DSC — A Valuable Tool in Heterocyclic Synthesis

Many decomposition and ring closure reactions in the azide series (e.g. a cyclization and rearrangement reaction sequence from the azido ester 1 via the ethoxy oxazole 2 to the oxazolone 3), intramolecular rearrangement reactions (e.g. via a-oxoketenes), self condensation of p-octopamine and also reactions with two reactants and the influence of solvents at the reaction conditions were studied using DSC (Differential Scanning Calorimetry).     

phenoVein—A Tool for Leaf Vein Segmentation and Analysis

Precise measurements of leaf vein traits are an important aspect of plant phenotyping for ecological and genetic research. Here, we present a powerful and user-friendly image analysis tool named phenoVein. It is dedicated to automated segmenting and analyzing of leaf veins in images acquired with different imaging modalities (microscope, macrophotography, etc.), including options for comfortable manual correction. Advanced image filtering emphasizes veins from the background and compensates for local brightness inhomogeneities. The most important traits being calculated are total vein length, vein density, piecewise vein lengths and widths, areole area, and skeleton graph statistics, like the number of branching or ending points. For the determination of vein widths, a model-based vein edge estimation approach has been implemented. Validation was performed for the measurement of vein length, vein width, and vein density of Arabidopsis (Arabidopsis thaliana), proving the reliability of phenoVein. We demonstrate the power of phenoVein on a set of previously described vein structure mutants of Arabidopsis (hemivenata, ondulata3, and asymmetric leaves2-101) compared with wild-type accessions Columbia-0 and Landsberg erecta-0. phenoVein is freely available as open-source software.Leaf veins are an important aspect of leaf structure and responsible for both the mechanical support of leaves and the long-distance transport of water, nutrients, and photoassimilates (Onoda et al., 2011; Malinowski, 2013). The molecular mechanisms by which vascular tissues acquire their identities are yet largely unknown (Roschzttardtz et al., 2014), and there is high interest in analyzing and evaluating traits of veins or leaf venation networks and their genetic regulation. The impact of vein density on photosynthesis is a major investigated topic (Sack and Scoffoni, 2013). During the last decade, a positive correlation between leaf venation and photosynthesis has been observed (Sack and Holbrook, 2006; Brodribb et al., 2007). An optimization of photosynthetic rates was shown to occur by spatial coordination between leaf vein and stomatal densities (Zhang et al., 2012; Carins Murphy et al., 2014; Fiorin et al., 2015). Additionally, there is interest in the impact of vein density on interveinal distances (Dengler et al., 1994; McKown and Dengler, 2009) and the effect of climate, habitat, or growth form on vein density (Sack and Scoffoni, 2013; Scoffoni et al., 2015) or vein width with respect to leaf hydraulic conductance (Feild and Brodribb, 2013; Xiong et al., 2015). Other researchers are particularly interested in the evolution from C3 to C4 plants, which requires higher vein density (Gowik and Westhoff, 2011) and led to selecting for variation of vein density within species (e.g. in a mutant collection by Feldman et al., 2014).Leaf venation studies analyzing traits of veins and venation networks are generally performed on microscopic images of leaves that are properly cleared after harvest. For very small leaves, e.g. the cotyledons or the first leaves (leaves 2–5) of Arabidopsis (Arabidopsis thaliana), basic traits, such as total vein length or vein density (vein length per leaf area), can be achieved manually. However, for larger leaves, manual vein segmentation may become tedious, and at least partially automated analysis is needed for studies on large series of leaf collections. Furthermore, the quantification of vein widths and in particular mean values of vein width of certain vein pieces of interest can hardly be achieved manually. Dedicated image processing tools are, therefore, needed to support researchers for fast and reliable data analysis.A number of software tools have been published that are either specifically made or adapted to analyze leaf veins. These programs have some common properties, like image processing functionalities for vein/areole segmentation and trait extraction. However, they differ in handling strategies or vein parameter analysis methods. A general overview on plant image analysis tools is collected in an online database at http://www.plant-image-analysis.org (Lobet et al., 2013). Programs allowing automated or semiautomated analysis of leaf venation parameters are, for example, a method to extract leaf venation patterns (Rolland-Lagan et al., 2009), the leaf extraction and analysis framework graphical user interface LeafGUI (Price et al., 2011), the leaf image analysis interface LIMANI (Dhondt et al., 2012), the user-interactive vessel generation analysis tool VESGEN (Vickerman et al., 2009; Parsons-Wingerter et al., 2014), and the software network extraction from images NEFI (Dirnberger et al., 2015). Nevertheless, for the analysis of large-scale leaf vein phenotyping experiments, there are certain needs that are only partly covered by each of the approaches and programs mentioned above. Specifically, the following properties are needed: (1) automated vein segmentation with optional manual correction; (2) invariance of the segmentation procedure to inhomogeneous illumination or brightness variations in the leaf image; (3) automated determination of total vein length and projected leaf area; (4) a well-defined and automated determination of vein widths, which is, as far as possible, independent of user chosen thresholds; (5) ability to process large high-resolution images of whole leafs; and (6) full transparency of the source code as well as offline availability of the tool. To provide these functionalities, we developed the user-friendly analysis tool phenoVein. It features automated leaf vein segmentation based on advanced image filtering techniques and includes determination of various vein traits, particularly a model-based vein width estimation. phenoVein allows easy and fast visual control and manual correction on the automatically achieved skeleton of the veins enabled by a real-time overlay of the segmented leaf vein structures on the original image. The length measurement algorithm of phenoVein was validated against complete manual segmentation. We evaluated the impact of image resolution on the results, which has recently been discussed (Price et al., 2014; Sack et al., 2014), and tested whether the orientation (angle) of a leaf on an image may affect the results as suspected from image analysis theory on binary skeleton length measurements (Russ, 2011). To show the powerful phenotyping capabilities of phenoVein, we analyzed the venation traits of leaves of Arabidopsis at different developmental stages (cotyledons, pooled leaves 1 + 2, and leaf 6) harvested from previously described venation mutants and corresponding wild-type lines: asymmetric leaves2-101 (as2-101), ondulata3 (ond3), and hemivenata2 (hve-2) versus Columbia-0 (Col-0) and Landsberg erecta-0 (Ler-0; Semiarti et al., 2001; Alonso-Peral et al., 2006; Robles et al., 2010; Pérez-Pérez et al., 2011). We offer the source code of phenoVein to the public as open-source software that can be further adapted or improved (for details, see “Materials and Methods”).     

