A Farewell to Flat Biology. Three-dimensional Cell Culture Models in Cancer Drug Target Identification and Validation

Cells of epithelial origin, e.g. from breast and prostate cancers, effectively differentiate into complex multicellular structures when cultured in three-dimensions (3D) instead of conventional two-dimensional (2D) adherent surfaces. The spectrum of different organotypic morphologies is highly dependent on the culture environment that can be either non-adherent or scaffold-based. When embedded in physiological extracellular matrices (ECMs), such as laminin-rich basement membrane extracts, normal epithelial cells differentiate into acinar spheroids reminiscent of glandular ductal structures. Transformed cancer cells, in contrast, typically fail to undergo acinar morphogenic patterns, forming poorly differentiated or invasive multicellular structures. The 3D cancer spheroids are widely accepted to better recapitulate various tumorigenic processes and drug responses. So far, however, 3D models have been employed predominantly in the Academia, whereas the pharmaceutical industry has yet to adopt a more widely and routine use. This is mainly due to poor characterisation of cell models, lack of standardised workflows and high throughput cell culture platforms, and the availability of proper readout and quantification tools. In this thesis, a complete workflow has been established entailing well-characterised 3D cell culture models for prostate cancer, a standardised 3D cell culture routine based on high-throughput-ready platform, automated image acquisition with concomitant morphometric image analysis, and data visualisation, in order to enable large-scale high-content screens. Our integrated suite of software and statistical analysis tools were optimised and validated using a comprehensive panel of prostate cancer cell lines and 3D models. The tools quantify multiple key cancer-relevant morphological features, ranging from cancer cell invasion through multicellular differentiation to growth, and detect dynamic changes both in morphology and function, such as cell death and apoptosis, in response to experimental perturbations including RNA interference and small molecule inhibitors. Our panel of cell lines included many non-transformed and most currently available classic prostate cancer cell lines, which were characterised for their morphogenetic properties in 3D laminin-rich ECM. The phenotypes and gene expression profiles were evaluated concerning their relevance for pre-clinical drug discovery, disease modelling and basic research. In addition, a spontaneous model for invasive transformation was discovered, displaying a highdegree of epithelial plasticity. This plasticity is mediated by an abundant bioactive serum lipid, lysophosphatidic acid (LPA), and its receptor LPAR1. The invasive transformation was caused by abrupt cytoskeletal rearrangement through impaired G protein alpha 12/13 and RhoA/ROCK, and mediated by upregulated adenylyl cyclase/cyclic AMP (cAMP)/protein kinase A, and Rac/ PAK pathways. The spontaneous invasion model tangibly exemplifies the biological relevance of organotypic cell culture models. Overall, this thesis work underlines the power of novel morphometric screening tools in drug discovery.

Assessment of pelvic floor by three-dimensional-ultrasound in primiparous women according to delivery mode: initial experience from a single reference service in Brazil

PURPOSE: To evaluate changes to the pelvic floor of primiparous women with different delivery modes, using three-dimensional ultrasound. METHODS: A prospective cross-sectional study on 35 primiparae divided into groups according to the delivery mode: elective cesarean delivery (n=10), vaginal delivery (n=16), and forceps delivery (n=9). Three-dimensional ultrasound on the pelvic floor was performed on the second postpartum day with the patient in a resting position. A convex volumetric transducer (RAB4-8L) was used, in contact with the large labia, with the patient in the gynecological position. Biometric measurements of the urogenital hiatus were taken in the axial plane on images in the rendering mode, in order to assess the area, anteroposterior and transverse diameters, average thickness, and avulsion of the levator ani muscle. Differences between groups were evaluated by determining the mean differences and their respective 95% confidence intervals. The proportions of levator ani muscle avulsion were compared between elective cesarean section and vaginal birth using Fisher's exact test. RESULTS: The mean areas of the urogenital hiatus in the cases of vaginal and forceps deliveries were 17.0 and 20.1 cm², respectively, versus 12.4 cm² in the Control Group (elective cesarean). Avulsion of the levator ani muscle was observed in women who underwent vaginal delivery (3/25), however there was no statistically significant difference between cesarean section and vaginal delivery groups (p=0.5). CONCLUSION: Transperineal three-dimensional ultrasound was useful for assessing the pelvic floor of primiparous women, by allowing pelvic morphological changes to be differentiated according to the delivery mode.

