Joint iterative reconstruction and 3D rigid alignment for X-ray tomography.

X-ray tomography is widely used for three-dimensional structure determination in many areas of science, from the millimeter to the nanometer scale. The resolution and quality of the 3D reconstruction is limited by the availability of alignment parameters that correct for the mechanical shifts of the sample or sample stage for the images that constitute a scan. In this paper we describe an algorithm for marker-free, fully automated and accurately aligned and reconstructed X-ray tomography data. Our approach solves the tomographic reconstruction jointly with projection data alignment based on a rigid-body deformation model. We demonstrate the robustness of our method on both synthetic phantom and experimental data and show that our method is highly efficient in recovering relatively large alignment errors without prior knowledge of a low resolution approximation of the 3D structure or a reasonable estimate of alignment parameters.

Spicules and skeletons: mantle musculature of two species of dorid nudibranchs (Gastropoda: Nudibranchia: Doridina).

Molluscs often possess complex calcified elements in addition to the shell, but how these elements function and relate to other tissues is often poorly understood. Dorid nudibranchs typically possess innumerable calcareous spicules arranged in complex networks. To describe how these spicules interact with muscles and connective tissue, we reconstructed tomographic digital models using serial sections and synchrotron micro-computed tomography. In two species with dramatically different spicule network morphologies, musculature was divided into a dorsal layer of crossed fibres, a ventral layer of branching radial fibres, and scattered dorsoventral fibres in between. These two species differed in the size of their dorsal tubercles, which was reflected in the organization of dorsal musculature, and in the amount and organization of connective tissue. In Platydoris sanguinea Bergh, 1905, dense mats of spicules sandwiched a layer of connective tissue with fewer spicules and muscle insertions only onto the ventral spicules. In Cadlina luteomarginata MacFarland, 1966, thick tracts of spicules are surrounded by a sheath of connective tissue. Muscles surround and insert into the dorsal tubercle spicule layer. Thus, both species appear to use the spicule network for muscle antagonism and transfer of motion, but the different arrangement of elements suggests that they use this skeleton in quite different ways.

Les mollusques présentent fréquemment des éléments calcifiés complexes en plus de leur coquille, mais le fonctionnement de ces éléments et leur relation avec d'autres tissus ne sont souvent pas bien compris. Les nudibranches doridiens possèdent typiquement d'innombrables spicules calcaires disposés en réseaux complexes. Pour décrire l'interaction de ces spicules avec les muscles et les tissus conjonctifs, nous avons reconstitué des modèles numériques tomographiques en utilisant des séries de coupes et la microtomodensitométrie par synchrotron. Chez deux espèces dont les réseaux de spicules présentent des morphologies très différentes, la musculature est divisée en une couche dorsale de fibres entrecroisées, une couche ventrale de fibres radiales ramifiées et, entre les deux, des fibres dorsoventrales dispersées. Ces deux espèces diffèrent sur le plan de la taille de leurs tubercules dorsaux, ce qui se reflète dans l'organisation de la musculature dorsale, et de la quantité et de l'organisation du tissu conjonctif. Chez Platydoris sanguinea Bergh, 1905, de denses tapis de spicules bordent de part et d'autre une couche de tissu conjonctif comptant moins de spicules et des insertions de muscles seulement sur les spicules ventraux. Chez Cadlina luteomarginata MacFarland, 1966, d'épais faisceaux de spicules sont entourés d'une gaine de tissu conjonctif. Des muscles entourent la couche de spicules du tubercule dorsal et la pénètrent. Ainsi, les deux espèces semblent utiliser le réseau de spicules pour l'antagonisme de muscles et le transfert de mouvement, mais les différentes configurations d'éléments indiqueraient qu'elles utilisent ce squelette de manières très différentes.

Thyroid cytology-histology correlation using the RCPath terminology for thyroid cytology reporting.