NORMA: The Network Makeup Artist——A Web Tool for Network Annotation Visualization

The Network Makeup Artist(NORMA) is a web tool for interactive network annotation visualization and topological analysis, able to handle multiple networks and annotations simultaneously. Precalculated annotations(e.g., Gene Ontology, Pathway enrichment, community detection,or clustering results) can be uploaded and visualized in a network, either as colored pie-chart nodes or as color-filled areas in a 2D/3D Venn-diagram-like style. In the case where no annotation exists,algorithms for automated...     

Bottleneck Allocation Methodology: An Integrated Manufacturing Management Model—A Systems Study

Bottleneck allocation methodology (BAM) attempts to blend the best features of other popular production planning philosophies. As a result, BAM could offer a better-integrated schedule with more flexible production planning results. This paper does a literature search of previous methodologies and demonstrates how BAM is an integration of these philosophies. This paper also demonstrates the operation of the BAM process.     

Should We Have Blind Faith in Bioinformatics Software? Illustrations from the SNAP Web-Based Tool

Bioinformatics tools have gained popularity in biology but little is known about their validity. We aimed to assess the early contribution of 415 single nucleotide polymorphisms (SNPs) associated with eight cardio-metabolic traits at the genome-wide significance level in adults in the Family Atherosclerosis Monitoring In earLY Life (FAMILY) birth cohort. We used the popular web-based tool SNAP to assess the availability of the 415 SNPs in the Illumina Cardio-Metabochip genotyped in the FAMILY study participants. We then compared the SNAP output with the Cardio-Metabochip file provided by Illumina using chromosome and chromosomal positions of SNPs from NCBI Human Genome Browser (Genome Reference Consortium Human Build 37). With the HapMap 3 release 2 reference, 201 out of 415 SNPs were reported as missing in the Cardio-Metabochip by the SNAP output. However, the Cardio-Metabochip file revealed that 152 of these 201 SNPs were in fact present in the Cardio-Metabochip array (false negative rate of 36.6%). With the more recent 1000 Genomes Project release, we found a false-negative rate of 17.6% by comparing the outputs of SNAP and the Illumina product file. We did not find any ‘false positive’ SNPs (SNPs specified as available in the Cardio-Metabochip by SNAP, but not by the Cardio-Metabochip Illumina file). The Cohen’s Kappa coefficient, which calculates the percentage of agreement between both methods, indicated that the validity of SNAP was fair to moderate depending on the reference used (the HapMap 3 or 1000 Genomes). In conclusion, we demonstrate that the SNAP outputs for the Cardio-Metabochip are invalid. This study illustrates the importance of systematically assessing the validity of bioinformatics tools in an independent manner. We propose a series of guidelines to improve practices in the fast-moving field of bioinformatics software implementation.     

