Relation between age, body weight, and medial retropharyngeal lymph node size in apparently healthy dogs.

The aims of this study were to determine the size of the medial retropharyngeal lymph nodes in apparently healthy dogs using ultrasonography and to investigate relationships between body weight (1.8-59 kg), age (1.0-15 years), and medial retropharyngeal lymph node sizes (width, height, and length). The sample population consisted of 100 apparently healthy, volunteered, adult dogs. The data were normally distributed, thus mean, SD, and Pearson's correlation were used. Repeatability of ultrasound measures was assessed as the percentage of differences between duplicate measures that were within 2 SDs of the differences: all measures were at least 93% repeatable (differences typically were < or = 0.25 cm and always < 1 cm). No difference between sexes was observed. The medial retropharyngeal lymph node increased in size with increased body weight (r = 0.46 to 0.59) and decreased in size with increased age (r = -0.30 to -0.50). Although statistically significant, the actual variation is not likely clinically important due to the small range of sizes, measurement error, and various combinations of age and body weight. Therefore, regardless of body weight or age, the average width is 1.0 cm, height is 0.5 cm, and length is 2.5 cm and maximum width is 2 cm, height is 1 cm, and length is 5 cm. Based on the maximal difference between duplicate measures (with some exception), any change > or = 0.4 cm with width or height, or > or = 1.0 cm in length, in a follow up measurement probably represents a true biological change rather than measurement error.     

Molecular expression of caprine estrogen receptor gene 1 in reproductive and non‐reproductive tissues

During the last decades, physiological effects of oestrogens have been increasingly explored by scientists and biotechnologists. Estrogens exert a wide range of effects on a large variety of cell types. Oestrogen and its receptors are essential for sexual development and reproduction. Estrogen receptor alpha is a nuclear receptor activated by the hormone oestrogen. In male, ERα is encoded by the gene estrogen receptor gene 1 (ESR1), responsible for better fertility. The ESR1 is involved in the reabsorption of luminal fluid during the transit of spermatozoa from the testis to the head of the epididymis which is important for their survival and maturation during epididymal storage. The absence of ESR1 leads to reduced epididymal sperm content, reduced sperm motility and fertilizing ability. Therefore, this is a good startby to study the expression pattern of estrogen receptor 1 gene in high‐fertile (G1) and low‐fertile (G2) bucks of Jamunapari and Barbari breeds identified on the basis of seminal quality traits and fertility trials. RNA was extracted from the tissues by TRIzol method. The identification and expression pattern of caprine ESR1 gene was analysed by real‐time PCR (Roche LC‐480). Our work shows that the relative quantification by RT‐PCR indicates more fold in head of epididymis as compared to spleen of caprine ESR1 gene. Furthermore, the RT‐PCR indicated that fertile bucks of Jamunapari breed have more fold value as compared to Barbari breed in respect of reproductive organ.     

The theropod ancestry of birds: new evidence from the late cretaceous of madagascar

A partial skeleton of a primitive bird, Rahona ostromi, gen. et sp. nov., has been discovered from the Late Cretaceous of Madagascar. This specimen, although exhibiting avian features such as a reversed hallux and ulnar papillae, retains characteristics that indicate a theropod ancestry, including a pubic foot and hyposphene-hypantra vertebral articulations. Rahona has a robust, hyperextendible second digit on the hind foot that terminates in a sicklelike claw, a unique characteristic of the theropod groups Troodontidae and Dromaeosauridae. A phylogenetic analysis places Rahona with Archaeopteryx, making Rahona one of the most primitive birds yet discovered.     

Developing a reliable strategy to infer the effective soil hydraulic properties from field evaporation experiments for agro-hydrological models

The Richards equation has been widely used for simulating soil water movement. However, the take-up of agro-hydrological models using the basic theory of soil water flow for optimizing irrigation, fertilizer and pesticide practices is still low. This is partly due to the difficulties in obtaining accurate values for soil hydraulic properties at a field scale. Here, we use an inverse technique to deduce the effective soil hydraulic properties, based on measuring the changes in the distribution of soil water with depth in a fallow field over a long period, subject to natural rainfall and evaporation using a robust micro Genetic Algorithm. A new optimized function was constructed from the soil water contents at different depths, and the soil water at field capacity. The deduced soil water retention curve was approximately parallel but higher than that derived from published pedo-tranfer functions for a given soil pressure head. The water contents calculated from the deduced soil hydraulic properties were in good agreement with the measured values. The reliability of the deduced soil hydraulic properties was tested in reproducing data measured from an independent experiment on the same soil cropped with leek. The calculation of root water uptake took account for both soil water potential and root density distribution. Results show that the predictions of soil water contents at various depths agree fairly well with the measurements, indicating that the inverse analysis is an effective and reliable approach to estimate soil hydraulic properties, and thus permits the simulation of soil water dynamics in both cropped and fallow soils in the field accurately.     