AIMS: The Royal College of Pathologists Thy1-5 thyroid cytology guidance, 2009, second edition 2016, invites audits of its use. This report documents the experience of one department, assessing percentage usage of each Thy category, correlation with subsequent histology and comparison with other published studies. METHODS: Thyroid cytology and subsequent histology reports for 7 years (1 January 2008-31 December 2014) were reviewed, excluding referrals. Years 2008-2010 were compared with 2011-2014. RESULTS: There were 1090 specimens in 2008-2010, 1239 in 2011-2014. Thy usage for 2008-2010/2011-2014, respectively was: Thy1 16.1%/9.8%; Thy1c 10.6%/10.7%; Thy2/2c 52.4%/45.2%; Thy3a 9.6%/14.4%; Thy3f 5.8%/10.9%; Thy4 2.3%/3.6%; Thy5 1.8%/5.4%. 772 specimens had subsequent histology: 415 non-neoplastic lesions; 357 neoplasms (110 benign, 247 malignant). Risk of malignancy (ROM) (including non-histology cases) for 2008-2010/2011-2014: Thy1/1c 5.2%/4.0%; Thy2/2c 1.4%/1.4%; Thy3a 10.0%/14.5%; Thy3f 25.4%/26.7%. Positive predictive values (PPVs) for neoplasia (histology cases only): Thy3a 20.3%/56.9%; Thy3f 60.0%/64.8%; Thy4 58.3%/90.9%; Thy5 100%/100%. PPVs for malignancy (histology cases only): Thy3a 10.2%/36.1%; Thy3f 35.4%/33.3%; Thy4 50.0%/81.8%; Thy5 100%/100%. The Thy3a/Thy5 ratio for 2011-2014 was 2.7. CONCLUSIONS: Numerical reporting categories facilitate audit and comparison with other published results. Technique-related inadequates (Thy1) have reduced but cystic lesions (Thy1c) are stable, in keeping with increased use of ultrasound scanning (USS). Thy2/2c has reduced, probably reflecting increased USS selection of non-benign nodules for sampling. ROMs for Thy1/1c/2/2c are low. Usage of all positive categories, Thy3a, Thy3f, Thy4 and Thy5, has increased. As others have reported for atypia of undetermined significance or follicular lesion of undetermined significance, Thy3a is followed by malignancy more frequently than expected. There is stable prediction of malignancy by Thy3f and Thy5, the latter being 100% throughout.

Three-dimensional imaging of human stem cells using soft X-ray tomography.

Three-dimensional imaging of human stem cells using transmission soft X-ray tomography (SXT) is presented for the first time. Major organelle types--nuclei, nucleoli, mitochondria, lysosomes and vesicles--were discriminated at approximately 50 nm spatial resolution without the use of contrast agents, on the basis of measured linear X-ray absorption coefficients and comparison of the size and shape of structures to transmission electron microscopy (TEM) images. In addition, SXT was used to visualize the distribution of a cell surface protein using gold-labelled antibody staining. We present the strengths of SXT, which include excellent spatial resolution (intermediate between that of TEM and light microscopy), the lack of the requirement for fixative or contrast agent that might perturb cellular morphology or produce imaging artefacts, and the ability to produce three-dimensional images of cells without microtome sectioning. Possible applications to studying the differentiation of human stem cells are discussed.

Parent and caregiver knowledge, beliefs and responses to seizures in Jamaican children

OBJECTIVE: To determine the knowledge and beliefs about seizures and actions during seizures of parents/ caregivers of children hospitalised for convulsive seizures. DESIGN AND METHODS: This was a cross-sectional study of parents and caregivers of children with acute convulsive seizures hospitalised at the Bustamante Hospital, Kingston, Jamaica between May 1 and October 31, 2013. Subjects were identified by admission records. Parents/caregivers were invited to participate. A questionnaire on the knowledge, beliefs and response of parents/ caregivers during the child’s current seizure episode was administered face to face. Data were analysed for frequencies; comparisons between groups using Chi Square analysis for categorical variables, and the Mann-Whitney U test for data not normally distributed. RESULTS: Fifty participants were enrolled; 39 (78%) mothers; mean age (SD) was 33.8 (10.1) years. All sought medical care first. Twenty-two (44%) had plausible beliefs about the cause of seizures. Twenty-seven (54%) knew of appropriate actions during a seizure, 10 (20%) knew of appropriate precautions and 11 (22%) responded appropriately during the seizure. Eleven (22%) reported receiving seizure education. Witnessing a previous seizure, education level and seizure education were positively associated with knowledge of seizures (p < 0.05). Socioeconomic status was higher in those with plausible beliefs about seizures and lower in those who took appropriate action during a seizure (p<0.05). CONCLUSION: Parents/caregivers of children with convulsive seizures have appropriate health-care seeking behaviour but inadequate knowledge. Seizure education should be prioritised to improve parental knowledge of and response to convulsive seizures.

Coded aperture imaging for fluorescent x-rays.

