Dinosaur tracks from the Kilmaluag Formation (Bathonian, Middle Jurassic) of Score Bay, Isle of Skye, Scotland, UK

Tracks of a juvenile theropod dinosaur with footprint lengths of between 2 and 9 cm as well as adults of the same ichnospecies with footprints of about 15–25 cm in length were found in the Bathonian (Middle Jurassic) Kilmaluag Formation of Score Bay, northwestern Trotternish Peninsula, Isle of Skye, Scotland, UK. Two footprint sizes occur together on the same bedding plane in the central portion of Score Bay, both in situ and on loose blocks. Another horizon containing footprints above this was also identified. The footprints from the lowest horizon were produced in a desiccated silty mud that was covered with sand. A close association of both adults and juveniles with similar travel direction indicated by the footprints may suggest post-hatching care in theropod dinosaurs. Other footprints, produced on a rippled sandy substrate, have been found on the slightly higher bedding plane at this locality. Loose blocks found 130 m to the northeast in the central part of Score Bay have not been correlated with any in situ sediments, but were preserved in a similar manner to those from the higher bedding plane. These tracks represent the youngest dinosaur remains yet found in Scotland

A Methodology for Flash Drought Identification: Application of Flash Drought Frequency across the United StatesJORDAN

With the increasing use of the term ‘‘flash drought’’ within the scientific community, Otkin et al. provide a general definition that identifies flash droughts based on their unusually rapid rate of intensi- fication. This study presents an objective percentile-based methodology that builds upon that work by identifying flash droughts using standardized evaporative stress ratio (SESR) values and changes in SESR over some period of time. Four criteria are specified to identify flash droughts: two that emphasize the vegetative impacts of flash drought and two that focus on the rapid rate of intensification. The method- ology was applied to the North American Regional Reanalysis (NARR) to develop a 38-yr flash drought climatology (1979–2016) across the United States. It was found that SESR derived from NARR data compared well with the satellite-based evaporative stress index for four previously identified flash drought events. Furthermore, four additional flash drought cases were compared with the U.S. Drought Monitor (USDM), and SESR rapidly declined 1–2 weeks before a response was evident with the USDM. From the climatological analysis, a hot spot of flash drought occurrence was revealed over the Great Plains, the Corn Belt, and the western Great Lakes region. Relatively few flash drought events occurred over mountainous and arid regions. Flash droughts were categorized based on their rate of intensification, and it was found that the most intense flash droughts occurred over the central Great Plains, Corn Belt, and western Great Lakes region

A Methodology for Flash Drought Identification: Application of Flash Drought Frequency across the United States

With the increasing use of the term ‘‘flash drought’’ within the scientific community, Otkin et al. provide a general definition that identifies flash droughts based on their unusually rapid rate of intensification. This study presents an objective percentile-based methodology that builds upon that work by identifying flash droughts using standardized evaporative stress ratio (SESR) values and changes in SESR over some period of time. Four criteria are specified to identify flash droughts: two that emphasize the vegetative impacts of flash drought and two that focus on the rapid rate of intensification. The methodology was applied to the North American Regional Reanalysis (NARR) to develop a 38-yr flash drought climatology (1979–2016) across the United States. It was found that SESR derived from NARR data compared well with the satellite-based evaporative stress index for four previously identified flash drought events. Furthermore, four additional flash drought cases were compared with the U.S. Drought Monitor (USDM), and SESR rapidly declined 1–2 weeks before a response was evident with the USDM. From the climatological analysis, a hot spot of flash drought occurrence was revealed over the Great Plains, the Corn Belt, and the western Great Lakes region. Relatively few flash drought events occurred over mountainous and arid regions. Flash droughts were categorized based on their rate of intensification, and it was found that the most intense flash droughts occurred over the central Great Plains, Corn Belt, and western Great Lakes region

Tracking a northern fulmar from a Scottish nesting site to the Charlie-Gibbs Fracture Zone : Evidence of linkage between coastal breeding seabirds and Mid-Atlantic Ridge feeding sites

Peer reviewedPublisher PD

Mouse allergen, lung function, and atopy in Puerto Rican children

Objective: To examine the relation between mouse allergen exposure and asthma in Puerto Rican children. Methods: Mus m 1, Der p 1, Bla g 2, and Fel d 1 allergens were measured in dust samples from homes of Puerto Rican children with (cases) and without (controls) asthma in Hartford, CT (n = 449) and San Juan (SJ), Puerto Rico (n = 678). Linear or logistic regression was used for the multivariate analysis of mouse allergen (Mus m 1) and lung function (FEV1 and FEV1/FVC) and allergy (total IgE and skin test reactivity (STR) to ≥1 allergen) measures. Results: Homes in SJ had lower mouse allergen levels than those in Hartford. In multivariate analyses, mouse allergen was associated with higher FEV1 in cases in Hartford (+70.6 ml, 95% confidence interval (CI) = 8.6-132.7 ml, P = 0.03) and SJ (+45.1 ml, 95% CI = -0.5 to 90.6 ml, P = 0.05). In multivariate analyses of controls, mouse allergen was inversely associated with STR to ≥1 allergen in non-sensitized children (odds ratio [OR] for each log-unit increment in Mus m 1 = 0.7, 95% CI = 0.5-0.9, P<0.01). In a multivariate analysis including all children at both study sites, each log-increment in mouse allergen was positively associated with FEV1 (+28.3 ml, 95% CI = 1.4-55.2 ml, P = 0.04) and inversely associated with STR to ≥1 allergen (OR for each log-unit increment in Mus m 1 = 0.8, 95% CI = 0.6-0.9, P<0.01). Conclusions: Mouse allergen is associated with a higher FEV1 and lower odds of STR to ≥1 allergen in Puerto Rican children. This may be explained by the allergen itself or correlated microbial exposures. © 2012 Forno et al