Anatomical and functional characteristics of the pelvic floor in nulliparous women submitted to three-dimensional endovaginal ultrasonography: case control study and evaluation of interobserver agreement

PURPOSE: To determine anatomical and functional pelvic floor measurements performed with three-dimensional (3-D) endovaginal ultrasonography in asymptomatic nulliparous women without dysfunctions detected in previous dynamic 3-D anorectal ultrasonography (echo defecography) and to demonstrate the interobserver reliability of these measurements. METHODS: Asymptomatic nulliparous volunteers were submitted to echo defecography to identify dynamic dysfunctions, including anatomical (rectocele, intussusceptions, entero/sigmoidocele and perineal descent) and functional changes (non-relaxation or paradoxical contraction of the puborectalis muscle) in the posterior compartment and assessed with regard to the biometric index of levator hiatus, pubovisceral muscle thickness, urethral length, anorectal angle, anorectal junction position and bladder neck position with the 3-D endovaginal ultrasonography. All measurements were compared at rest and during the Valsalva maneuver, and perineal and bladder neck descent was determined. The level of interobserver agreement was evaluated for all measurements. RESULTS: A total of 34 volunteers were assessed by echo defecography and by 3-D endovaginal ultrasonography. Out of these, 20 subjects met the inclusion criteria. The 14 excluded subjects were found to have posterior dynamic dysfunctions. During the Valsalva maneuver, the hiatal area was significantly larger, the urethra was significantly shorter and the anorectal angle was greater. Measurements at rest and during the Valsalva maneuver differed significantly with regard to anorectal junction and bladder neck position. The mean values for normal perineal descent and bladder neck descent were 0.6 cm and 0.5 cm above the symphysis pubis, respectively. The intraclass correlation coefficient ranged from 0.62-0.93. CONCLUSIONS: Functional biometric indexes, normal perineal descent and bladder neck descent values were determined for young asymptomatic nulliparous women with the 3-D endovaginal ultrasonography. The method was found to be reliable to measure pelvic floor structures at rest and during Valsalva, and might therefore be suitable for identifying dysfunctions in symptomatic patients.

Comparison of Two- and Three-dimensional Ultrasonography in the Evaluation of Lesion Level in Fetuses with Spina Bifida

Purpose To evaluate the precision of both two- and three-dimensional ultrasonography in determining vertebral lesion level (the first open vertebra) in patients with spina bifida. Methods This was a prospective longitudinal study comprising of fetuses with open spina bifida who were treated in the fetal medicine division of the department of obstetrics of Hospital das Clínicas of the Universidade de São Paulo between 2004 and 2013. Vertebral lesion level was established by using both two- and three-dimensional ultrasonography in 50 fetuses (two examiners in each method). The lesion level in the neonatal period was established by radiological assessment of the spine. All pregnancies were followed in our hospital prenatally, and delivery was scheduled to allow immediate postnatal surgical correction. Results Two-dimensional sonography precisely estimated the spina bifida level in 53% of the cases. The estimate error was within one vertebra in 80% of the cases, in up to two vertebrae in 89%, and in up to three vertebrae in 100%, showing a good interobserver agreement. Three-dimensional ultrasonography precisely estimated the lesion level in 50% of the cases. The estimate error was within one vertebra in 82% of the cases, in up to two vertebrae in 90%, and in up to three vertebrae in 100%, also showing good interobserver agreement. Whenever an estimate error was observed, both two- and three-dimensional ultrasonography scans tended to underestimate the true lesion level (55.3% and 62% of the cases, respectively). Conclusions No relevant difference in diagnostic performance was observed between the two- and three-dimensional ultrasonography. The use of three-dimensional ultrasonography showed no additional benefit in diagnosing the lesion level in the fetuses with spina bifida. Errors in both methods showed a tendency to underestimate lesion level.

