Ex vivo assessment of chemotherapy-induced apoptosis and associated molecular changes in patient tumor samples

BACKGROUND: There are inherent conceptual problems in investigating the pharmacodynamics of cancer drugs in vivo. One of the few possible approaches is serial biopsies in patients. However, this type of research is severely limited by methodological and ethical constraints. MATERIALS AND METHODS: A modified 3-dimensional tissue culture technique was used to culture human tumor samples, which had been collected during routine cancer operations. Twenty tumor samples of patients with non-small cell lung cancer (NSCLC) were cultured ex vivo for 120 h and treated with mitomycin C, taxotere and cisplatin. The cytotoxic activity of the anticancer agents was quantified by assessing the metabolic activity of treated tumor cultures and various assays of apoptosis and gene expression were performed. RESULTS: The proliferative activity of the tissue was maintained in culture as assessed by Ki-67 staining. Mitomycin C, cisplatin and taxotere reduced the metabolic activity of the tumor tissue cultures by 51%, 29% and 20%, respectively, at 120 h. The decrease in metabolic activity corresponded to the induction of apoptosis as demonstrated by the typical morphological changes, such as chromatin condensation and nuclear fragmentation. In addition, activated caspase-3 could be verified in apoptotic cells by immunohistochemistry. To verify functional aspects of apoptosis, the induction of chemotherapy-induced cell death was inhibited with the caspase inhibitor z-VAD.fmk. RNA was extracted from the tissue cultures after 120 h of ex vivo drug treatment and was of sufficient quality to allow quantitative PCR. CONCLUSION: The 3-dimensional ex vivo culture technique is a useful method to assess the molecular effects of pharmacological interventions in human cancer samples in vitro. This culture technique could become an important tool for drug development and for the prediction of in vivo drug efficacy.

Feasibility of T2* mapping for the evaluation of hip joint cartilage at 1.5T using a three-dimensional (3D), gradient-echo (GRE) sequence: a prospective study

This study defines the feasibility of utilizing three-dimensional (3D) gradient-echo (GRE) MRI at 1.5T for T(2)* mapping to assess hip joint cartilage degenerative changes using standard morphological MR grading while comparing it to delayed gadolinium-enhanced MRI of cartilage (dGEMRIC). MRI was obtained from 10 asymptomatic young adult volunteers and 33 patients with symptomatic femoroacetabular impingement (FAI). The protocol included T(2)* mapping without gadolinium-enhancement utilizing a 3D-GRE sequence with six echoes, and after gadolinium injection, routine hip sequences, and a dual-flip-angle 3D-GRE sequence for dGEMRIC T(1) mapping. Cartilage was classified as normal, with mild changes, or with severe degenerative changes based on morphological MRI. T(1) and T(2)* findings were subsequently correlated. There were significant differences between volunteers and patients in normally-rated cartilage only for T(1) values. Both T(1) and T(2)* values decreased significantly with the various grades of cartilage damage. There was a statistically significant correlation between standard MRI and T(2)* (T(1)) (P < 0.05). High intraclass correlation was noted for both T(1) and T(2)*. Correlation factor was 0.860 to 0.954 (T(2)*-T(1) intraobserver) and 0.826 to 0.867 (T(2)*-T(1) interobserver). It is feasible to gather further information about cartilage status within the hip joint using GRE T(2)* mapping at 1.5T.

