (OR 0.62; 95% CI: 0.46–0.83). In addition, parents were less likely (OR 0.41; 95% CI: 0.31–0.56) to participate if their child was overweight vs. obese. Among the 115 refusers with obese children, 21% cited as a reason for refusal that their children did not have a weight problem, vs. 30% among the 214 refusers with overweight children. In conclusion, parents of preschool‐age children with a BMI 85–95th%ile are less likely to have their children participate in an obesity prevention trial than parents of children with BMI >95th%ile. One reason appears to be that they less frequently consider their children to have a weight problem.     

Calling time on alien plantscapes

Both urban and rural environments around the globe have become dominated by alien plant species to the extent that plantscapes from one region or country have become difficult to distinguish from many others. This process of plant community homogenisation comes at a cost to cultural identity and undermines people's sense of place. Although invasive alien plant species have received considerable attention in recent decades, issues with non-invasive alien plant species have largely been ignored, and yet they contribute significantly to biotic homogeneity and impose an ever accumulating invasion debt: a debt that increases in proportion with their population sizes. By contrast, an abundance of native species in the places where people live is important for strengthening commitment to biodiversity conservation. Is there therefore sufficient evidence of harm from increasing numbers of non-invasive alien plants to justify local and central governments introducing measures to substantially reduce the proportion of non-invasive aliens in both urban and rural environments?     

PIDDosome‐induced p53‐dependent ploidy restriction facilitates hepatocarcinogenesis

Polyploidization frequently precedes tumorigenesis but also occurs during normal development in several tissues. Hepatocyte ploidy is controlled by the PIDDosome during development and regeneration. This multi‐protein complex is activated by supernumerary centrosomes to induce p53 and restrict proliferation of polyploid cells, otherwise prone for chromosomal instability. PIDDosome deficiency in the liver results in drastically increased polyploidy. To investigate PIDDosome‐induced p53‐activation in the pathogenesis of liver cancer, we chemically induced hepatocellular carcinoma (HCC) in mice. Strikingly, PIDDosome deficiency reduced tumor number and burden, despite the inability to activate p53 in polyploid cells. Liver tumors arise primarily from cells with low ploidy, indicating an intrinsic pro‐tumorigenic effect of PIDDosome‐mediated ploidy restriction. These data suggest that hyperpolyploidization caused by PIDDosome deficiency protects from HCC. Moreover, high tumor cell density, as a surrogate marker of low ploidy, predicts poor survival of HCC patients receiving liver transplantation. Together, we show that the PIDDosome is a potential therapeutic target to manipulate hepatocyte polyploidization for HCC prevention and that tumor cell density may serve as a novel prognostic marker for recurrence‐free survival in HCC patients.