Breeding site fidelity, and breeding pair infidelity in the endangered Carnaby’s Cockatoo Calyptorhynchus latirostris

The ecology and behaviour of the endangered Carnaby’s Cockatoo Calyptorhynchus latirostris have been studied in detail at Coomallo Creek in the northern wheatbelt of Western Australia from 1969 until the present. Results of research on this breeding population conducted on individually marked birds from 1970 to 1990 were compared with results from analyses of DNA taken from nestlings in the study area from 2003, 2005, and each year from 2009 to 2013. Analyses of DNA confirmed earlier findings about the stability of adult breeding pairs, and that females used the same breeding hollow they used previously, provided the hollow was not occupied when they returned to breed. When moving to another hollow, they chose a hollow in the same vicinity of the previous hollow. Analyses in 22 cases where DNA was obtained from both nestlings of a breeding attempt revealed that in six (27.3%) cases, the second egg was fertilised by a male not paired with the female. These extra-pair copulations were not suspected during the earlier study based on observations of individually marked birds

Charting a new frontier of science by integrating mathematical modeling to understand and predict complex biological systems

Biological systems are staggeringly complex. To untangle this complexity and make predictions about biological systems is a continuous goal of biological research. One approach to achieve these goals is to emphasize the use of quantitative measures of biological processes. Advances in quantitative biology data collection and analysis across scales (molecular, cellular, organismal, ecological) has transformed how we understand, categorize, and predict complex biological systems. Simultaneously, thanks to increased computational power, mathematicians, engineers and physical scientists -- collectively termed theoreticians -- have developed sophisticated models of biological systems at different scales. But there is still a disconnect between the two fields. This surge of quantitative data creates an opportunity to apply, develop, and evaluate mathematical models of biological systems and explore novel methods of analysis. The novel modeling schemes can also offer deeper understanding of principles in biology. In the context of this paper, we use “models” to refer to mathematical representations of biological systems. This data revolution puts scientists in a unique position to leverage information-rich datasets to improve descriptive modeling. Moreover, advances in technology allow inclusion of heterogeneity and variability within these datasets and mathematical models. This inclusion may lead to identifying previously undetermined variables driving or maintaining heterogeneity and diversity. Improved inclusion of variation may even improve biologically meaningful predictions about how systems will respond to perturbations. Although some of these practices are mainstream in specific sub-fields of biology, such practices are not widespread across all fields of biological sciences. With resources dedicated to better integrating biology and mathematical modeling, we envision a transformational improvement in the ability to describe and predict complex biological systems

Transcriptome sequencing reveals altered long intergenic non-coding RNAs in lung cancer

BACKGROUND: Long intergenic non-coding RNAs (lncRNAs) represent an emerging and under-studied class of transcripts that play a significant role in human cancers. Due to the tissue- and cancer-specific expression patterns observed for many lncRNAs it is believed that they could serve as ideal diagnostic biomarkers. However, until each tumor type is examined more closely, many of these lncRNAs will remain elusive. RESULTS: Here we characterize the lncRNA landscape in lung cancer using publicly available transcriptome sequencing data from a cohort of 567 adenocarcinoma and squamous cell carcinoma tumors. Through this compendium we identify over 3,000 unannotated intergenic transcripts representing novel lncRNAs. Through comparison of both adenocarcinoma and squamous cell carcinomas with matched controls we discover 111 differentially expressed lncRNAs, which we term lung cancer-associated lncRNAs (LCALs). A pan-cancer analysis of 324 additional tumor and adjacent normal pairs enable us to identify a subset of lncRNAs that display enriched expression specific to lung cancer as well as a subset that appear to be broadly deregulated across human cancers. Integration of exome sequencing data reveals that expression levels of many LCALs have significant associations with the mutational status of key oncogenes in lung cancer. Functional validation, using both knockdown and overexpression, shows that the most differentially expressed lncRNA, LCAL1, plays a role in cellular proliferation. CONCLUSIONS: Our systematic characterization of publicly available transcriptome data provides the foundation for future efforts to understand the role of LCALs, develop novel biomarkers, and improve knowledge of lung tumor biology. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-014-0429-8) contains supplementary material, which is available to authorized users

Hearing Care and Management Priority Among Parents of Children with Down Syndrome: A Grounded Theory