Two-dimensional assembly and local redox-activity of molecular hybrid structures in an electrochemical environment

The self-assembly and redox-properties of two viologen derivatives, N-hexyl-N-(6-thiohexyl)-4,4-bipyridinium bromide (HS-6V6-H) and N,N-bis(6-thiohexyl)-4,4-bipyridinium bromide (HS-6V6-SH), immobilized on Au(111)-(1x1) macro-electrodes were investigated by cyclic voltammetry, surface enhanced infrared spectroscopy (SEIRAS) and in situ scanning tunneling microscopy (STM). Depending on the assembly conditions one could distinguish three different types of adlayers for both viologens: a low coverage disordered and an ordered striped phase of flat oriented molecules as well as a high coverage monolayer composed of tilted viologen moieties. Both molecules, HS-6V6-H and HS-6V6-SH, were successfully immobilized on Au(poly) nano-electrodes, which gave a well-defined redox-response in the lower pA–current range. An in situ STM configuration was employed to explore electron transport properties of single molecule junctions Au(T)|HS-6V6-SH(HS-6V6-H)|Au(S). The observed sigmoidal potential dependence, measured at variable substrate potential ES and at constant bias voltage (ET–ES), was attributed to electronic structure changes of the viologen moiety during the one-electron reduction/re-oxidation process V2+ V+. Tunneling experiments in asymmetric, STM-based junctions Au(T)-S-6V6-H|Au(S) revealed current (iT)–voltage (ET) curves with a maximum located at the equilibrium potential of the redox-process V2+ V+. The experimental iT–ET characteristics of the HS-6V6-H–modified tunneling junction were tentatively attributed to a sequential two-step electron transfer mechanism.

LakeMIP Kivu: evaluating the representation of a large, deep tropical lake by a set of one-dimensional lake models

The African great lakes are of utmost importance for the local economy (fishing), as well as being essential to the survival of the local people. During the past decades, these lakes experienced fast changes in ecosystem structure and functioning, and their future evolution is a major concern. In this study, for the first time a set of one-dimensional lake models are evaluated for Lake Kivu (2.28°S; 28.98°E), East Africa. The unique limnology of this meromictic lake, with the importance of salinity and subsurface springs in a tropical high-altitude climate, presents a worthy challenge to the seven models involved in the Lake Model Intercomparison Project (LakeMIP). Meteorological observations from two automatic weather stations are used to drive the models, whereas a unique dataset, containing over 150 temperature profiles recorded since 2002, is used to assess the model’s performance. Simulations are performed over the freshwater layer only (60 m) and over the average lake depth (240 m), since salinity increases with depth below 60 m in Lake Kivu and some lake models do not account for the influence of salinity upon lake stratification. All models are able to reproduce the mixing seasonality in Lake Kivu, as well as the magnitude and seasonal cycle of the lake enthalpy change. Differences between the models can be ascribed to variations in the treatment of the radiative forcing and the computation of the turbulent heat fluxes. Fluctuations in wind velocity and solar radiation explain inter-annual variability of observed water column temperatures. The good agreement between the deep simulations and the observed meromictic stratification also shows that a subset of models is able to account for the salinity- and geothermal-induced effects upon deep-water stratification. Finally, based on the strengths and weaknesses discerned in this study, an informed choice of a one-dimensional lake model for a given research purpose becomes possible.

Two-dimensional supramolecular polymers: controlled formation and visualization on the surface

Self – assembly is a powerful tool for the construction of highly organized nanostructures. Therefore, the possibility to control and predict pathways of molecular ordering on the nanoscale level is a critical issue for the production of materials with tunable and adaptive macroscopic properties. 2D polymers are attractive objects for the field of material sciences due to their exceptional properties. [1] As shown before, amphiphilic oligopyrenotides (produced via automated solid-phase synthesis) form rod–like supramolecular polymers in water. [2] These assemblies form 1D objects. [3] By applying certain changes to the design of the oligopyrenotide units the dimensionality of the formed assemblies can be influenced. Herein, we demonstrate that Py3 (see Figure 1) forms defined supramolecular assemblies under thermodynamic conditions in water. To study Py3 self-assembly, we carried out whole set of spectroscopic (UV/vis, fluorescence, DLS) and microscopic experiments (AFM). The obtained results suggest that oligopyrenotides with the present type of geometry and linker length leads to formation of 2D supramolecular assemblies.