Quantum Hall effect in 2 dimensional GaInAs structure

Transport properties of GaAs / δ – Mn / GaAs / InxGa1-xAs / GaAs structure with Mn δ – layer, which is separated from InxGa1-xAs quantum well (QW) by 3 nm thick GaAs spacer was investigated. This structure with high mobility was characterized by X-ray difractometry and reflectometry. Transport and electrical properties of the structure were measured by using Pulsed Magnetic Field System (PMFS). During investigation of the Shubnikov – de Haas and the Hall effects the main parameters of QW structure such as cyclotron mass, Fermi level, g – factor, Dingle temperature and concentration of holes were estimated. Obtained results show high quality of the prepared structure. However, anomalous Hall effect at temperatures 2.09 K, 3 K, 4.2 K is not clearly observed. Attempts to identify magnetic moment were made. For this purpose the polarity of the filed was changed to the opposite at each shot. As a result hysteresis loop was not observed in the magnetic field dependences of the anomalous Hall resistivity.This can be attributed to the imperfection of the experimental setup.

Effect of wave frequency on the nonlinear interaction between Görtler vortices and three-dimensional Tollmien-Schlichting waves

The nonlinear interaction between Görtler vortices (GV) and three-dimensional Tollmien-Schlichting (TS) waves nonlinear interaction is studied with a spatial, nonparallel model based on the Parabolized Stability Equations (PSE). In this investigation the effect of TS wave frequency on the nonlinear interaction is studied. As verified in previous investigations using the same numerical model, the relative amplitudes and growth rates are the dominant parameters in GV/TS wave interaction. In this sense, the wave frequency influence is important in defining the streamwise distance traveled by the disturbances in the unstable region of the stability diagram and in defining the amplification rates that they go through.

Development of a three-dimensional nonlinear viscoelastic constitutive model of solid propellant

A three dimensional nonlinear viscoelastic constitutive model for the solid propellant is developed. In their earlier work, the authors have developed an isotropic constitutive model and verified it for one dimensional case. In the present work, the validity of the model is extended to three-dimensional cases. Large deformation, dewetting and cyclic loading effects are treated as the main sources of nonlinear behavior of the solid propellant. Viscoelastic dewetting criteria is used and the softening of the solid propellant due to dewetting is treated by the modulus decrease. The nonlinearities during cyclic loading are accounted for by the functions of the octahedral shear strain measure. The constitutive equation is implemented into a finite element code for the analysis of propellant grains. A commercial finite element package ‘ABAQUS’ is used for the analysis and the model is introduced into the code through a user subroutine. The model is evaluated with different loading conditions and the predicted values are in good agreement with the measured ones. The resulting model applied to analyze a solid propellant grain for the thermal cycling load.

An experimental investigation of the effects of nozzle ellipticity on the flow structure of co-flow jet diffusion flames

The flow structure of cold and ignited jets issuing into a co-flowing air stream was experimentally studied using a laser Doppler velocimeter. Methane was employed as the jet fluid discharging from circular and elliptic nozzles with aspect ratios varying from 1.29 to 1.60. The diameter of the circular nozzle was 4.6 mm and the elliptic nozzles had approximately the same exit area as that of the circular nozzle. These non-circular nozzles were employed in order to increase the stability of attached jet diffusion flames. The time-averaged velocity and r.m.s. value of the velocity fluctuation in the streamwise and transverse directions were measured over the range of co-flowing stream velocities corresponding to different modes of flame blowout that are identified as either lifted or attached flames. On the basis of these measurements, attempts were made to explain the existence of an apparent optimum aspect ratio for the blowout of attached flames observed at higher values of co-flowing stream velocities. The insensitivity of the blowout limits of lifted flames to nozzle geometry observed in our previous work at low co-flowing stream velocities was also explained. Measurements of the fuel concentration at the jet centerline indicated that the mixing process was enhanced with the 1.38 aspect ratio jet compared with the 1.60 aspect ratio jet. On the basis of the obtained experimental data, it was suggested that the higher blowout limits of attached flames for an elliptic jet of 1.38 aspect ratio was due to higher entrainment rates.

