TreeToReads - a pipeline for simulating raw reads from phylogenies.

BackgroundUsing phylogenomic analysis tools for tracking pathogens has become standard practice in academia, public health agencies, and large industries. Using the same raw read genomic data as input, there are several different approaches being used to infer phylogenetic tree. These include many different SNP pipelines, wgMLST approaches, k-mer algorithms, whole genome alignment and others; each of these has advantages and disadvantages, some have been extensively validated, some are faster, some have higher resolution. A few of these analysis approaches are well-integrated into the regulatory process of US Federal agencies (e.g. the FDA's SNP pipeline for tracking foodborne pathogens). However, despite extensive validation on benchmark datasets and comparison with other pipelines, we lack methods for fully exploring the effects of multiple parameter values in each pipeline that can potentially have an effect on whether the correct phylogenetic tree is recovered.ResultsTo resolve this problem, we offer a program, TreeToReads, which can generate raw read data from mutated genomes simulated under a known phylogeny. This simulation pipeline allows direct comparisons of simulated and observed data in a controlled environment. At each step of these simulations, researchers can vary parameters of interest (e.g., input tree topology, amount of sequence divergence, rate of indels, read coverage, distance of reference genome, etc) to assess the effects of various parameter values on correctly calling SNPs and reconstructing an accurate tree.ConclusionsSuch critical assessments of the accuracy and robustness of analytical pipelines are essential to progress in both research and applied settings

The Iowa Homemaker vol.7, no.10

The Iowa Homemaker Has a Birthday by Ruth Morrison, page 1 Chow Mein versus Chop Suey by Frances Thomas, page 2 Veishea, 1928 by Ruth M. Davis, page 3 News Bits by Margaret Davidson and Rosemary Koeberle, page 4 Sandwiches for Your Spring Menu by Caroline E. Morrell, page 5 4-H Club by Mrs. Edith Barker, page 6 State Association Page by Marcia E. Turner, page 8 Home Economics Research at Iowa State by Melba Nisewanger, page 10 Editorial, page 11 Who’s There and Where by Vera Caulum, page 12 Window Boxes by Gladys Parker, page 1

Bostonia: The Boston University Alumni Magazine. Volume 11

Founded in 1900, Bostonia magazine is Boston University's main alumni publication, which covers alumni and student life, as well as university activities, events, and programs

Age-Related Success with Elective Single versus Double Blastocyst Transfer

Background. Although the optimal outcome of assisted reproductive technology (ART) is a healthy singleton pregnancy, the rate of twin gestation from ART in women over the age of 35 is persistently high. Methods/Findings. We compared clinical pregnancy rates (PRs), ongoing pregnancy/live birth rates, and multiple gestation rates (MGRs) in 108 women who chose elective single blastocyst transfer (eSBT) to 415 women who chose elective double blastocyst transfer (eDBT) at a hospital-based IVF center. There was no significant difference in PR between eSBT and eDBT (57.4% versus 50.2%, P = 0.47) nor between eSBT and eDBT within each age group: <35, 35–37, 38–40, and >40. The risk of multiple gestations, however, was greatly increased between eSBT and eDBT (1.6 versus 32.4%, P < 0.00005), and this difference did not vary across age groups. Conclusion(s). Women undergoing eDBT are at uniformly high risk of multiple gestation regardless of age. eSBT appears to significantly lower the risk of multiple gestation without compromising PR

Testing models of mRNA localization reveals robustness regulated by reducing transport between cells

Robust control of gene expression in both space and time is of central importance in the regulation of cellular processes and for multicellular development. However, the mechanisms by which robustness is achieved are generally not identified or well understood. For example, messenger RNA (mRNA) localization by molecular motor-driven transport is crucial for cell polarization in numerous contexts, but the regulatory mechanisms that enable this process to take place in the face of noise or significant perturbations are not fully understood. Here, we use a combined experimental-theoretical approach to characterize the robustness of gurken/transforming growth factor-α mRNA localization in Drosophila egg chambers, where the oocyte and 15 surrounding nurse cells are connected in a stereotypic network via intracellular bridges known as ring canals. We construct a mathematical model that encodes simplified descriptions of the range of steps involved in mRNA localization, including production and transport between and within cells until the final destination in the oocyte. Using Bayesian inference, we calibrate this model using quantitative single molecule fluorescence in situ hybridization data. By analyzing both the steady state and dynamic behaviors of the model, we provide estimates for the rates of different steps of the localization process as well as the extent of directional bias in transport through the ring canals. The model predicts that mRNA synthesis and transport must be tightly balanced to maintain robustness, a prediction that we tested experimentally using an overexpression mutant. Surprisingly, the overexpression mutant fails to display the anticipated degree of overaccumulation of mRNA in the oocyte predicted by the model. Through careful model-based analysis of quantitative data from the overexpression mutant, we show evidence of saturation of the transport of mRNA through ring canals. We conclude that this saturation engenders robustness of the localization process in the face of significant variation in the levels of mRNA synthesis

The Iowa Homemaker vol.8, no.1

The Maples by Melba NIsewanger, page 1 Infantile Tetany – Its Cause and Cure by Mrs. Helen C. Morling, page 2 You Need Another Oven by Ethyl Cessna Morgan, page 3 -Makes a Girl Healthy by Rosemary Koeberle, page 4 “Home Economics on Display” by Ruth M. Davis, page 5 Girls’ 4-H Clubs by Lulu Tregoning, page 6 State Association Page by Marcia E. Turner, page 8 Home Economics Research at Iowa State by Melba Nisewanger, page 10 Editorial, page 11 Who’s There and Where by Vera Caulum, page 1

