Computed tomography for in vivo deep over‐1000 nm near‐infrared fluorescence imaging

This study aims to develop a novel cross‐sectional imaging of fluorescence in over‐1000 nm near‐infrared (OTN‐NIR), which allows in vivo deep imaging, using computed tomography (CT) system. Cylindrical specimens of composite of OTN‐NIR fluorophore, NaGdF₄ co‐doped with Yb³⁺ and Ho³⁺ (ex: 980 nm, em: 1150 nm), were embedded in cubic agar (10.5–12 mm) or in the peritoneal cavity of mice and placed on a rotatable stage. When the fluorescence from inside of the samples was serially captured from multiple angles, the images were disrupted by the reflection and refraction of emitted light on the sample‐air interface. Immersing the sample into water filled in a rectangular bath suppressed the disruption at the interface and successfully reconstructed the position and concentration of OTN‐NIR fluorophores on the cross‐sectional images using a CT technique. This is promising as a novel three‐dimensional imaging technique for OTN‐NIR fluorescent image projections of small animals captured from multiple angles.     

Seasonality and 3D‐visualization of brooding in the hermaphroditic ophiuroid Amphiura capensis

This article describes the reproductive biology and developing young of Amphiura capensis, a small brooding brittle star found in the intertidal zones of Namibia and South Africa. Each month from October 2014 to September 2015, 20 specimens were collected from Mouille Point, Cape Town, South Africa, and dissected for internal examination of brooding characteristics. Disc diameters of 238 analyzed adults ranged 2.5–8.7 mm, with a mean of 6.15 mm (SD = 1.10 mm). Brooding was exhibited in 60.5% of all sampled individuals, of which 30.6% contained young of only one of six subjectively chosen size classes, 31.9% contained two size classes, and the rest (37.5%) contained more than two size classes at the same time. Young within the same bursa were commonly of the same size class, which suggests sequential brooding. However, multiple size classes of young were often present within different bursae of the same parent, which thus exhibited characteristics of both sequential and simultaneous brooding. Of 584 brooded young retrieved from dissections, an average of 2.5 (SD = 3.2) and a maximum of 14 young were recorded within a single parent. As no larval stages were observed, development was assumed to be direct. Three‐dimensional visualizations of μCT scans revealed the positions of the brooded young to be quite different from those in other species, facing with their mouths downwards instead of upwards, and not all pressed against the adult's bursal wall. Brooding occurred throughout the year, but numbers of young peaked in austral winter, coinciding with warmer water temperatures at this site. The duration of brooded development was estimated to be ~6 months, comparable with other species with similar reproductive biology.     

Alternative dental measurements: proposals and relationships with other measurements

Most archaeological and fossil teeth are heavily worn, and this greatly limits the usefulness of tooth crown diameter measurements, as they are usually defined at the widest points of the crown. There are alternatives, particularly measurements at the cervix of the tooth, where the crown joints the root, and measurements along a diagonal axis in molars, that are much less affected by wear. These would allow a wider range of specimens to be included, e.g., in the study of dental reduction in Upper Palaeolithic and Mesolithic Homo sapiens. In addition, they would allow the little-worn teeth of children to be compared directly with well-worn teeth in adults. These alternatives, however, have been little used, and as yet there have not been any studies of the repeatability with which they can be measured, or of the extent to which they are related to the more usual crown diameters. The present study is based on a group of unworn teeth, where direct comparisons could be made between the alternative measurements, which are not much affected by wear, with the usual crown diameters, which are very much affected. In an interobserver-error study of this material, cervical and diagonal measurements could be recorded as reliably as the usual crown diameters. The buccolingual cervical measurement was strongly correlated with the normal bucclingual crown diameter in all teeth, whereas the mesiodistal cervical measurement was highly correlated with the normal mesiodistal crown diameter in incisors and canines, but less so in premolars and molars. The molar diagonal measurements showed high correlations with all other measurements. Crown areas (robustness index) calculated from the usual diameters were strongly correlated with crown areas calculated from cervical measurements, and crown areas calculated from molar diagonals were strongly correlated with both other areas. Despite the long usage of the more usual maximum crown diameters, the alternative dental measurements could be measured just as reliably, could record similar information about tooth crown size, and would be better measures for the worn dentitions seen in archaeological and fossil material.     