Three-dimensional conformal breast irradiation in the prone position

The prone position can be used for the planning of adjuvant radiotherapy after conservative breast surgery in order to deliver less irradiation to lung and cardiac tissue. In the present study, we compared the results of three-dimensional conformal radiotherapy planning for five patients irradiated in the supine and prone position. Tumor stage was T1N0M0 in four patients and T1N1M0 in one. All patients had been previously submitted to conservative breast surgery. Breast size was large in three patients and moderate in the other two. Irradiation in the prone position was performed using an immobilization foam pad with a hole cut into it to accommodate the breast so that it would hang down away from the chest wall. Dose-volume histograms showed that mean irradiation doses reaching the ipsilateral lung were 8.3 ± 3.6 Gy with the patient in the supine position and 1.4 ± 1.0 Gy with the patient in the prone position (P = 0.043). The values for the contralateral lung were 1.3 ± 0.7 and 0.3 ± 0.1 Gy (P = 0.043) and the values for cardiac tissue were 4.6 ± 1.6 and 3.0 ± 1.7 Gy (P = 0.079), respectively. Thus, the dose-volume histograms demonstrated that lung tissue irradiation was significantly lower with the patient in the prone position than in the supine position. Large-breasted women appeared to benefit most from irradiation in the prone position. Prone position breast irradiation appears to be a simple and effective alternative to the conventional supine position for patients with large breasts, since they are subjected to lower pulmonary doses which may cause less pulmonary side effects in the future.

Multicellular spheroids of bone marrow stromal cells: a three-dimensional in vitro culture system for the study of hematopoietic cell migration

Cell fate decisions are governed by a complex interplay between cell-autonomous signals and stimuli from the surrounding tissue. In vivo cells are connected to their neighbors and to the extracellular matrix forming a complex three-dimensional (3-D) microenvironment that is not reproduced in conventional in vitro systems. A large body of evidence indicates that mechanical tension applied to the cytoskeleton controls cell proliferation, differentiation and migration, suggesting that 3-D in vitro culture systems that mimic the in vivo situation would reveal biological subtleties. In hematopoietic tissues, the microenvironment plays a crucial role in stem and progenitor cell survival, differentiation, proliferation, and migration. In adults, hematopoiesis takes place inside the bone marrow cavity where hematopoietic cells are intimately associated with a specialized three 3-D scaffold of stromal cell surfaces and extracellular matrix that comprise specific niches. The relationship between hematopoietic cells and their niches is highly dynamic. Under steady-state conditions, hematopoietic cells migrate within the marrow cavity and circulate in the bloodstream. The mechanisms underlying hematopoietic stem/progenitor cell homing and mobilization have been studied in animal models, since conventional two-dimensional (2-D) bone marrow cell cultures do not reproduce the complex 3-D environment. In this review, we will highlight some of the mechanisms controlling hematopoietic cell migration and 3-D culture systems.

Three-dimensional kinematic analysis of upper and lower limb motion during gait of post-stroke patients

The aim of this study was to analyze the alterations of arm and leg movements of patients during stroke gait. Joint angles of upper and lower limbs and spatiotemporal variables were evaluated in two groups: hemiparetic group (HG, 14 hemiparetic men, 53 ± 10 years) and control group (CG, 7 able-bodied men, 50 ± 4 years). The statistical analysis was based on the following comparisons (P ≤ 0.05): 1) right versus left sides of CG; 2) affected (AF) versus unaffected (UF) sides of HG; 3) CG versus both the affected and unaffected sides of HG, and 4) an intracycle comparison of the kinematic continuous angular variables between HG and CG. This study showed that the affected upper limb motion in stroke gait was characterized by a decreased range of motion of the glenohumeral (HG: 6.3 ± 4.5, CG: 20.1 ± 8.2) and elbow joints (AF: 8.4 ± 4.4, UF: 15.6 ± 7.6) on the sagittal plane and elbow joint flexion throughout the cycle (AF: 68.2 ± 0.4, CG: 46.8 ± 2.7). The glenohumeral joint presented a higher abduction angle (AF: 14.2 ± 1.6, CG: 11.5 ± 4.0) and a lower external rotation throughout the cycle (AF: 4.6 ± 1.2, CG: 22.0 ± 3.0). The lower limbs showed typical alterations of the stroke gait patterns. Thus, the changes in upper and lower limb motion of stroke gait were identified. The description of upper limb motion in stroke gait is new and complements gait analysis.