You cannot fight fire with fire: a demographic model suggests alternative approaches to manage multiple herbicide‐resistant Avena fatua

Multiple herbicide‐resistant (MHR ) weed populations pose significant agronomic and economic threats and demand the development and implementation of ecologically based tactics for sustainable management. We investigated the influence of nitrogen fertiliser rate (56, 112, 168, or 224 kg N ha^?1) and spring wheat seeding density (67.3 kg ha^?1 or 101 kg ha^?1) on the demography of one herbicide susceptible and two MHR Avena fatua populations under two cropping systems (continuous cropping and crop‐fallow rotation). To represent a wide range of environmental conditions, data were obtained in field conditions over 3 years (2013–2015). A stochastic density‐dependent population dynamics model was constructed using the demographic data to project A. fatua populations. Elasticity analysis was used to identify demographic processes with negative impacts on population growth. In both cropping systems, MHR seedbank densities were negatively impacted by increasing nitrogen fertilisation rate and wheat density. Overall, MHR seedbank densities were larger in the wheat‐ fallow compared with the continuous wheat cropping system and seedbank densities stabilised near zero in the high nitrogen and high spring wheat seeding rate treatment. In both cropping systems, density‐dependent seed production was the most influential parameter impacting population growth rate. This study demonstrated that while the short‐term impact of weed management tactics can be investigated by field experiments, evaluation of long‐term consequences requires the use of population dynamics models. Demographic models, such as the one constructed here, will aid in selecting ecologically based weed management tactics, such as appropriate resource availability and modification to crop competitive ability to reduce the impact of MHR .     

A Comprehensive Genotype and Environment Assessment of Wheat Grain Ash Content in Oregon and Washington: Analysis of Variation

A comprehensive analysis of the variation in wheat grain ash content has not been previously conducted. This study assessed the relative contribution of genotype and environment to variation in ash content, with a particular aim of ascertaining the potential for manipulating the trait using contemporary adapted germplasm. A total of 2,240 samples were drawn from four years of multilocation field plots grown in the wheat production areas of Oregon and Washington states. Genotypes included commercial cultivars and advanced breeding lines of soft and hard winter, and soft and hard spring wheats with red and white kernel color, several soft white club wheats, and one soft white spring waxy wheat cultivar. In addition to ash, protein content, test weight, and Single Kernel Characterization System kernel hardness, weight and size were also measured. In total, 20 separate fully balanced ANOVA results were conducted. Whole model R² values were highly significant, 0.62–0.91. Nineteen of the 20 ANOVA results indicated significant genotype effects, but the effects were not large. In contrast, environment effects were always highly significant with F values often one to two orders of magnitude larger than the genotype F values. The grand mean for all samples was 1.368% ash. For individual data sets, genotype means across environments varied ≈0.1–0.3% ash. The genotypes judged noteworthy because they had the highest least squares mean ash content were OR9900553 and ClearFirst soft white winter, NuHills hard red winter, Waxy‐Pen and Cataldo soft white spring, and WA8010 and Lochsa hard spring wheats. Genotypes with lowest least squares mean ash were Edwin (club) soft white winter, OR2040073H hard red winter, WA7952 soft white spring, and WA8038 hard spring wheats. In conclusion, wheat grain ash is more greatly influenced by crop year and location than by genotype. However, sufficient genotype variation is present to plausibly manipulate this grain trait through traditional plant breeding.     

Tools for knowledge acquisition within the NeuroScholar system and their application to anatomical tract-tracing data

Background

Knowledge bases that summarize the published literature provide useful online references for specific areas of systems-level biology that are not otherwise supported by large-scale databases. In the field of neuroanatomy, groups of small focused teams have constructed medium size knowledge bases to summarize the literature describing tract-tracing experiments in several species. Despite years of collation and curation, these databases only provide partial coverage of the available published literature. Given that the scientists reading these papers must all generate the interpretations that would normally be entered into such a system, we attempt here to provide general-purpose annotation tools to make it easy for members of the community to contribute to the task of data collation.

Results

In this paper, we describe an open-source, freely available knowledge management system called 'NeuroScholar' that allows straightforward structured markup of the PDF files according to a well-designed schema to capture the essential details of this class of experiment. Although, the example worked through in this paper is quite specific to neuroanatomical connectivity, the design is freely extensible and could conceivably be used to construct local knowledge bases for other experiment types. Knowledge representations of the experiment are also directly linked to the contributing textual fragments from the original research article. Through the use of this system, not only could members of the community contribute to the collation task, but input data can be gathered for automated approaches to permit knowledge acquisition through the use of Natural Language Processing (NLP).

Conclusion

We present a functional, working tool to permit users to populate knowledge bases for neuroanatomical connectivity data from the literature through the use of structured questionnaires. This system is open-source, fully functional and available for download from [1].