Linear temporal logic for biologists in BMA

Medical Research Council, Royal SocietyThis is the author accepted manuscript. The final version is available from Springer via http://www.springer.com/in/book/978331945176

Development of Motorized Azimuthal Scanners for Ultrasonic NDE Of Composites

Composites are a material class for which nondestructive material property characterization is as important as flaw detection. Fiber reinforced composite laminates often possess strong in-plane elastic anisotropy attributable to the specific fiber orientation and layup sequence. Many of these elastic anisotropies may be investigated using ultrasound [1–6], among which angular measurements are often used. Hsu et al [3,4] used angular scan of acousto-ultrasonic signals to investigate fiber reinforced composite laminates. By placing and rotating two contact transducers on the same side of crossedplied composite laminates, the angular dependence of the acousto-ultrasonic signal was measured and found to have good correlation with the fiber orientation of the sample. Angular measurement of normal-incident shear wave has also been used to detect errors in layup sequence and ply orientation in both green (before cured) and cured composites [4–6]. The transmitted signals of normal incident shear wave in a “crossed polarizer” configuration were found to be particularly sensitive to ply misorientation and layup sequence in a laminate. For green composites, sandwiched between aluminum delay lines, EMATs (electro-meganetic transducer) were used so that the problem of changing coupling condition during the angular scan was avoided. This technique was believed to hold good potential as a practical NDE tool for detecting layup errors during the manufacturing process [5]

A qualitative exploration of physical, mental and ocular fatigue in patients with primary Sjögren's Syndrome

Introduction Primary Sjögren's Syndrome (pSS) affects exocrine glands such as those producing the tear film, leading to dry and painful eyes, but is also associated with fatigue. The experience of fatigue in pSS, and its relationship with sicca symptoms, is poorly understood. Methods Twenty people diagnosed with pSS were recruited to participate in a semi-structured qualitative interview about their symptoms experience. Interviews were audio-recorded, transcribed verbatim and analysed using thematic analysis. Results People with pSS described physical tiredness, mental fatigue and ocular fatigue. Mental fatigue was characterised by difficulties in attention, particularly, the ability to follow conversations and short-term memory problems. Participants linked their experience of fatigue to feeling of depression, frustration, irritation and anxiety, and therefore, fatigue was suggested to have had a large impact on their psychological well-being. People with pSS also described a range of ocular symptoms including pain, dryness, and itching, which were compounded by fatigue. For some, eye fatigue was pervasive, and daily activities involving the eyes such as reading, using the computer and driving were impaired. In some cases, the level of ocular discomfort was so severe it prevented sleep, which in turn impacted on general fatigue levels. Conclusions People with pSS experience fatigue in a range of ways; physical, mental and ocular fatigue were described. Fatigue was suggested to exacerbate other ocular symptoms, posed serious physical limitations and caused psychological distress. Further research into the nature of fatigue and ocular symptoms in pSS is required

Use of a Chirp Waveform in Pulsed Eddy Current Crack Detection

When an electrical conductor containing a surface-breaking crack is subjected to a short pulse of electromagnetic radiation, the reflected field contains transient features related to the depth of the crack. This has been demonstrated in both theoretical calculations [1] and in experiments [2,3] on shallow (0.13 mm to 1.3 mm) slots in a low conductivity titanium alloy. Specifically, these results show that the peak crack signal is delayed in time by an amount proportional to the square of the crack depth, and that the signal decay times also increase with increasing depth

Long-Term Results of Conservative Surgery and Radiotherapy for Ductal Carcinoma In Situ Using Lung Density Correction: The University of Michigan Experience

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72520/1/j.1524-4741.2007.00447.x.pd

A Toolbox for Discrete Modelling of Cell Signalling Dynamics

In an age where the volume of data regarding biological systems exceeds our ability to analyse it, many researchers are looking towards systems biology and computational modelling to help unravel the complexities of gene and protein regulatory networks. In order to make such techniques more accessible to mainstream researchers, tools such as the BioModelAnalyzer (BMA) have been developed to provide a user-friendly graphical interface for discrete modelling of biological systems. Here we use the BMA to build a library of target functions of known molecular interactions, translated from ordinary differential equations (ODEs). We then show that these BMA target functions can be used to reconstruct complex networks, which can correctly predict many known genetic perturbations. This new library supports the accessibility ethos behind the creation of BMA, providing a toolbox for the construction of complex cell signalling models without the need for extensive experience in computer programming or mathematical modelling, and allows for construction and simulation of complex biological systems with only small amounts of quantitative data.Royal Societ

Bringing LTL Model Checking to Biologists

The BioModelAnalyzer (BMA) is a web based tool for the development of discrete models of biological systems. Through a graphical user interface, it allows rapid development of complex models of gene and protein interaction networks and stability analysis without requiring users to be proficient computer programmers. Whilst stability is a useful specification for testing many systems, testing temporal specifications in BMA presently requires the user to perform simulations. Here we describe the LTL module, which includes a graphical and natural language interfaces to testing LTL queries. The graphical interface allows for graphical construction of the queries and presents results visually in keeping with the current style of BMA. The Natural language interface complements the graphical interface by allowing a gentler introduction to formal logic and exposing educational resources

Social Network Characteristics and Psychological Well-Being: A Replication and Extension

This article represents a replication and extension of a previous study by Israel and her colleagues that investigated the relationship between psychological well-being and social network characteristics. The present research included both a comparable sample of white women (N=104) between the ages of 60 and 68 (as in the original study), and a more extensive adult population of men and women (N=718) between the ages of 50 and 95. The network characteristics examined are categorized along three broad dimensions: Structure—linkages in the overall network (size and density); interaction-nature of the linkages themselves (frequency, geographic dispersion, and reciprocity); and functions that networks provide (affective support and instrumental support). The results indicate a predominance of comparable findings for both the replication and extension studies. Of the eight network characteristics examined, the results of five of the regression analyses were the same across all three studies. The network characteristics of size, density, geographic dispersion, reciprocal instrumental support, and instrumental support did not make a significant contribution to the variance in psychological well-being. Of the other three network characteristics, the effect of frequency of interaction varied across the studies, and a pattern of significant results was found for affective support and reciprocal affective support. A discussion of this evidence in light of current literature and implications for practice and research is included.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/67842/2/10.1177_109019818701400406.pd

Craniofacial dysmorphology in Down syndrome is caused by increased dosage of Dyrk1a and at least three other genes

Down syndrome (DS), trisomy of human chromosome 21 (Hsa21), occurs in 1 in 800 live births and is the most common human aneuploidy. DS results in multiple phenotypes, including craniofacial dysmorphology, which is characterised by midfacial hypoplasia, brachycephaly and micrognathia. The genetic and developmental causes of this are poorly understood. Using morphometric analysis of the Dp1Tyb mouse model of DS and an associated mouse genetic mapping panel, we demonstrate that four Hsa21-orthologous regions of mouse chromosome 16 contain dosage-sensitive genes that cause the DS craniofacial phenotype, and identify one of these causative genes as Dyrk1a. We show that the earliest and most severe defects in Dp1Tyb skulls are in bones of neural crest (NC) origin, and that mineralisation of the Dp1Tyb skull base synchondroses is aberrant. Furthermore, we show that increased dosage of Dyrk1a results in decreased NC cell proliferation and a decrease in size and cellularity of the NC-derived frontal bone primordia. Thus, DS craniofacial dysmorphology is caused by an increased dosage of Dyrk1a and at least three other genes