Mathematical principles for the design of isostatic mount systems for dynamic structures

Isostatic mounts are used in applications like telescopes and robotics to move and hold part of a structure in a desired pose relative to the rest, by driving some controls rather than driving the subsystem directly. To achieve this successfully requires an understanding of the structure of the coupled space of configurations and controls, and of the singularities of the mapping from the coupled space to the space of controls. It is crucial to avoid such singularities because generically they lead to large constraint forces and internal stresses which can cause distortion. In this paper we outline design principles for isostatic mount systems for dynamic structures, with particular emphasis on robots

Simulation, modelling and development of the metris RCA

In partnership with Metris UK we discuss the utilisation of modelling and simulation methods in the development of a revolutionary 7-axis Robot CMM Arm (RCA). An offline virtual model is described, facilitating pre-emptive collision avoidance and assessment of optimal placement of the RCA relative to scan specimens. Workspace accessibility of the RCA is examined under a range of geometrical assumptions and we discuss the effects of arbitrary offsets resulting from manufacturing tolerances. Degeneracy is identified in the number of ways a given pose may be attained and it is demonstrated how a simplified model may be exploited to solve the inverse kinematics problem of finding the “correct” set of joint angles. We demonstrate how the seventh axis may be utilised to avoid obstacles or otherwise awkward poses, giving the unit greater dexterity than traditional CMMs. The results of finite element analysis and static force modelling on the RCA are presented which provide an estimate of the forces exerted on the internal measurement arm in a range of poses

Characteristics, accuracy and reverification of robotised articulated arm CMMs

VDI article 2617 specifies characteristics to describe the accuracy of articulated arm coordinate measuring machines (AACMMs) and outlines procedures for checking them. However the VDI prescription was written with a former generation of machines in mind: manual arms exploiting traditional touch probe technologies. Recent advances in metrology have given rise to noncontact laser scanning tools and robotic automation of articulated arms – technologies which are not adequately characterised using the VDI specification. In this paper we examine the “guidelines” presented in VDI 2617, finding many of them to be ambiguous and open to interpretation, with some tests appearing even to be optional. The engineer is left significant flexibility in the execution of the test procedures and the manufacturer is free to specify many of the test parameters. Such flexibility renders the VDI tests of limited value and the results can be misleading. We illustrate, with examples using the Nikon RCA, how a liberal interpretation of the VDI guidelines can significantly improve accuracy characterisation and suggest ways in which to mitigate this problem. We propose a series of stringent tests and revised definitions, in the same vein as VDI 2617 and similar US standards, to clarify the accuracy characterisation process. The revised methodology includes modified acceptance and reverification tests which aim to accommodate emerging technologies, laser scanning devices in particular, while maintaining the spirit of the existing and established standards. We seek to supply robust re-definitions for the accepted terms “zero point” and “useful arm length”, pre-supposing nothing about the geometry of the measuring device. We also identify a source of error unique to robotised AACMMs employing laser scanners – the forward-reverse pass error. We show how eliminating this error significantly improves the repeatability of a device and propose a novel approach to the testing of probing error based on statistical uncertainty

Automated SNP detection from a large collection of white spruce expressed sequences: contributing factors and approaches for the categorization of SNPs

BACKGROUND: High-throughput genotyping technologies represent a highly efficient way to accelerate genetic mapping and enable association studies. As a first step toward this goal, we aimed to develop a resource of candidate Single Nucleotide Polymorphisms (SNP) in white spruce (Picea glauca [Moench] Voss), a softwood tree of major economic importance. RESULTS: A white spruce SNP resource encompassing 12,264 SNPs was constructed from a set of 6,459 contigs derived from Expressed Sequence Tags (EST) and by using the bayesian-based statistical software PolyBayes. Several parameters influencing the SNP prediction were analysed including the a priori expected polymorphism, the probability score (P(SNP)), and the contig depth and length. SNP detection in 3' and 5' reads from the same clones revealed a level of inconsistency between overlapping sequences as low as 1%. A subset of 245 predicted SNPs were verified through the independent resequencing of genomic DNA of a genotype also used to prepare cDNA libraries. The validation rate reached a maximum of 85% for SNPs predicted with either P(SNP )≥ 0.95 or ≥ 0.99. A total of 9,310 SNPs were detected by using P(SNP )≥ 0.95 as a criterion. The SNPs were distributed among 3,590 contigs encompassing an array of broad functional categories, with an overall frequency of 1 SNP per 700 nucleotide sites. Experimental and statistical approaches were used to evaluate the proportion of paralogous SNPs, with estimates in the range of 8 to 12%. The 3,789 coding SNPs identified through coding region annotation and ORF prediction, were distributed into 39% nonsynonymous and 61% synonymous substitutions. Overall, there were 0.9 SNP per 1,000 nonsynonymous sites and 5.2 SNPs per 1,000 synonymous sites, for a genome-wide nonsynonymous to synonymous substitution rate ratio (Ka/Ks) of 0.17. CONCLUSION: We integrated the SNP data in the ForestTreeDB database along with functional annotations to provide a tool facilitating the choice of candidate genes for mapping purposes or association studies

