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Background With recent advances in microscopy, recordings of cell behaviour can result in terabyte-size datasets. The lattice light sheet microscope (LLSM) images cells at high speed and high 3D resolution, accumulating data at 100 frames/second over hours, presenting a major challenge for interrogating these datasets. The surfaces of vertebrate cells can rapidly deform to create projections that interact with the microenvironment. Such surface projections include spike-like filopodia and wave-like ruffles on the surface of macrophages as they engage in immune surveillance. LLSM imaging has provided new insights into the complex surface behaviours of immune cells, including revealing new types of ruffles. However, full use of these data requires systematic and quantitative analysis of thousands of projections over hundreds of time steps, and an effective system for analysis of individual structures at this scale requires efficient and robust methods with minimal user intervention. Results We present LLAMA, a platform to enable systematic analysis of terabyte-scale 4D microscopy datasets. We use a machine learning method for semantic segmentation, followed by a robust and configurable object separation and tracking algorithm, generating detailed object level statistics. Our system is designed to run on high-performance computing to achieve high throughput, with outputs suitable for visualisation and statistical analysis. Advanced visualisation is a key element of LLAMA: we provide a specialised tool which supports interactive quality control, optimisation, and output visualisation processes to complement the processing pipeline. LLAMA is demonstrated in an analysis of macrophage surface projections, in which it is used to i) discriminate ruffles induced by lipopolysaccharide (LPS) and macrophage colony stimulating factor (CSF-1) and ii) determine the autonomy of ruffle morphologies. Conclusions LLAMA provides an effective open source tool for running a cell microscopy analysis pipeline based on semantic segmentation, object analysis and tracking. Detailed numerical and visual outputs enable effective statistical analysis, identifying distinct patterns of increased activity under the two interventions considered in our example analysis. Our system provides the capacity to screen large datasets for specific structural configurations. LLAMA identified distinct features of LPS and CSF-1 induced ruffles and it identified a continuity of behaviour between tent pole ruffling, wave-like ruffling and filopodia deployment.

Developmental branching morphogenesis establishes organ architecture, and it is driven by iterative interactions between epithelial and mesenchymal progenitor cell populations. We describe an approach for analyzing this interaction and how it contributes to organ development. After initial in vivo cell labeling with the nucleoside analog 5-ethynyl-2'-deoxyuridine (EdU) and tissue-specific antibodies, optical projection tomography (OPT) and confocal microscopy are used to image the developing organ. These imaging data then inform a second analysis phase that quantifies (using Imaris and Tree Surveyor software), models and integrates these events at a cell and tissue level in 3D space and across developmental time. The protocol establishes a benchmark for assessing the impact of genetic change or fetal environment on organogenesis that does not rely on ex vivo organ culture or section-based reconstruction. By using this approach, examination of two developmental stages for an organ such as the kidney can be undertaken by a postdoctoral-level researcher in 6 weeks, with a full developmental analysis in mouse achievable in 5 months.

We construct face two-colourable triangulations of the graph 2Kn in an orientable surface; equivalently biembeddings of two twofold triple systems of order n, for all n ≡ 4 (mod 12). The biembeddings have a cyclic automorphism and the construction employs index 1 current graphs.

The parity vectors of two Latin squares of the same side n provide a necessary condition for the two squares to be biembeddable in an orientable surface. We investigate constraints on the parity vector of a Latin square resulting from structural properties of the square, and show how the parity vector of a direct product may be obtained from the parity vectors of the constituent factors. Parity vectors for Cayley tables of all Abelian groups, some non-Abelian groups, Steiner quasigroups and Steiner loops are determined. Finally, we give a lower bound on the number of main classes of Latin squares of side n that admit no self-embeddings.

A defining set of a t-(v, k, λ) design is a subcollection of its blocks which is contained in no other t-design with the given parameters, on the same point set. A minimal defining set is a defining set, none of whose proper subcollections is a defining set. The spectrum of minimal defining sets of a design D is the set {|M| | M is a minimal defining set of D}. We show that if a t-(v, k, λ) design D is contained in a design F, then for every minimal defining set d D of D there exists a minimal defining set d F of F such that $${d_D = d_F\cap D}$$. The unique simple design with parameters $${{\left(v,k, {v-2\choose k-2}\right)}}$$is said to be the full design on v elements; it comprises all possible k-tuples on a v set. Every simple t-(v, k, λ) design is contained in a full design, so studying minimal defining sets of full designs gives valuable information about the minimal defining sets of all t-(v, k, λ) designs. This paper studies the minimal defining sets of full designs when t = 2 and k = 3. Several families of non-isomorphic minimal defining sets of these designs are found. For given v, a lower bound on the size of the smallest and an upper bound on the size of the largest minimal defining set are given. The existence of a continuous section of the spectrum comprising approximately v values is shown, where just two values were known previously.