Using Prior Information from the Medical Literature in GWAS of Oral Cancer Identifies Novel Susceptibility Variant on Chromosome 4 - the AdAPT Method

Background: Genome-wide association studies (GWAS) require large sample sizes to obtain adequate statistical power, but it may be possible to increase the power by incorporating complementary data. In this study we investigated the feasibility of automatically retrieving information from the medical literature and leveraging this information in GWAS. Methods: We developed a method that searches through PubMed abstracts for pre-assigned keywords and key concepts, and uses this information to assign prior probabilities of association for each single nucleotide polymorphism (SNP) with the phenotype of interest - the Adjusting Association Priors with Text (AdAPT) method. Association results from a GWAS can subsequently be ranked in the context of these priors using the Bayes False Discovery Probability (BFDP) framework. We initially tested AdAPT by comparing rankings of known susceptibility alleles in a previous lung cancer GWAS, and subsequently applied it in a two-phase GWAS of oral cancer. Results: Known lung cancer susceptibility SNPs were consistently ranked higher by AdAPT BFDPs than by p-values. In the oral cancer GWAS, we sought to replicate the top five SNPs as ranked by AdAPT BFDPs, of which rs991316, located in the ADH gene region of 4q23, displayed a statistically significant association with oral cancer risk in the replication phase (per-rare-allele log additive p-value [p(trend)] = 2.5 x 10(-3)). The combined OR for having one additional rare allele was 0.83 (95% CI: 0.76-0.90), and this association was independent of previously identified susceptibility SNPs that are associated with overall UADT cancer in this gene region. We also investigated if rs991316 was associated with other cancers of the upper aerodigestive tract (UADT), but no additional association signal was found. Conclusion: This study highlights the potential utility of systematically incorporating prior knowledge from the medical literature in genome-wide analyses using the AdAPT methodology. AdAPT is available online (url: http://services.gate.ac.uk/lld/gwas/service/config)

Reconstructing an Ancestral Mammalian Immune Supercomplex from a Marsupial Major Histocompatibility Complex

The first sequenced marsupial genome promises to reveal unparalleled insights into mammalian evolution. We have used theMonodelphis domestica (gray short-tailed opossum) sequence to construct the first map of a marsupial major histocompatibility complex (MHC). The MHC is the most gene-dense region of the mammalian genome and is critical to immunity and reproductive success. The marsupial MHC bridges the phylogenetic gap between the complex MHC of eutherian mammals and the minimal essential MHC of birds. Here we show that the opossum MHC is gene dense and complex, as in humans, but shares more organizational features with non-mammals. The Class I genes have amplified within the Class II region, resulting in a unique Class I/II region. We present a model of the organization of the MHC in ancestral mammals and its elaboration during mammalian evolution. The opossum genome, together with other extant genomes, reveals the existence of an ancestral “immune supercomplex” that contained genes of both types of natural killer receptors together with antigen processing genes and MHC genes

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.

BACKGROUND: We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. RESULTS: The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. CONCLUSIONS: Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution

Identification of cancer risk and associated behaviour: implications for social marketing campaigns for cancer prevention

Background Community misconception of what causes cancer is an important consideration when devising communication strategies around cancer prevention, while those initiating social marketing campaigns must decide whether to target the general population or to tailor messages for different audiences. This paper investigates the relationships between demographic characteristics, identification of selected cancer risk factors, and associated protective behaviours, to inform audience segmentation for cancer prevention social marketing. Methods Data for this cross-sectional study (n = 3301) are derived from Cancer Council New South Wales’ 2013 Cancer Prevention Survey. Descriptive statistics and logistic regression models were used to investigate the relationship between respondent demographic characteristics and identification of each of seven cancer risk factors; demographic characteristics and practice of the seven ‘protective’ behaviours associated with the seven cancer risk factors; and identification of cancer risk factors and practising the associated protective behaviours, controlling for demographic characteristics. Results More than 90% of respondents across demographic groups identified sun exposure and smoking cigarettes as moderate or large cancer risk factors. Around 80% identified passive smoking as a moderate/large risk factor, and 40–60% identified being overweight or obese, drinking alcohol, not eating enough vegetables and not eating enough fruit. Women and older respondents were more likely to identify most cancer risk factors as moderate/large, and to practise associated protective behaviours. Education was correlated with identification of smoking as a moderate/large cancer risk factor, and with four of the seven protective behaviours. Location (metropolitan/regional) and country of birth (Australia/other) were weak predictors of identification and of protective behaviours. Identification of a cancer risk factor as moderate/large was a significant predictor for five out of seven associated cancer-protective behaviours, controlling for demographic characteristics. Conclusions These findings suggest a role for both audience segmentation and whole-of-population approaches in cancer-prevention social marketing campaigns. Targeted campaigns can address beliefs of younger people and men about cancer risk factors. Traditional population campaigns can enhance awareness of being overweight, alcohol consumption, and poor vegetable and fruit intake as cancer risk factors