The Ideal Review Process Is a Three-Way Street

In response to the increasing difficulty of obtaining high quality peer reviews, our invited paper describes the concept of review avoidance and why this phenomenon occurs. In reaffirming the professional responsibilities and potential benefits of reviewing, we also emphasize the interdependent nature of the ideal peer review process. We suggest that the review process is a three-way street where the respective roles and responsibilities of authors, editors and editorial teams, and reviewers are inextricably linked. We present thematic illustrations of undesirable reviewer comments, and a brief synthesis of broad themes in the literature on high-quality reviewing. The synthesis is complemented by a master reviewer’s fine-grained perspective on crafting high quality reviews. A final Appendix presents additional sources that may be informative for prospective reviewers, submitting authors, and those mentors and colleagues who may wish to provide guidance and training to them

Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community

Background: A steep drop in the cost of next-generation sequencing during recent years has made the technology affordable to the majority of researchers, but downstream bioinformatic analysis still poses a resource bottleneck for smaller laboratories and institutes that do not have access to substantial computational resources. Sequencing instruments are typically bundled with only the minimal processing and storage capacity required for data capture during sequencing runs. Given the scale of sequence datasets, scientific value cannot be obtained from acquiring a sequencer unless it is accompanied by an equal investment in informatics infrastructure. Results: Cloud BioLinux is a publicly accessible Virtual Machine (VM) that enables scientists to quickly provision on-demand infrastructures for high-performance bioinformatics computing using cloud platforms. Users have instant access to a range of pre-configured command line and graphical software applications, including a full-featured desktop interface, documentation and over 135 bioinformatics packages for applications including sequence alignment, clustering, assembly, display, editing, and phylogeny. Each tool's functionality is fully described in the documentation directly accessible from the graphical interface of the VM. Besides the Amazon EC2 cloud, we have started instances of Cloud BioLinux on a private Eucalyptus cloud installed at the J. Craig Venter Institute, and demonstrated access to the bioinformatic tools interface through a remote connection to EC2 instances from a local desktop computer. Documentation for using Cloud BioLinux on EC2 is available from our project website, while a Eucalyptus cloud image and VirtualBox Appliance is also publicly available for download and use by researchers with access to private clouds. Conclusions: Cloud BioLinux provides a platform for developing bioinformatics infrastructures on the cloud. An automated and configurable process builds Virtual Machines, allowing the development of highly customized versions from a shared code base. This shared community toolkit enables application specific analysis platforms on the cloud by minimizing the effort required to prepare and maintain them

Head Start and child care providers’ motivators, barriers and facilitators to practicing family-style meal service

This paper presents a qualitative investigation of the motivators, barriers, and facilitators for practicing family-style meal service (FSMS) from the perspective of 18 child care providers serving preschool children in Head Start (HS), Child and Adult Care Food Program (CACFP) funded, and non-CACFP child-care centers. Providers were selected based on maximum variation purposive sampling and semi-structured interviews were conducted until saturation was reached. Provider responses were systematically coded using thematic analysis. HS and CACFP providers reported being motivated to practice FSMS because it created pleasant mealtimes, opportunities to role model healthy eating, and healthful child development. CACFP and non-CACFP providers reported not using FSMS because it was resource intensive, messy, and seemed to violate CACFP policy. HS and CACFP providers offered suggestions to overcome these barriers. They suggested that FSMS eventually becomes easier with practice, children can self-regulate their energy intake, and teaching children self-help skills during play time can avoid messes during mealtimes. Findings from this study have implications for programming, policy, and research

Sterile Testis Complementation with Spermatogonial Lines Restores Fertility to DAZL-Deficient Rats and Maximizes Donor Germline Transmission

Despite remarkable advances in assisted reproductive capabilities ∼4% of all couples remain involuntarily infertile. In almost half of these cases, a lack of conception can in some measure be attributed to the male partner, wherein de novo Y-chromosomal deletions of sperm-specific Deleted-in-Azoospermia (DAZ) genes are particularly prevalent. In the current study, long-term cultures of rat spermatogonial stem cells were evaluated after cryo-storage for their potential to restore fertility to rats deficient in the DAZ-like (DAZL) gene. Detailed histological analysis of DAZL-deficient rat testes revealed an apparently intact spermatogonial stem cell compartment, but clear failure to produce mature haploid gametes resulting in infertility. After proliferating >1 million-fold in cell number during culture post-thaw, as few as 50,000 donor spermatogonia transplanted into only a single testis/recipient effectively restored fecundity to DAZL-deficient rats, yielding 100% germline transmission to progeny by natural mating. Based on these results, the potency and efficacy of this donor stem cell line for restoring fertility to azoospermic rodents is currently unprecedented. Prospectively, similar successes in humans could be directly linked to the feasibility of obtaining enough fully functional spermatogonial stem cells from minimal testis biopsies to be therapeutically effective. Thus, regeneration of sperm production in this sterile recipient provides an advanced pre-clinical model for optimizing the efficacy of stem cell therapies to cure a paradoxically increasing number of azoospermic men. This includes males that are rendered infertile by cancer therapies, specific types of endocrine or developmental defects, and germline-specific de novo mutations; all of whom may harbor healthy sources of their own spermatogonial stem cells for treatment

Peripheral mechanisms contributing to the glucocorticoid hypersensitivity in proopiomelanocortin null mice treated with corticosterone.