We employ a coded aperture pattern in front of a pixilated charge couple device detector to image fluorescent x-rays (6-25 KeV) from samples irradiated with synchrotron radiation. Coded apertures encode the angular direction of x-rays, and given a known source plane, allow for a large numerical aperture x-ray imaging system. The algorithm to develop and fabricate the free standing No-Two-Holes-Touching aperture pattern was developed. The algorithms to reconstruct the x-ray image from the recorded encoded pattern were developed by means of a ray tracing technique and confirmed by experiments on standard samples.

Detection of ß-amyloid peptide (1-16) and amyloid precursor protein (APP770) using spectroscopic ellipsometry and QCM techniques: a step forward towards Alzheimers disease diagnostics.

A highly sensitive method of spectroscopic ellipsometry in total internal reflection mode (TIRE) was exploited for detecting ß-amyloid peptide (Aß(1-16)) in the direct immune reaction with monoclonal DE2 antibodies (raised against Aß(1-16)) electrostatically immobilised on the surface of gold. A rapid detection of Aß(1-16) in a wide range of concentrations from 5 µg/ml down to 0.05 ng/ml was achieved using a cost-effective and label-free direct immunoassay format. TIRE dynamic spectral measurements proved that the immune reaction between DE2 monoclonal antibodies and Aß(1-16) is highly specific with the affinity constant K(D)=1.46×10(-8) mol/l. The same DE2 antibodies were utilised for detection of amyloid precursor protein APP(770), a larger protein containing Aß(1-16) domain, using the quartz crystal microbalance (QCM) measurements in liquid. A combination of QCM and TIRE kinetics results allowed the evaluation of the originally unknown concentration of APP(770) in complete medium solution containing other proteins, salts, and amino acids.

Analysis of ergosterol for the detection of mold in soils by automated on-fiber derivatization headspace extraction-SPME-GC/MS.

The estimate of ergosterol ([5,7,22-ergostatrien-3beta-ol] has been used by many to relate its concentration to the amount of mold in soils. This new method using on-fiber derivatization-solid phase microextraction-GC/MS method for the analysis of ergosterol presents a quick and straightforward method where low detection limits (1.5 ppb) and good limit of quantitation range (3 ppb to 90 ppm) can be achieved with careful control of analytical parameters. After saponification of real soil samples, sampling without extensive workup can be performed and analysis by a standard addition method can be utilized to deduce the original sample concentration of ergosterol. Peak area extraction analysis by MS SIM on selected characteristic fragment ions gives results with RSD < or = 2.2%.

Educating for personalized medicine: a perspective from oncology.

The personalized-medicine concept represents the future of oncology medicine. New genomics technologies will characterize patients biologically in ways that will drive more efficient and effective cancer treatment. Yet the introduction of these technologies is disruptive to current practices in clinical oncology, as well as to current regulatory and reimbursement strategies. The efficient introduction of personalized medicine will require education in addition to behavioral and policy changes by the various involved stakeholders.

Impaired intercellular adhesion and immature adherens junctions in merlin-deficient human primary schwannoma cells.

Schwannomas that occur spontaneously or in patients with neurofibromatosis Type 2, lack both alleles for the tumor suppressor and plasma membrane-cytoskeleton linker merlin. We have shown that human primary schwannoma cells display activation of the RhoGTPases Rac1 and Cdc42 which results in highly dynamic and ongoing protrusive activity like ruffling. Ruffling is an initial and temporally limited step in the formation of intercellular contacts like adherens junctions that are based on the cadherin-catenin system. We tested if there is a connection between Rac1-induced ongoing ruffling and the maintenance, stabilization and functionality of adherens junctions and if this is of relevance in human, merlin-deficient schwannoma cells. We show intense ongoing ruffling is not limited to membranes of single human primary schwannoma cells, but occurs also in membranes of contacting cells, even when confluent. Live cell imaging shows that newly formed contacts are released after a short time, suggesting disturbed formation or stabilization of adherens junctions. Morphology, high phospho-tyrosine levels and cortactin staining indicate that adherens junctions are immature in human primary schwannoma cells, whereas they display characteristics of mature adherens junctions in human primary Schwann cells. When merlin is reintroduced, human primary schwannoma cells show only initial ruffling in contacting cells and adherens junctions appear more mature. We therefore propose that ongoing Rac-induced ruffling causes immature adherens junctions and leads to impaired, nonfunctional intercellular adhesion in aggregation assays in merlin-deficient schwannoma cells that could be an explanation for increased proliferation rates due to loss of contact inhibition or tumor development in general.