Objective: This study qualitatively explored the factors that influence how parents of children who are Deaf or hard-of-hearing with Down syndrome prioritize hearing care and management and developed an associated theory to explain that priority. Design: Grounded theory was used for the purposes of this qualitative study. Data were collected using in-depth interviews which were analyzed using a three-tiered qualitative coding process. Study Sample: Eighteen mothers of children who are Deaf or hard-of-hearing with Down syndrome participated in this study. Results: The higher the extent of engaged professional support, perception of benefit for child, parent activation, and family engagement, the higher the priority for hearing care and management will likely be among parents of children who are Deaf or hard-of-hearing with Down syndrome. Conclusions: Understanding how parents of children who are Deaf or hard-of-hearing with Down syndrome decide to prioritize hearing care and management has implications for how hearing health providers and others provide care to parents to enhance priority for hearing-related needs

NRG Oncology-Radiation Therapy Oncology Group Study 1014: 1-Year Toxicity Report From a Phase 2 Study of Repeat Breast-Preserving Surgery and 3-Dimensional Conformal Partial-Breast Reirradiation for In-Breast Recurrence.

PURPOSE: To determine the associated toxicity, tolerance, and safety of partial-breast reirradiation. METHODS AND MATERIALS: Eligibility criteria included in-breast recurrence occurring \u3e1 year after whole-breast irradiation, \u3c3 \u3ecm, unifocal, and resected with negative margins. Partial-breast reirradiation was targeted to the surgical cavity plus 1.5 cm; a prescription dose of 45 Gy in 1.5 Gy twice daily for 30 treatments was used. The primary objective was to evaluate the rate of grade ≥3 treatment-related skin, fibrosis, and/or breast pain adverse events (AEs), occurring ≤1 year from re-treatment completion. A rate of ≥13% for these AEs in a cohort of 55 patients was determined to be unacceptable (86% power, 1-sided α = 0.07). RESULTS: Between 2010 and 2013, 65 patients were accrued, and the first 55 eligible and with 1 year follow-up were analyzed. Median age was 68 years. Twenty-two patients had ductal carcinoma in situ, and 33 had invasive disease: 19 ≤1 cm, 13 \u3e1 to ≤2 cm, and 1 \u3e2 cm. All patients were clinically node negative. Systemic therapy was delivered in 51%. All treatment plans underwent quality review for contouring accuracy and dosimetric compliance. All treatment plans scored acceptable for tumor volume contouring and tumor volume dose-volume analysis. Only 4 (7%) scored unacceptable for organs at risk contouring and organs at risk dose-volume analysis. Treatment-related skin, fibrosis, and/or breast pain AEs were recorded as grade 1 in 64% and grade 2 in 7%, with only 1 ( CONCLUSION: Partial-breast reirradiation with 3-dimensional conformal radiation therapy after second lumpectomy for patients experiencing in-breast failures after whole-breast irradiation is safe and feasible, with acceptable treatment quality achieved. Skin, fibrosis, and breast pain toxicity was acceptable, and grade 3 toxicity was rare

A novel LC–ESI-MS method for the simultaneous determination of etravirine, darunavir and ritonavir in human blood plasma

The new potent combination of antiretrovirals etravirine, darunavir, and ritonavir requires a new bioanalytical method for clinical pharmacology investigations and potential therapeutic drug monitoring. The development and validation of a novel LC–MS method for the simultaneous quantification of the most recently FDA-approved protease inhibitor and non-nucleoside reverse transcriptase inhibitor is described. This novel method was developed and validated using a sub-2 μm particle column, and provides excellent chromatographic separation and peak shape for all three analytes and internal standard. The method was validated over the range of 0.002–2.0 μg/mL. Intra- and inter-day accuracy of all analytes ranged from 88 to 106%, and intra- and inter-day precision was <7%. Dilution of samples 2-, 5-, and 10-fold maintained accuracy and precision, using a sample volume as low as 10 μL. Finally, the applicability of the method was investigated with clinical samples and external quality assurance proficiency testing samples

Urban blue space renovation and local resident and visitor well-being:A case study from Plymouth, UK