Two-dimensional supramolecular polymers

One of the biggest issues of modern materials science is developing of strategies to create large and ordered assemblies in the form of discrete nanoscale objects. Oligopyrenotides (OPs) represent novel class of amphiphilic molecules which tend to self-assemble forming highly ordered structures. As has been already shown OPs are able to form 1D («rod-like») supramolecular polymer [1]. Since programmed arraying of polyaromatic hydrocarbons in structurally defined objects could offer enhanced performance over the individual components, prediction and controlling of their spatial arrangement remains challenging. Herein we demonstrate that certain changes to design of pyrene’s molecular core allow Py3 form 2D supramolecular assemblies («nanosheets») instead of 1D. Two dimensional supramolecular polymers are attractive objects due to their exceptional properties which originate from in-plan alignment of molecular units in the sheets with constant thickness ~ 2 nm [2]. These assemblies have high degree of internal order: the interior consists of hydrophobic pyrenes and alkyl chains, whereas the exterior exists as a net of hydrophilic, negatively charged phosphates. The Py3 units are hold up by non-covalent interactions what makes these assemblies totally reversible. Moreover the polymerization occurs via nucleation-elongation mechanism. To study Py3 self-assembly, we carried out whole set of spectroscopic (UV/vis, fluorescence, DLS) and microscopic experiments (AFM)

Two-dimensional supramolecular polymers

One of the biggest issues of modern materials science is developing of strategies to create large and ordered assemblies in the form of discrete nanoscale objects. Oligopyrenotides (OPs) represent novel class of amphiphilic molecules which tend to self-assemble forming highly ordered structures. As has been already shown OPs are able to form 1D («rod-like») supramolecular polymer [1]. Since programmed arraying of polyaromatic hydrocarbons in structurally defined objects could offer enhanced performance over the individual components, prediction and controlling of their spatial arrangement remains challenging. Herein we demonstrate that certain changes to design of pyrene’s molecular core allow Py3 form 2D supramolecular assemblies («nanosheets») instead of 1D. Two dimensional supramolecular polymers are attractive objects due to their exceptional properties which originate from in-plan alignment of molecular units in the sheets with constant thickness ~ 2 nm [2]. These assemblies have high degree of internal order: the interior consists of hydrophobic pyrenes and alkyl chains, whereas the exterior exists as a net of hydrophilic, negatively charged phosphates. The Py3 units are hold up by non-covalent interactions what makes these assemblies totally reversible. Moreover the polymerization occurs via nucleation-elongation mechanism. To study Py3 self-assembly, we carried out whole set of spectroscopic (UV/vis, fluorescence, DLS) and microscopic experiments (AFM)

A Multi-Dimensional Approach to Evaluating Family Preservation Programs

The current study evaluates the effectiveness of family preservation programs funded by the Mississippi Department of Human Services. This venture encompassed scrutiny and assessment of improvements in child functioning, positive changes in parental functioning and family functioning and the decrease in foster care placement. Further, this evaluation assessed client and staff satisfaction. It also included an assessment of the perceived impact this program had on the community. Results indicate that the family preservation programs were effective in improving the self-esteem of participants, family cohesion, and adaptability. There were no significant changes in child placement, teen births, or abuse rates. Client and staff satisfaction were high on all quality dimensions. The majority of the sample of community members felt that the family preservation programs were effective in the community.

Reactive mass transport modelling of a three-dimensional vertical fault zone with a finger-like convective flow regime