Topotecan has demonstrated activity in ovarian carcinomas. In order to increase the tumour response rate and to define the maximum tolerated dose (MTD) of topotecan, we decided to develop a high-dose phase I regimen supported by stem cell support. High-doses schedules using a 1-day single administration have MTDs of 10.5 (24 h continuous infusion (CI)) or 22.5 mg/m2 (30 min infusion). Five-day CI induces grade IV mucositis at high doses (MTD12 mg/m2). We chose to administer topotecan in a 5-day schedule with a 30 min daily infusion. Patients were scheduled to receive one cycle of therapy. The first dose level was 4.0 mg/m2/day x 5 days. Limiting toxicities were defined as toxic death, grade IV non-haematopoietic or haematopoietic toxicity6 weeks. From August 1998 to April 2002, 49 patients were included. Forty-three patients have completed one course and 15 have received two cycles. One patient treated at level 7 mg/m2/day died of sepsis. Median duration of grade IV neutropenia was 9 days. Two episodes of grade IV diarrhoea were observed at level 9.5 mg/m2/day. Pharmacokinetic data were linear within the dose range of 4-9.0 mg/m2/day. The MTD was reached at 9 mg/m2/day x 5 days.

A K 4 - e trade consists of two disjoint decompositions of some simple graph H into copies of K 4 - e. The number of vertices of H is referred to as the foundation of the trade, while the number of copies of K 4 - e in each of the decompositions is called the volume of the trade. We determine the values of v and s for which there exists a K 4 - e trade of volume s and foundation v.

The deformation characteristics of quenched and aged Ti-V alloys in the composition range 20 to 40 wt pct vanadium have been examined by optical metallography and transmission electron microscopy. A coarse lenticular deformation product similar in appearance to previously reported strain induced “martensites” was found to be associated with the occurrence of the omega phase. These features proved to be {112}〈111〉 twins. In the omega bearing alloys prolonged aging resulted in a transition of the deformation mode from twinning to slip at a point which corresponded either to the onset of embrittlement or alpha phase precipitation.

Beta phase titanium-vanadium alloys in the composition range 20 to 40 wt pct vanadium were studied to determine the dependence of mechanical properties and texture formation on deformation modes. Changes in twinning probability and slip characteristics with vanadium content are reflected in wide variations in sheet textures in both as-rolled and rolled and recrystallized samples. These sheet textures exhibit strongly anisotropic strength properties which may be qualitatively related to the type of texture.

All of the eleven tested bi-and tricyclic sugar acetals were found to be competitive inhibitors of glucose exit from human red cells. The highest-affinity agents were those locked into a Cl conformation by fusion with am-dioxane ring attached to a phenyl group (methyl-4,6-O-benzylidene-d-glucopyranoside,K i =0.73mm; 4,6-O-benzylidene-d-glucopyranose,K i =0.13mm at 23°C). All of the isopropylidene acetals had less affinity thand-glucose (Sen-WiddasK m=2.5mm) for the transport system. Sugars in which two or more hydroxyl group were cross-linked by isopropylidene group apprently penetrated the red cell membrane by simple diffusion, as shown by a lack of (1) saturation in the entry process (2) competition for entry with other acetals ord-glucose, and (3) inhibition by phloretins or Hg2+ on entry rates.

The strength characteristics and microstructures of aged Ni−Mo alloys containing ordered (Ni4Mo) precipitates were studied as a function of aging time and temperature. It was found that 17 at. pct Mo alloy aged at 750°C produced a uniform dispersion of cuboidal β precipitates which coarsened with time producing a gradual increase in flow stress. The flow stress increment was found to vary in qualitative agreement with both order strengthening and coherency strain models. Both these models give over-estimates of the strengthening increment. A negative dependence of flow stress on temperature is attributed to coherency strain contributions.

The influence of wire processing variables on the formation of subgrain structures and strengthening in three aluminum conductor materials is described. Electrical conductor grade aluminum, an Al-Fe-Mg alloy and an Al-Fe-Co alloy each develop subgrain structures with mean linear intercepts (•L) in the range of 0.4 to 1.5 μm with several sequences of wiredrawing and partial annealing. The yield strengths of these wires were found to obey a a = σ0 +k(•L) m relationship, with an exponentm = -1 independent of the processing sequence used to arrive at the structure. The role of precipitate particles in the alloys is to raisek above that for EC-A1 while Mg in solid solution increases σ0. The precipitates also affect the development of the substructure during the wiredrawing and annealing.

The structure and kinetics of aged Cu-15 Ni-8 Sn with and without prior deformation was investigated by means of X-ray diffraction and transmission electron microscopy. Deformation prior to aging is known to accelerate the hardening process in this alloy. The purpose of the study was to determine whether the strengthing mechanisms are kinetically enhanced through modified alloy decomposition or through other mechanisms. Deformation does not affect most of the features of structure development, including DO22 ordering in the tin-rich phase. However, for a given aging treatment, cold worked material shows a reduced strain modulation. The accelerated strengthening response in cold worked alloys cannot be attributed to an accelerated or altered decomposition process. It is suggested that the coarsened spinodal structure and the dislocation structure interact in a synergistic way to give the observed strengthening acceleration.