3D‐liquid chromatography as a complex mixture characterization tool for knowledge‐based downstream process development

Knowledge‐based development of chromatographic separation processes requires efficient techniques to determine the physicochemical properties of the product and the impurities to be removed. These characterization techniques are usually divided into approaches that determine molecular properties, such as charge, hydrophobicity and size, or molecular interactions with auxiliary materials, commonly in the form of adsorption isotherms. In this study we demonstrate the application of a three‐dimensional liquid chromatography approach to a clarified cell homogenate containing a therapeutic enzyme. Each separation dimension determines a molecular property relevant to the chromatographic behavior of each component. Matching of the peaks across the different separation dimensions and against a high‐resolution reference chromatogram allows to assign the determined parameters to pseudo‐components, allowing to determine the most promising technique for the removal of each impurity. More detailed process design using mechanistic models requires isotherm parameters. For this purpose, the second dimension consists of multiple linear gradient separations on columns in a high‐throughput screening compatible format, that allow regression of isotherm parameters with an average standard error of 8%. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1283–1291, 2016     

The combination of two‐dimensional and three‐dimensional analysis methods contributes to the understanding of glioblastoma spatial heterogeneity

Heterogeneity is regarded as the major factor leading to the poor outcomes of glioblastoma (GBM) patients. However, conventional two‐dimensional (2D) analysis methods, such as immunohistochemistry and immunofluorescence, have limited capacity to reveal GBM spatial heterogeneity. Thus, we sought to develop an effective analysis strategy to increase the understanding of GBM spatial heterogeneity. Here, 2D and three‐dimensional (3D) analysis methods were compared for the examination of cell morphology, cell distribution and large intact structures, and both types of methods were employed to dissect GBM spatial heterogeneity. The results showed that 2D assays showed only cross‐sections of specimens but provided a full view. To visualize intact GBM specimens in 3D without sectioning, the optical tissue clearing methods CUBIC and iDISCO+ were used to clear opaque specimens so that they would become more transparent, after which the specimens were imaged with a two‐photon microscope. The 3D analysis methods showed specimens at a large spatial scale at cell‐level resolution and had overwhelming advantages in comparison to the 2D methods. Furthermore, in 3D, heterogeneity in terms of cell stemness, the microvasculature, and immune cell infiltration within GBM was comprehensively observed and analysed. Overall, we propose that 2D and 3D analysis methods should be combined to provide much greater detail to increase the understanding of GBM spatial heterogeneity.     

An audit of cervical cytology in HIV‐positive women

O. E. O. Hotonu, J. Hussey, M. S. T. Basta, V. Wadehra, P. Cross and M. L. Schmid
An audit of cervical cytology in HIV‐positive women Objective: To investigate whether a cohort of human immunodeficiency virus‐positive (HIV+) women were having annual cervical cytology as recommended by the English National Health Service cervical screening programme (NHSCSP) guidelines. Methods: An audit of cervical cytology in an HIV+ cohort of 187 women by obtaining their last cervical cytology result and recall from local cytology services. Results: Of the 187 women in the audit, two were ineligible, leaving 185 women, 167 (90.3%) of whom were aged 25–64 years and eligible for screening. Of the 185 women, 126 (68.1%) had a cytology history, 50 (27%) had never had cervical cytology and nine (4.9%) had inadequate details to ascertain whether or not they had a cytology history. Of the 126 with a cytology record, 34 (27%) had a current cytological abnormality, which was low grade in 25 (19.8%) and high grade in nine (7.1%). Among women aged 25–64 years attending the clinic, these percentages were significantly higher than expected for England as a whole (P < 0.001). Of 126 women with a cytology record, 29 (23%) were overdue for their recall date and of these the previous test was abnormal in 14 (48.3%). Cytology tests were taken within the community setting in 61 (48.4%), whereas 65 (51.6%) were seen either at an HIV sexual health clinic or were under colposcopy follow‐up. Of 91 women with negative cytology only 50 (54.9%) were recommended for repeat in 12 months. Conclusion: This audit demonstrates a high rate of cytological abnormalities among HIV+ women compared with the screening population at large. Implementation of NHSCSP guidelines has been difficult and requires improved care pathways between HIV clinics, primary care and laboratories.     