Proopiomelanocortin (POMC) deficiency causes severe obesity through hyperphagia of hypothalamic origin. However, low glucocorticoid levels caused by adrenal insufficiency mitigate against insulin resistance, hyperphagia and fat accretion in Pomc-/- mice. Upon exogenous glucocorticoid replacement, corticosterone-supplemented (CORT) Pomc-/- mice show exaggerated responses, including excessive fat accumulation, hyperleptinaemia and insulin resistance. To investigate the peripheral mechanisms underlying this glucocorticoid hypersensitivity, we examined the expression levels of key determinants and targets of glucocorticoid action in adipose tissue and liver. Despite lower basal expression of 11beta-hydroxysteroid dehydrogenase type 1 (11beta-HSD1), which generates active glucocorticoids within cells, CORT-mediated induction of 11beta-HSD1 mRNA levels was more pronounced in adipose tissues of Pomc-/- mice. Similarly, CORT treatment increased lipoprotein lipase mRNA levels in all fat depots in Pomc-/- mice, consistent with exaggerated fat accumulation. Glucocorticoid receptor (GR) mRNA levels were selectively elevated in liver and retroperitoneal fat of Pomc-/- mice but were corrected by CORT in the latter depot. In liver, CORT increased phosphoenolpyruvate carboxykinase mRNA levels specifically in Pomc-/- mice, consistent with their insulin-resistant phenotype. Furthermore, CORT induced hypertension in Pomc-/- mice, independently of adipose or liver renin-angiotensin system activation. These data suggest that CORT-inducible 11beta-HSD1 expression in fat contributes to the adverse cardiometabolic effects of CORT in POMC deficiency, whereas higher GR levels may be more important in liver

Low-Energy (\u3c 20 eV) and High-Energy (1000 eV) Electron-Induced Methanol Radiolysis of Astrochemical Interest

We report the first infrared study of the low-energy (\u3c 20 eV) electron-induced reactions of condensed methanol. Our goal is to simulate processes which occur when highenergy cosmic rays interact with interstellar and cometary ices, where methanol, a precursor of several prebiotic species, is relatively abundant. The interactions of high-energy radiation, such as cosmic rays (Emax ~1020 eV), with matter produce large numbers of low-energy secondary electrons, which are known to initiate radiolysis reactions in the condensed phase. Using temperature programmed desorption (TPD) and infrared reflection absorption spectroscopy (IRAS), we have investigated low-energy (5–20 eV) and high-energy (~1000 eV) electron-induced reactions in condensed methanol (CH3OH). IRAS has the benefit that it does not require thermal processing prior to product detection. Using IRAS, we have found evidence for the formation of ethylene glycol (HOCH2CH2OH), formaldehyde (CH2O), dimethyl ether (CH3OCH3), methane (CH4), carbon dioxide (CO2), carbon monoxide (CO), and the hydroxyl methyl radical (•CH2OH) upon both low-energy and high-energy electron irradiation of condensed methanol at ~85 K. Additionally, TPD results, presented herein, are similar for methanol films irradiated with both 1000 eV and 20 eV electrons. These IRAS and TPD findings are qualitatively consistent with the hypothesis that high-energy condensed phase radiolysis is mediated by low-energy electron-induced reactions. Moreover, methoxymethanol (CH3OCH2OH) could serve as a tracer molecule for electron-induced reactions in the interstellar medium. The results of experiments such as ours may provide a fundamental understanding of how complex organic molecules (COM) are synthesized in cosmic ices

Lung epithelial tip progenitors integrate glucocorticoid- and STAT3-mediated signals to control progeny fate.

Insufficient alveolar gas exchange capacity is a major contributor to lung disease. During lung development, a population of distal epithelial progenitors first produce bronchiolar-fated and subsequently alveolar-fated progeny. The mechanisms controlling this bronchiolar-to-alveolar developmental transition remain largely unknown. We developed a novel grafting assay to test if lung epithelial progenitors are intrinsically programmed or if alveolar cell identity is determined by environmental factors. These experiments revealed that embryonic lung epithelial identity is extrinsically determined. We show that both glucocorticoid and STAT3 signalling can control the timing of alveolar initiation, but that neither pathway is absolutely required for alveolar fate specification; rather, glucocorticoid receptor and STAT3 work in parallel to promote alveolar differentiation. Thus, developmental acquisition of lung alveolar fate is a robust process controlled by at least two independent extrinsic signalling inputs. Further elucidation of these pathways might provide therapeutic opportunities for restoring alveolar capacity.Medical Research Council (G0900424, ER), the March of Dimes (5-FY11-119, ER), the Wellcome Trust (093029, ER), Newton Trust (14.07h, ER), Wellcome Trust PhD programme for Clinicians (MN), Postdoctoral Fellowship from the Government of the Basque Country (UL), MRC studentship (RVR), British Heart Foundation Studentship (EJB), COST BM1201. Core grants from the Wellcome Trust (092096) and Cancer Research UK (C6946/A14492).This is the final version of the article. It first appeared from the Company of Biologists at http://dx.doi.org/10.1242/dev.134023