Anticancer drug discovery and development throughout the world.

This year's American Society of Clinical Oncology International Symposium devoted 2 hours to a lively discussion of various aspects of anticancer drug discovery and development throughout the world. The scientific program started with an overview of efforts directed toward promoting international collaboration in natural product-derived anticancer drug discovery. This was followed by a discussion on the importance of interethnic differences and pharmacogenetics in anticancer drug development. Thereafter, this part of the program was completed by a description of the activities of the newly created Singapore-Hong Kong-Australia Drug Development Consortium and an overview of the contribution of Japan to anticancer drug development. The logistics and regulatory aspects of clinical trials with new anticancer agents in different parts of the world were then presented, with an emphasis on Europe, North America, and Japan. The program was completed with a panel discussion of the efforts to harmonize the exchange of clinical data originating from one region of the globe with other territories, with input from official representatives of the United States Food and Drug Administration and the Medical Devices Evaluation Center of Japan.

Transforming growth factor beta (TGFbeta) mediates Schwann cell death in vitro and in vivo: examination of c-Jun activation, interactions with survival signals, and the relationship of TGFbeta-mediated death to Schwann cell differentiation.

In some situations, cell death in the nervous system is controlled by an interplay between survival factors and negative survival signals that actively induce apoptosis. The present work indicates that the survival of Schwann cells is regulated by such a dual mechanism involving the negative survival signal transforming growth factor beta (TGFbeta), a family of growth factors that is present in the Schwann cells themselves. We analyze the interactions between this putative autocrine death signal and previously defined paracrine and autocrine survival signals and show that expression of a dominant negative c-Jun inhibits TGFbeta-induced apoptosis. This and other findings pinpoint activation of c-Jun as a key downstream event in TGFbeta-induced Schwann cell death. The ability of TGFbeta to kill Schwann cells, like normal Schwann cell death in vivo, is under a strong developmental regulation, and we show that the decreasing ability of TGFbeta to kill older cells is attributable to a decreasing ability of TGFbeta to phosphorylate c-Jun in more differentiated cells.

Expression of amyloid precursor protein in human astrocytes in vitro: isoform-specific increases following heat shock.

The beta-amyloid protein deposited in senile plaques and cerebral blood vessels in the Alzheimer's disease brain is derived from the larger transmembrane spanning amyloid precursor protein. The present study investigates the effects of heat shock on the expression and processing of amyloid precursor protein in a normal human fetal astrocytic cell line CC2565 using reverse transcription-polymerase chain reaction, in situ hybridization histochemistry and western blot analysis. Heat shock led to an increase in the messenger RNA encoding Kunitz protease inhibitor isoforms of amyloid precursor protein, which peaked at 4h post-heat shock. This increase was confined to the messenger RNA encoding amyloid precursor protein-751, with a decrease in amyloid precursor protein-770 and no change in amyloid precursor protein-695. This shift in splicing was accompanied by a significant decrease in secreted amyloid precursor protein and an increase in beta-secretase processing within the cell. These findings demonstrate that astrocytes in vitro demonstrate a striking response to heat shock. This is unlikely to be due to a direct action on the promoter region of the gene, since the response is specific for one splice variant; amyloid precursor protein-751 messenger RNA. This increase in expression is further accompanied by a decrease in secretion of amyloid precursor protein, implying a shift in processing towards an intracellular route, possibly via the actions of the beta-secretase enzyme, which is known to be potentially amyloidogenic. Such a mechanism may contribute to amyloidosis in the intact brain in response to cellular stress, such as head injury.

Extradural neural axis compartment.

The lengthy, continuous, slender extradural neural axis compartment (EDNAC), which extends from the coccyx to the orbit, has been not so much discovered as recognized. Through this compartment run arteries, myelinated and unmyelinated nerves, and valveless veins. Adipose tissue is abundant in the orbital and spinal segments, possibly due to movement requirements, although it is very sparse in the skull base segment, the last segment to be recognized as a continuation of the EDNAC, which connects Breschet's veins to the orbit. The lateral sellar compartment (in older terminology, the cavernous sinus) is an enlarged segment of this EDNAC along the skull base connecting the orbit with the extradural space through the superior orbital fissure and down the dorsum to Breschet's veins of the basilar process of the occipital bone. Understanding the continuity of the EDNAC should help the student understand any segment, particularly the skull base. As Batson noted, "Living anatomy is slowly editing and replacing the anatomy of the dead room."