High‐speed X‐ray‐induced luminescence computed tomography

X‐ray‐induced luminescence computed tomography (XLCT) is an emerging molecular imaging. Challenges in improving spatial resolution and reducing the scan time in a whole‐body field of view (FOV) still remain for practical in vivo applications. In this study, we present a novel XLCT technique capable of obtaining three‐dimensional (3D) images from a single snapshot. Specifically, a customed two‐planar‐mirror component is integrated into a cone beam XLCT imaging system to obtain multiple optical views of an object simultaneously. Furthermore, a compressive sensing based algorithm is adopted to improve the efficiency of 3D XLCT image reconstruction. Numerical simulations and experiments were conducted to validate the single snapshot X‐ray‐induced luminescence computed tomography (SS‐XLCT). The results show that the 3D distribution of the nanophosphor targets can be visualized much faster than conventional cone beam XLCT imaging method that was used in our comparisons while maintaining comparable spatial resolution as in conventional XLCT imaging. SS‐XLCT has the potential to harness the power of XLCT for rapid whole‐body in vivo molecular imaging of small animals.     

Scaffold‐free inkjet printing of three‐dimensional zigzag cellular tubes

The capability to print three‐dimensional (3D) cellular tubes is not only a logical first step towards successful organ printing but also a critical indicator of the feasibility of the envisioned organ printing technology. A platform‐assisted 3D inkjet bioprinting system has been proposed to fabricate 3D complex constructs such as zigzag tubes. Fibroblast (3T3 cell)‐based tubes with an overhang structure have been successfully fabricated using the proposed bioprinting system. The post‐printing 3T3 cell viability of printed cellular tubes has been found above 82% (or 93% with the control effect considered) even after a 72‐h incubation period using the identified printing conditions for good droplet formation, indicating the promising application of the proposed bioprinting system. Particularly, it is proved that the tubular overhang structure can be scaffold‐free fabricated using inkjetting, and the maximum achievable height depends on the inclination angle of the overhang structure. As a proof‐of‐concept study, the resulting fabrication knowledge helps print tissue‐engineered blood vessels with complex geometry. Biotechnol. Bioeng. 2012; 109: 3152–3160. © 2012 Wiley Periodicals, Inc.     

Three‐dimensional ring‐oven washing technique for a paper‐based immunodevice

Washing is a standard step for enzyme‐linked immunosorbent assays (ELISA) performed on a paper‐based chip, in which nonspecific‐binding antibodies and antigens should be removed completely from the paper surface. In this study, a novel three‐dimensional (3D) washing strategy using a heating ring‐oven was carried out on a paper‐based chip. Compared with a plane washing mode by a ring‐oven, this 3D washing strategy obtained a lower background, as gravity played an important role in the washing step. The paper‐based chip was placed on a 3D plastic holder and the waste area was connected to a heating ring. Use of a heating waste area meant that the nonspecific‐binding protein was continuously carried to the waste area through gravity and capillary action. The angle between the plastic holder and the ring plane was carefully selected. The effect of washing on different parts of the detection area was investigated by upconversion fluorescence and chemiluminescence (CL). This novel 3D washing strategy was performed for carcinoembryonic antigen detection through CL and a lower detection limit of 2 pg ml^?1 was obtained. This approach provides an effective washing strategy to remove nonspecific‐binding antibody from a paper‐based immunodevice.     

Three‐dimensional reconstruction of the odontophoral cartilages of Caenogastropoda (Mollusca: Gastropoda) using micro‐CT: Morphology and phylogenetic significance