The effect of climate on Burgundy vintage quality rankings

Aim: Based on consensus rankings from prominent rating authorities, we examined the importance of a suite of climatic variables, organized by winegrape phenological stage, in distinguishing between high- and low-ranked vintages in Burgundy. Methods and Results: Vintage ratings of Burgundy wines acquired from 12 sources were evaluated to develop consensus rankings for red and white wines from 1961–2015. Climate variables (air temperature, precipitation, degree-day accumulations, etc.) were organized by mean phenological stage and compared between good and poor vintages using Mann-Whitney U tests and multivariate stepwise discriminant function analysis. High temperatures, particularly during the growing season, were found to be the most consistently important climatic factor in distinguishing good-quality vintages from poor-quality vintages. The best red vintages had a greater diurnal temperature range during the growing season, whereas the top white vintages were not distinguished by unusually warm conditions, but the bottom-ranked white vintages were particularly cool and wet. The impact of rainfall varied across the growing season, with top-ranked Burgundy wines benefitting from rainfall during the bud break period and dry conditions during the ripening phase. Conclusions: The most important climatic factor in distinguishing between top- and bottom-ranked vintages is growing season temperature, especially high diurnal temperature range (for reds) and high average maximum temperatures (for whites). Good Burgundy vintages are more likely when there is ample rainfall during the bud break period in April and dry conditions during the véraison and ripening phases. Significance and Impact of the Study: As viticulturalists adapt to regional climate trends, a better understanding of how specific climate variables affect wine quality becomes increasingly important in viticulture management

Carbon dioxide and ocean acidification observations in UK waters. Synthesis report with a focus on 2010–2015

Key messages: 1.1 The process of ocean acidification is now relatively well-documented at the global scale as a long-term trend in the open ocean. However, short-term and spatial variability can be high. 1.2 New datasets made available since Charting Progress 2 make it possible to greatly improve the characterisation of CO2 and ocean acidification in UK waters. 3.1 Recent UK cruise data contribute to large gaps in national and global datasets. 3.2 The new UK measurements confirm that pH is highly variable, therefore it is important to measure consistently to determine any long term trends. 3.3 Over the past 30 years, North Sea pH has decreased at 0.0035±0.0014 pH units per year. 3.4 Upper ocean pH values are highest in spring, lowest in autumn. These changes reflect the seasonal cycles in photosynthesis, respiration (decomposition) and water mixing. 3.5 Carbonate saturation states are minimal in the winter, and lower in 7 more northerly, colder waters. This temperature-dependence could have implications for future warming of the seas. 3.6 Over the annual cycle, North-west European seas are net sinks of CO2. However, during late summer to autumn months, some coastal waters may be significant sources. 3.7 In seasonally-stratified waters, sea-floor organisms naturally experience lower pH and saturation states; they may therefore be more vulnerable to threshold changes. 3.8 Large pH changes (0.5 - 1.0 units) can occur in the top 1 cm of sediment; however, such effects are not well-documented. 3.9 A coupled forecast model estimates the decrease in pH trend within the North Sea to be -0.0036±0.00034 pH units per year, under a high greenhouse gas emissions scenario (RCP 8.5). 3.10 Seasonal estimates from the forecast model demonstrate areas of the North Sea that are particularly vulnerable to aragonite undersaturation

Digital human modelling for virtual fitting trials

A recognised difficulty with the conventional use of Digital Human Modelling (DHM) systems is that they typically use percentile data to describe anthropometry and joint constraints. Hence any model is a synthesis of the set of data rather than a representation of any particular human. Implicit in this is that an acceptable degree of correlation exists between body dimensions whereas it has long been known that only weak correlations exist. The consequences are obvious in that products are designed/evaluated against models of humans that do not exist. An alternative approach is to use pre-defined families of manikins that together ‘enclose’ and represent the necessary diversity of human form. In the real world, rather than the digital world, ergonomists use real people in ‘fitting trials’. These people might be selected on the basis of the need for diversity covering the range of anthropometry that is thought necessary for the product evaluation but the practical considerations rarely allow an exhaustive evaluation. This paper describes an amalgam of the two approaches where the anthropometry and other aspects of more than 150 people has been collected experimentally. This data is used within the HADRIAN system as discrete sets of data rather than as the basis for a percentile representation. i.e. the data is maintained as sets relating to each individual and used to construct digital models of individuals. This is combined with a task description language that is used to drive the product or workplace evaluation in a way that is analogous to a physical fitting trial. The approach is being used within AUNT-SUE (Accessibility and User Needs in Transport – Sustainable Urban Environments) a wide–ranging research project looking at exclusion in public transport systems. The use of the HADRIAN approach is illustrated through a focus on the creation of a journey planner that meets the needs of a diverse range of people including the elderly and disabled

Wigs, disguises and child's play : solidarity in teacher education

It is generally acknowledged that much contemporary education takes place within a dominant audit culture, in which accountability becomes a powerful driver of educational practices. In this culture both pupils and teachers risk being configured as a means to an assessment and target-driven end: pupils are schooled within a particular paradigm of education. The article discusses some ethical issues raised by such schooling, particularly the tensions arising for teachers, and by implication, teacher educators who prepare and support teachers for work in situations where vocational aims and beliefs may be in in conflict with instrumentalist aims. The article offers De Certeau’s concept of ‘la perruque’ to suggest an opening to playful engagement for human ends in education, as a way of contending with and managing the tensions generated. I use the concept to recover a concept of solidarity for teacher educators and teachers to enable ethical teaching in difficult times