Numerical Investigations on Soil Structure Interaction of Multistorey Frames

Frames are the most widely used structural system for multistorey buildings. A building frame is a three dimensional discrete structure consisting of a number of high rise bays in two directions at right angles to each other in the vertical plane. Multistorey frames are a three dimensional lattice structure which are statically indeterminate. Frames sustain gravity loads and resist lateral forces acting on it. India lies at the north westem end of the Indo-Australian tectonic plate and is identified as an active tectonic area. Under horizontal shaking of the ground, horizontal inertial forces are generated at the floor levels of a multistorey frame. These lateral inertia forces are transferred by the floor slab to the beams, subsequently to the columns and finally to the soil through the foundation system. There are many parameters that affect the response of a structure to ground excitations such as, shape, size and geometry of the structure, type of foundation, soil characteristics etc. The Soil Structure Interaction (SS1) effects refer to the influence of the supporting soil medium on the behavior of the structure when it is subjected to different types of loads. Interaction between the structure and its supporting foundation and soil, which is a complete system, has been modeled with finite elements. Numerical investigations have been carried out on a four bay, twelve storeyed regular multistorey frame considering depth of fixity at ground level, at characteristic depth of pile and at full depth. Soil structure interaction effects have been studied by considering two models for soil viz., discrete and continuum. Linear static analysis has been conducted to study the interaction effects under static load. Free vibration analysis and further shock spectrum analysis has been conducted to study the interaction effects under time dependent loads. The study has been extended to four types of soil viz., laterite, sand, alluvium and layered.The structural responses evaluated in the finite element analysis are bending moment, shear force and axial force for columns, and bending moment and shear force for beams. These responses increase with increase in the founding depth; however these responses show minimal increase beyond the characteristic length of pile. When the soil structure interaction effects are incorporated in the analysis, the aforesaid responses of the frame increases upto the characteristic depth and decreases when the frame has been analysed for the full depth. It has been observed that shock spectrum analysis gives wide variation of responses in the frame compared to linear elastic analysis. Both increase and decrease in responses have been observed in the interior storeys. The good congruence shown by the two finite element models viz., discrete and continuum in linear static analysis has been absent in shock spectrum analysis.

Finite-size scaling analysis of the avalanches in the three-dimensional Gaussian random-field Ising model with metastable dynamics

A numerical study is presented of the third-dimensional Gaussian random-field Ising model at T=0 driven by an external field. Standard synchronous relaxation dynamics is employed to obtain the magnetization versus field hysteresis loops. The focus is on the analysis of the number and size distribution of the magnetization avalanches. They are classified as being nonspanning, one-dimensional-spanning, two-dimensional-spanning, or three-dimensional-spanning depending on whether or not they span the whole lattice in different space directions. Moreover, finite-size scaling analysis enables identification of two different types of nonspanning avalanches (critical and noncritical) and two different types of three-dimensional-spanning avalanches (critical and subcritical), whose numbers increase with L as a power law with different exponents. We conclude by giving a scenario for avalanche behavior in the thermodynamic limit.

Spanning avalanches in the three-dimensional Gaussian random-field Ising model with metastable dynamics: Field dependence and geometrical properties

Spanning avalanches in the 3D Gaussian Random Field Ising Model (3D-GRFIM) with metastable dynamics at T=0 have been studied. Statistical analysis of the field values for which avalanches occur has enabled a Finite-Size Scaling (FSS) study of the avalanche density to be performed. Furthermore, a direct measurement of the geometrical properties of the avalanches has confirmed an earlier hypothesis that several types of spanning avalanches with two different fractal dimensions coexist at the critical point. We finally compare the phase diagram of the 3D-GRFIM with metastable dynamics with the same model in equilibrium at T=0.