Odontophoral cartilages are located in the molluscan buccal mass and support the movement of the radula during feeding. The structural diversity of odontophoral cartilages is currently known only from limited taxa, but this information is important for interpreting phylogeny and for understanding the biomechanical operation of the buccal mass. Caenogastropods exhibit a wide variety of feeding strategies, but there is little comparative information on cartilage morphology within this group. The morphology of caenogastropod odontophoral cartilages is currently known only from dissection and histology, although preliminary results suggest that they may be structurally diverse. A comparative morphological survey of 18 caenogastropods and three noncaenogastropods has been conducted, sampling most major caenogastropod superfamilies. Three‐dimensional models of the odontophoral cartilages were generated using X‐ray microscopy (micro‐CT) and reconstruction by image segmentation. Considerable morphological diversity of the odontophoral cartilages was found within Caenogastropoda, including the presence of thin cartilaginous appendages, asymmetrically overlapping cartilages, and reflexed cartilage margins. Many basal caenogastropod taxa possess previously unidentified cartilaginous support structures below the radula (subradular cartilages), which may be homologous to the dorsal cartilages of other gastropods. As subradular cartilages were absent in carnivorous caenogastropods, adaptation to trophic specialization is likely. However, incongruence with specific feeding strategies or body size suggests that the morphology of odontophoral cartilages is constrained by phylogeny, representing a new source of morphological characters to improve the phylogenetic resolution of this group. J. Morphol. 2009. © 2008 Wiley‐Liss, Inc.     

Three‐dimensional multiphoton/optical coherence tomography for diagnostic applications in dermatology

A preliminary clinical trial using state‐of‐the‐art multiphoton tomography (MPT) and optical coherence tomography (OCT) for three‐dimensional (3D) multimodal in vivo imaging of normal skin, nevi, scars and pathologic skin lesions has been conducted. MPT enabled visualization of sub‐cellular details with axial and transverse resolutions of <2 μm and <0.5 μm, respectively, from a volume of 0.35 × 0.35 × 0.2 mm³ at a frame rate of 0.14 Hz (512 × 512 pixels). State‐of‐the‐art OCT, operating at a center wavelength of 1300 nm, was capable of acquiring 3D images depicting the layered architecture of skin with axial and transverse resolutions ～8 μm and ～20 μm, respectively, from a volume of 7 × 3.5 × 1.5 mm³ at a frame rate of 46 Hz (1024 × 1024 pixels). This study demonstrates the clinical diagnostic potential of MPT/OCT for pre‐screening relatively large areas of skin using 3D OCT to identify suspicious regions at microscopic level and subsequently using high resolution MPT to obtain zoomed in, sub‐cellular level information of the respective regions (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Three‐dimensional intravital imaging in bone research

Intravital imaging has emerged as a novel and efficient tool for visualization of in situ dynamics of cellular behaviors and cell‐microenvironment interactions in live animals, based on desirable microscopy techniques featuring high resolutions, deep imaging and low phototoxicity. Intravital imaging, especially based on multi‐photon microscopy, has been used in bone research for dynamics visualization of a variety of physiological and pathological events at the cellular level, such as bone remodeling, hematopoiesis, immune responses and cancer development, thus, providing guidance for elucidating novel cellular mechanisms in bone biology as well as guidance for new therapies. This review is aimed at interpreting development and advantages of intravital imaging in bone research, and related representative discoveries concerning bone matrices, vessels, and various cells types involved in bone physiologies and pathologies. Finally, current limitations, further refinement, and extended application of intravital imaging in bone research are concluded.      

A three‐dimensional analysis of bilateral directional asymmetry in the human clavicle

This study presents a novel three‐dimensional analysis using statistical atlases and automated measurements to assess diaphyseal morphology of the clavicle and its relationship to muscle asymmetry. A sample of 505 individuals (285 males, 220 females) from the William McCormick Clavicle Collection was CT scanned, segmented, and added to a statistical bone atlas that captures correspondence between homologous points on the bone surfaces. Muscle attachment sites were localized on the atlas and then propagated across the entire population. Cross‐sectional contours were extracted at 5% increments along the entire bone, as well as at muscle attachment sites and the clavicle waist; maximum and minimum dimensions of each cross‐sectional contour were calculated. In addition, the entire three‐dimensional surface was examined for asymmetry by analyzing the magnitude and directional differences between homologous points across all bone surfaces in the dataset. The results confirm the existing studies on clavicle asymmetry, namely that the left clavicle is longer than the right, but the right is more robust than the left. However, the patterns of asymmetry are sexually dimorphic. Males are significantly asymmetric in all dimensions and at muscle and ligament attachment sites (P < 0.05), whereas female asymmetry is more variable. We hypothesize that this is related to absolute and relative differences in male muscle strength compared to females. However, an area with no muscle attachments on the posterior midshaft was significantly asymmetric in both sexes. We suggest that this is a curvature difference caused by opposing muscle actions at the medial and lateral ends of the bone. Am J Phys Anthropol 2012. © 2012 Wiley Periodicals, Inc.     