The microstructures and hardening characteristics of Al and Al with dilute additions of soluble and insoluble impurities were compared during wire drawing at room temperature to true strains (e w ) of 4.95. Three stages of microstructure change are observed: formation of a dislocation cell structure; cell boundary sharpening and cell size refinement; dynamic recrystallization. A minimum effective cell size is reached at an intermediate strain level corresponding approximately to the onset of dynamic recrystallization. The amounts and types of impurities at levels less than 1 pct have a great effect on the details of the microstructural changes as well as the hardening characteristics. 99.98 pct pure Al alternately saturates and hardens frome w = 0 to 4.95. Al-0.6 Fe (insoluble) work softens neare w = 3.5. Al-0.2 Mg (soluble) and EC Al (with 0.15 pct soluble and insoluble impurities) both work harden at a diminishing rate toe w ≃1.25 then enter a linear hardening stage which persists toe w ≃5. A linear relation between yield strength and inverse cell size is established for EC Al and Al-0.2 Mg in the cell refinement strain range; however, the Petch slope is much less than that of similar Al alloys subjected to elevated temperature dynamic or static recovery. Al-0.6 Fe does not exhibit a consistent linear relation between yield strength and inverse cell size. These differences can be attributed to the degree of recovery and the interrelation between cell size, cell boundary character and total dislocation density.

Age hardening and accompanying phase transformations were studied in a Cu-15Ni-8Sn alloy using mechanical testing, X-ray diffraction and microscopy techniques on samples aged at 300 to 550°C. At 450°C and below, strengthening is accompanied by the formation of sideband peaks about the fundamental reflections corresponding to a modulated structure with A≃ 100A. This structure is metastable and with further aging is displaced by a discontinuous (cellular) precipitation reaction which causes the yield strength to drop. A peak yield strength increment of ≃450 MPa is achieved in samples aged at 350°C. Both the hardening and the discontinuous transformation growth rates are increased by extensive deformation prior to aging. Prior deformation decreases the time to peak strength but does not significantly affect the peak strength increment. The early stages of aging correlate well with a spinodal strengthening model proposed by Ditchek and Schwartz which considers squaring of the composition modulation wave.

A detailed cytogenetic study of male-viable and lethal deficiencies affecting the w-spl interval in Drosophila melanogaster has revealed the existence of genetic duplication such that, for example, the consequences of the loss of salivary chromosome band 3C3 are essentially compensated for by the presence of band 3C5-6, and vice versa. Although each of the duplicate elements possesses rst + and vt + activity, rst and vt phenotypes appear in males when 3C3 and part, but not all, of 3C5-6 are deleted. The degree of rst and vt expression can be correlated with the amount of material lost from 3C5-6. Deletions removing the entire 3C3-6 interval are male lethal. Despite the duplicate elements, at least one EMS-induced, presumptive point mutation expressing only rst is known; two others express both rst and vt. No loci other than rst and vt occur between W and spl. Band 3C2 appears to be associated with the w locus, which probably extends into the interband space between 3C1 and 3C2. The w locus is not involved in the rst-vt duplication in the 3C3-6 region. — The cytogenetic characteristics of the 3C region—a high coefficient of crossing over, frequent induced chromosome breakage, ectopic pairing, constriction, and an extended replication period—can be correlated with the fact that in 3C a relatively long stretch of DNA, nearly 2% of the entire X chromosome, is highly compacted into but few adjacent bands. These characteristics do not necessarily represent special properties of intercalary heterochromatin; they can be interpreted as reflecting the properties of any similarly organized euchromatic region.

A number of kinetic incompatibilities with classical carrier theory, previously noted in the behavior of the monosaccharide transport system in human erythrocytes, are accommodated by a revised picture of the arrangement of the sugar-recognizing entities in the cell membranes. The new schema, an extension from that recently proposed by Naftalin (Biochim. Biophys. Acta211:65, 1970), replaces the mobile carriers with binding sites fixed in a two-column matrix (bilayer). These sites are in a state of equilibrium between a more interfacially disposed conformation and a more “introverted” state not in direct contact with the adjacent aqueous pool (cell interior or outside medium); adsorbed sugars may migrate between the two layers only when the apposed sites are both in the introverted orientation. Occupation of the sites by any given sugar characteristically shifts the position of the introversion-extroversion equilibrium. Computer simulation of this model, under certain restricting conditions, shows reasonable correspondence with observations on the biological system which have been difficult to bring into accord with mobile-carrier theory, particularly the dissonance in the apparent binding characteristics given by several accepted experimental approaches. Moreover, the single “introversiveness” characteristic distinguishing the several substrates may alone serve (in place of differing binding affinities and inter-site transition probabilities) as the basis for the sugars' comparative “saturation” characteristics, and for their patterns of mutual competitive or accelerative interplay.

Polycrystalline samples of Ni4Mo have been examined at various stages of isothermal ageing at 700° C. The mechanical properties were measured on initially disordered samples at various stages of the ordering process. These properties were correlated with microstructural observations such as domain size, degree of order and fracture characteristics. The correlations are rationalised in terms of a model for the ordering process and its effect on dislocation motion.