RHEUMATOID ARTHRITIS—Present-Day Physical Therapy

Physical therapy is an important therapeutic agent for patients with rheumatoid arthritis. Well directed exercise balanced with rest is fundamental. Careful muscular reeducation is as important in the treatment of patients with arthritis as it is in caring for a patient with paralysis. Pain with slight malalignment and limitation in the joint will cause muscles to lose their sequence of action and so upset the rhythm of motion.Active exercise with a balanced use of assistance and resistance to movement, combined, as indicated, with traction upon the joint or stretching of constricted tissues may result in (1) stabilization of the joint, (2) increase in range of movement, (3) relaxation of antagonists, and (4) reduction of atrophy. The objectives of muscular exercise then are (1) reduction of pain, spasm and deformity, (2) development of muscular power, and (3) restoration of the normal rhythm of movement.     

DPPrimer – A Degenerate PCR Primer Design Tool

Designed degenerate primers unlike conventional primers are superior in matching and amplification of large number of genes, from related gene families. DPPrimer tool was designed to predict primers for PCR amplification of homologous gene from related or diverse plant species. The key features of this tool include platform independence and user friendliness in primer design. Embedded features such as search for functional domains, similarity score selection and phylogebetic tree further enhance the user friendliness of DPPrimer tool. Performance of DPPrimer tool was evaluated by successful PCR amplification of ADP-glucose phosphorylase genes from wheat, barley and rice.

Availability

DPPrimer is freely accessible at http://202.141.12.147/DGEN_tool/index.html     

Genetic Recombination Frequencies and Mapping Functions—A Simulated Laboratory Exercise for Students of Genetics

Suggestions are offered for teaching some aspects of water economy in plant cells. These include diffusion and osmosis, transport of water within plants, the part played by turgor in structural support and its implications for plant organs or whole plants. Wherever possible the degree of sophistication thought desirable at this level is indicated. Some appropriate practical demonstrations are referred to.     

High-Resolution Physical Map of the Immunoglobulin λ Variant Gene Cluster Assembled by Quantitative DNA Fiber Mapping

Quantitative DNA fiber mapping (QDFM) allows rapid construction of near-kilobase-resolution physical maps by hybridizing specific probes to individual stretched DNA molecules. We evaluated the utility of QDFM for the large-scale physical mapping of a rather unstable, repeat-rich 850-kb region encompassing the immunoglobulin λ variant (IGLV) gene segments. We mapped a minimal tiling path composed of 32 cosmid clones to three partially overlapping yeast artificial chromosome (YAC) clones and determined the physical size of each clone, the extent of overlap between clones, and contig orientation, as well as the sizes of gaps between adjacent contigs. Regions of germline DNA for which we had no YAC coverage were characterized by cosmid to cosmid hybridizations. Compared to other methods commonly used for physical map assembly, QDFM is a rapid, versatile technique delivering unambiguous data necessary for map closure and preparation of sequence-ready minimal tiling paths.     

The Mouse Grimace Scale: A Clinically Useful Tool?

Medical research has a heavy and continuing demand for rodent models across a range of disciplines. Behavioural assessment of pain in such models is highly time consuming, thus limiting the number of models and analgesics that can be studied. Facial expressions are widely used to assess pain in human infants. Recently the mouse grimace scale (MGS) has been developed and shown to be accurate and reliable, requiring only a short amount of training for the observer. This system therefore has the potential to become a highly useful tool both in pain research and clinical assessment of mouse pain. To date, the MGS has only been used as a research tool, however there is increasing interest in its use in cage-side clinical assessment. It is often wrongly assumed that MGS scores of animals not in pain (i.e. at baseline) are zero. Here, we aimed to assess the variability in baseline MGS scores between cohorts, sexes and strains of mice. Establishing the presence of a consistent baseline MGS score could lead to a valuable clinical pain assessment tool for mice when baseline information from the individual mouse may not be available as a comparator. Results demonstrated a significant difference in baseline MGS scores between both sexes (males > females) and strains of mice. The method used to score the facial action units (Live vs. retrospectively from still images) demonstrated significant differences in scores with live scores being significantly lower than retrospective scoring from images. The level of variation shown demonstrates the need for further research to be undertaken with regard to establishing baseline MGS scores for specific strains and sexes of mice, taking into account the method of scoring, prior to considering clinical implementation of this method in pain assessment.