Observational studies have suggested that people with better access to attractive, safe, and inclusive blue spaces enjoy higher psychological well-being, with particular benefits for those living in deprived urban areas. However, intervention studies are scarce. To help bridge this gap we conducted a repeat cross-sectional study exploring local resident and visitor well-being before and after a small-scale intervention aimed at improving the quality of an urban beach area in a deprived neighbourhood in Plymouth, United Kingdom. Physical alterations were co-created with local stakeholders and residents, and accompanied by a series of on-site community events. Key outcomes were self-reported psychological well-being, satisfaction with personal safety and community belonging, and perceptions of site quality. Adjusted linear models showed that positive well-being (B = 7.42; 95% CI = 4.18–10.67) and life satisfaction (B = 0.40; 95% CI = 0.11–0.70) were both higher after the intervention compared to before, with associations for life satisfaction stronger among those who visited the site in the last four weeks. Associations with positive well-being were partially mediated by greater satisfaction with community belonging; and associations with life satisfaction were partially and independently mediated by greater satisfaction with personal safety and community belonging. Although caution needs to be taken due to the repeat cross-sectional design and the sampling of site visitors as well as local residents, the findings support the idea that environmental improvements to urban blue spaces can foster better psychological well-being, and underline the importance of community involvement in the process

The Precision Array for Probing the Epoch of Reionization: 8 Station Results

We are developing the Precision Array for Probing the Epoch of Reionization (PAPER) to detect 21cm emission from the early Universe, when the first stars and galaxies were forming. We describe the overall experiment strategy and architecture and summarize two PAPER deployments: a 4-antenna array in the low-RFI environment of Western Australia and an 8-antenna array at our prototyping site in Green Bank, WV. From these activities we report on system performance, including primary beam model verification, dependence of system gain on ambient temperature, measurements of receiver and overall system temperatures, and characterization of the RFI environment at each deployment site. We present an all-sky map synthesized between 139 MHz and 174 MHz using data from both arrays that reaches down to 80 mJy (4.9 K, for a beam size of 2.15e-5 steradians at 154 MHz), with a 10 mJy (620 mK) thermal noise level that indicates what would be achievable with better foreground subtraction. We calculate angular power spectra ($C_\ell$) in a cold patch and determine them to be dominated by point sources, but with contributions from galactic synchrotron emission at lower radio frequencies and angular wavemodes. Although the cosmic variance of foregrounds dominates errors in these power spectra, we measure a thermal noise level of 310 mK at $\ell=100$ for a 1.46-MHz band centered at 164.5 MHz. This sensitivity level is approximately three orders of magnitude in temperature above the level of the fluctuations in 21cm emission associated with reionization.Comment: 13 pages, 14 figures, submitted to AJ. Revision 2 corrects a scaling error in the x axis of Fig. 12 that lowers the calculated power spectrum temperatur

Development of a liquid chromatography–tandem mass spectrometry assay of six antimicrobials in plasma for pharmacokinetic studies in premature infants

This method provides a simple extraction procedure, as well as a validated, sensitive, and specific liquid chromatography-tandem mass spectrometry assay for the simultaneous quantification of ampicillin, piperacillin, tazobactam, meropenem, acyclovir, and metronidazole in human plasma. The method was validated over concentration ranges specific for each compound, with a lower limit of quantification of 50–300 ng/mL and a sample volume of 50 μL. The method is accurate and precise, with within- and between-day accuracy ranging from 85–110% and 92–110%, respectively, and within- and between-day precision of 89–111% and 91–109%, respectively. Simplicity, low plasma volume, and high throughput make this method suitable for clinical pharmacokinetic studies in premature infants

Assessing the Potential Effects of Fungicides on Nontarget Gut Fungi (Trichomycetes) and Their Associated Larval Black Fly Hosts

Fungicides are moderately hydrophobic and have been detected in water and sediment, particularly in agricultural watersheds, but typically are not included in routine water quality monitoring efforts. This is despite their widespread use and frequent application to combat fungal pathogens. Although the efficacy of these compounds on fungal pathogens is well documented, little is known about their effects on nontarget fungi. This pilot study, a field survey in southwestern Idaho from April to December 2010 on four streams with varying pesticide inputs (two agricultural and two reference sites), was conducted to assess nontarget impact of fungicides on gut fungi, or trichomycetes. Tissues of larval black flies (Diptera: Simuliidae), hosts of gut fungi, were analyzed for pesticide accumulation. Fungicides were detected in hosts from streams within agricultural watersheds but were not detected in hosts from reference streams. Gut fungi from agricultural sites exhibited decreased percent infestation, density and sporulation within the gut, and black fly tissues had elevated pesticide concentrations. Differences observed between the sites demonstrate a potential effect on this symbiotic system. Future research is needed to parse out the details of the complex biotic and abiotic relationships; however, these preliminary results indicate that impacts to nontarget organisms could have far-reaching consequences within aquatic ecosystems