Representing and comparing protein folds and fold families using three‐dimensional shape‐density representations

The question of how best to compare and classify the (three‐dimensional) structures of proteins is one of the most important unsolved problems in computational biology. To help tackle this problem, we have developed a novel shape‐density superposition algorithm called 3D‐Blast which represents and superposes the shapes of protein backbone folds using the spherical polar Fourier correlation technique originally developed by us for protein docking. The utility of this approach is compared with several well‐known protein structure alignment algorithms using receiver‐operator‐characteristic plots of queries against the “gold standard” CATH database. Despite being completely independent of protein sequences and using no information about the internal geometry of proteins, our results from searching the CATH database show that 3D‐Blast is highly competitive compared to current state‐of‐the‐art protein structure alignment algorithms. A novel and potentially very useful feature of our approach is that it allows an average or “consensus” fold to be calculated easily for a given group of protein structures. We find that using consensus shapes to represent entire fold families also gives very good database query performance. We propose that using the notion of consensus fold shapes could provide a powerful new way to index existing protein structure databases, and that it offers an objective way to cluster and classify all of the currently known folds in the protein universe. Proteins 2012. © 2011 Wiley Periodicals, Inc.     

Phase Transformation Induced Capacitance Activation for 3D Graphene‐CoO Nanorod Pseudocapacitor

Development of a pseudocapacitor over the integration of metal oxide on carbonaceous materials is a promising step towards energy storage devices with high energy and power densities. Here, a self‐assembled cobalt oxide (CoO) nanorod cluster on three‐dimensional graphene (CoO‐3DG) is synthesized through a facile hydrothermal method followed by heat treatment. As an additive‐free electrode, CoO‐3DG exhibits good electrochemical performance. Compared with CoO nanorod clusters grown on Ni foam (i.e., CoO‐Ni, ≈680 F g^?1 at 1 A g^?1 and ≈400 F g^?1 at 20 A g^?1), CoO‐3DG achieves much higher capacitance (i.e., ≈980 F g^?1 at 1 A g^?1 and ≈600 F g^?1 at 20 A g^?1) with excellent cycling stability of 103% retention of specific capacitance after 10 000 cycles. Furthermore, it shows an interesting activation process and instability with a redox reaction for CoO. In addition, the phase transformation from CoO nanorods to Co₃O₄ nanostructures was observed and investigated after charge and discharge process, which suggests the activation kinetics and the phase transformable nature of CoO based nanostructure. These observations demonstrate phase transformation with morphological change induced capacitance increasement in the emergent class of metal oxide materials for electrochemical energy storage device.     

Direct Growth of Flower‐Like δ‐MnO2 on Three‐Dimensional Graphene for High‐Performance Rechargeable Li‐O2 Batteries

A challenge still remains to develop high‐performance and cost‐effective air electrode for Li‐O₂ batteries with high capacity, enhanced rate capability and long cycle life (100 times or above) despite recent advances in this field. In this work, a new design of binder‐free air electrode composed of three‐dimensional (3D) graphene (G) and flower‐like δ‐MnO₂ (3D‐G‐MnO₂) has been proposed. In this design, graphene and δ‐MnO₂ grow directly on the skeleton of Ni foam that inherits the interconnected 3D scaffold of Ni foam. Li‐O₂ batteries with 3D‐G‐MnO₂ electrode can yield a high discharge capacity of 3660 mAh g^?1 at 0.083 mA cm^?2. The battery can sustain 132 cycles at a capacity of 492 mAh g^?1 (1000 mAh g_carbon ^?1) with low overpotentials under a high current density of 0.333 mA cm^?2. A high average energy density of 1350 Wh Kg^?1 is maintained over 110 cycles at this high current density. The excellent catalytic activity of 3D‐G‐MnO₂ makes it an attractive air electrode for high‐performance Li‐O₂ batteries.