Development and characterisation of a novel three-dimensional inter-kingdom wound biofilm model

Chronic diabetic foot ulcers are frequently colonised and infected by polymicrobial biofilms that ultimately prevent healing. This study aimed to create a novel in vitro inter-kingdom wound biofilm model on complex hydrogel-based cellulose substrata to test commonly used topical wound treatments. Inter-kingdom triadic biofilms composed of Candida albicans, Pseudomonas aeruginosa, and Staphylococcus aureus were shown to be quantitatively greater in this model compared to a simple substratum when assessed by conventional culture, metabolic dye and live dead qPCR. These biofilms were both structurally complex and compositionally dynamic in response to topical therapy, so when treated with either chlorhexidine or povidone iodine, principal component analysis revealed that the 3-D cellulose model was minimally impacted compared to the simple substratum model. This study highlights the importance of biofilm substratum and inclusion of relevant polymicrobial and inter-kingdom components, as these impact penetration and efficacy of topical antiseptics

Modular organization of the white spruce (Picea glauca) transcriptome reveals functional organization and evolutionary signatures

Transcript profiling has shown the molecular bases of several biological processes in plants but few studies have developed an understanding of overall transcriptome variation. We investigated transcriptome structure in white spruce (Picea glauca), aiming to delineate its modular organization and associated functional and evolutionary attributes. Microarray analyses were used to: identify and functionally characterize groups of co-expressed genes; investigate expressional and functional diversity of vascular tissue preferential genes which were conserved among Picea species, and identify expression networks underlying wood formation. We classified 22 857 genes as variable (79%; 22 coexpression groups) or invariant (21%) by profiling across several vegetative tissues. Modular organization and complex transcriptome restructuring among vascular tissue preferential genes was revealed by their assignment to coexpression groups with partially overlapping profiles and partially distinct functions. Integrated analyses of tissue-based and temporally variable profiles identified secondary xylem gene networks, showed their remodelling over a growing season and identified PgNAC-7 (no apical meristerm (NAM), Arabidopsis transcription activation factor (ATAF) and cup-shaped cotyledon (CUC) transcription factor 007 in Picea glauca) as a major hub gene specific to earlywood formation. Reference profiling identified comprehensive, statistically robust coexpressed groups, revealing that modular organization underpins the evolutionary conservation of the transcriptome structure. © 2015 The Authors

Aspirin inhibits the acute venodilator response to furosemide in patients with chronic heart failure

OBJECTIVES: We sought to determine the effect of aspirin on the venodilator effect of furosemide in patients with chronic heart failure (CHF) BACKGROUND: Furosemide has an acute venodilator effect preceding its diuretic action, which is blocked by nonsteroidal anti-inflammatory drugs. The ability of therapeutic doses of aspirin to block this effect of furosemide in patients with CHF has not been studied. For comparison, the venodilator response to nitroglycerin (NTG) was also studied. METHODS: Eleven patients with CHF were randomized to receive placebo, aspirin at 75 mg/day or aspirin at 300 mg/day for 14 days in a double-blind, crossover study. The effect of these pretreatments on the change in forearm venous capacitance (FVC) after 20 mg of intravenous furosemide was measured over 20 min by using venous occlusion plethysmography. In a second study, the effect of 400 μg of sublingual NTG on FVC was documented in 11 similar patients (nine participated in the first study). RESULTS: Mean arterial pressure, heart rate and forearm blood flow did not change in response to furosemide. After placebo pretreatment, furosemide caused an increase in FVC of 2.2% (95% confidence interval [CI] −0.9% to 5.2%; mean response over 20 min). By comparison, FVC fell by −1.1% (95% CI −4.2% to 1.9%) after pretreatment with aspirin at 75 mg/day, and by −3.7% (95% CI −6.8% to −0.7%) after aspirin at 300 mg/day (p = 0.020). In the second study, NTG increased FVC by 2.1% (95% CI −1.6% to 5.8%) (p = 0.95 vs. furosemide). CONCLUSIONS: In patients with CHF, venodilation occurs within minutes of the administration of intravenous dose of furosemide. Our observation that aspirin inhibits this effect further questions the use of aspirin in patients with CHF

Analysis of lesion localisation at colonoscopy: outcomes from a multi-centre U.K. study

Background: Colonoscopy is currently the gold standard for detection of colorectal lesions, but may be limited in anatomically localising lesions. This audit aimed to determine the accuracy of colonoscopy lesion localisation, any subsequent changes in surgical management and any potentially influencing factors. Methods: Patients undergoing colonoscopy prior to elective curative surgery for colorectal lesion/s were included from 8 registered U.K. sites (2012–2014). Three sets of data were recorded: patient factors (age, sex, BMI, screener vs. symptomatic, previous abdominal surgery); colonoscopy factors (caecal intubation, scope guide used, colonoscopist accreditation) and imaging modality. Lesion localisation was standardised with intra-operative location taken as the gold standard. Changes to surgical management were recorded. Results: 364 cases were included; majority of lesions were colonic, solitary, malignant and in symptomatic referrals. 82% patients had their lesion/s correctly located at colonoscopy. Pre-operative CT visualised lesion/s in only 73% of cases with a reduction in screening patients (64 vs. 77%; p = 0.008). 5.2% incorrectly located cases at colonoscopy underwent altered surgical management, including conversion to open. Univariate analysis found colonoscopy accreditation, scope guide use, incomplete colonoscopy and previous abdominal surgery significantly influenced lesion localisation. On multi-variate analysis, caecal intubation and scope guide use remained significant (HR 0.35, 0.20–0.60 95% CI and 0.47; 0.25–0.88, respectively). Conclusion: Lesion localisation at colonoscopy is incorrect in 18% of cases leading to potentially significant surgical management alterations. As part of accreditation, colonoscopists need lesion localisation training and awareness of when inaccuracies can occur

Multimodality treatment of brain metastases: an institutional survival analysis of 275 patients

<p>Abstract</p> <p>Background</p> <p>Whole brain radiation therapy (WBRT), surgical resection, stereotactic radiosurgery (SRS), and combinations of the three modalities are used in the management of patients with metastatic brain tumors. We present the previously unreported survival outcomes of 275 patients treated for newly diagnosed brain metastases at Cancer Care Northwest and Gamma Knife of Spokane between 1998 and 2008.</p> <p>Methods</p> <p>The effects treatment regimen, age, Eastern Cooperative Oncology Group-Performance Status (ECOG-PS), primary tumor histology, number of brain metastases, and total volume of brain metastases have on patient overall survival were analyzed. Statistical analysis was performed using Kaplan-Meier survival curves, Andersen 95% confidence intervals, approximate confidence intervals for log hazard-ratios, and multivariate Cox proportional hazard models.</p> <p>Results</p> <p>The median clinical follow up time was 7.2 months. On multivariate analysis, survival statistically favored patients treated with SRS alone when compared to patients treated with WBRT alone (p < 0.001), patients treated with resection with SRS when compared to patients treated with SRS alone (p = 0.020), patients in ECOG-PS class 0 when compared to patients in ECOG-PS classes 2 (p = 0.04), 3 (p < 0.001), and 4 (p < 0.001), patients in the non-small-cell lung cancer group when compared to patients in the combined melanoma and renal-cell carcinoma group (p < 0.001), and patients with breast cancer when compared to patients with non-small-cell lung cancer (p < 0.001).</p> <p>Conclusions</p> <p>In our analysis, patients benefited from a combined modality treatment approach and physicians must consider patient age, performance status, and primary tumor histology when recommending specific treatments regimens.</p