For a three-dimensional vertically-oriented fault zone, we consider the coupled effects of fluid flow, heat transfer and reactive mass transport, to investigate the patterns of fluid flow, temperature distribution, mineral alteration and chemically induced porosity changes. We show, analytically and numerically, that finger-like convection patterns can arise in a vertically-oriented fault zone. The onset and patterns of convective fluid flow are controlled by the Rayleigh number which is a function of the thermal properties of the fluid and the rock, the vertical temperature gradient, and the height and the permeability of the fault zone. Vigorous fluid flow causes low temperature gradients over a large region of the fault zone. In such a case, flow across lithological interfaces becomes the most important mechanism for the formation of sharp chemical reaction fronts. The degree of rock buffering, the extent and intensity of alteration, the alteration mineralogy and in some cases the formation of ore deposits are controlled by the magnitude of the flow velocity across these compositional interfaces in the rock. This indicates that alteration patterns along compositional boundaries in the rock may provide some insights into the convection pattern. The advective mass and heat exchanges between the fault zone and the wallrock depend on the permeability contrast between the fault zone and the wallrock. A high permeability contrast promotes focussed convective flow within the fault zone and diffusive exchange of heat and chemical reactants between the fault zone and the wallrock. However, a more gradual permeability change may lead to a regional-scale convective flow system where the flow pattern in the fault affects large-scale fluid flow, mass transport and chemical alteration in the wallrocks

Three-dimensional imaging methods for quantitative analysis of facial soft tissues and skeletal morphology in patients with orofacial clefts: a systematic review.

BACKGROUND Current guidelines for evaluating cleft palate treatments are mostly based on two-dimensional (2D) evaluation, but three-dimensional (3D) imaging methods to assess treatment outcome are steadily rising. OBJECTIVE To identify 3D imaging methods for quantitative assessment of soft tissue and skeletal morphology in patients with cleft lip and palate. DATA SOURCES Literature was searched using PubMed (1948-2012), EMBASE (1980-2012), Scopus (2004-2012), Web of Science (1945-2012), and the Cochrane Library. The last search was performed September 30, 2012. Reference lists were hand searched for potentially eligible studies. There was no language restriction. STUDY SELECTION We included publications using 3D imaging techniques to assess facial soft tissue or skeletal morphology in patients older than 5 years with a cleft lip with/or without cleft palate. We reviewed studies involving the facial region when at least 10 subjects in the sample size had at least one cleft type. Only primary publications were included. DATA EXTRACTION Independent extraction of data and quality assessments were performed by two observers. RESULTS Five hundred full text publications were retrieved, 144 met the inclusion criteria, with 63 high quality studies. There were differences in study designs, topics studied, patient characteristics, and success measurements; therefore, only a systematic review could be conducted. Main 3D-techniques that are used in cleft lip and palate patients are CT, CBCT, MRI, stereophotogrammetry, and laser surface scanning. These techniques are mainly used for soft tissue analysis, evaluation of bone grafting, and changes in the craniofacial skeleton. Digital dental casts are used to evaluate treatment and changes over time. CONCLUSION Available evidence implies that 3D imaging methods can be used for documentation of CLP patients. No data are available yet showing that 3D methods are more informative than conventional 2D methods. Further research is warranted to elucidate it.

Evaluation of 3-dimensional superimposition techniques on various skeletal structures of the head using surface models.

OBJECTIVES To test the applicability, accuracy, precision, and reproducibility of various 3D superimposition techniques for radiographic data, transformed to triangulated surface data. METHODS Five superimposition techniques (3P: three-point registration; AC: anterior cranial base; AC + F: anterior cranial base + foramen magnum; BZ: both zygomatic arches; 1Z: one zygomatic arch) were tested using eight pairs of pre-existing CT data (pre- and post-treatment). These were obtained from non-growing orthodontic patients treated with rapid maxillary expansion. All datasets were superimposed by three operators independently, who repeated the whole procedure one month later. Accuracy was assessed by the distance (D) between superimposed datasets on three form-stable anatomical areas, located on the anterior cranial base and the foramen magnum. Precision and reproducibility were assessed using the distances between models at four specific landmarks. Non parametric multivariate models and Bland-Altman difference plots were used for analyses. RESULTS There was no difference among operators or between time points on the accuracy of each superimposition technique (p>0.05). The AC + F technique was the most accurate (D<0.17 mm), as expected, followed by AC and BZ superimpositions that presented similar level of accuracy (D<0.5 mm). 3P and 1Z were the least accurate superimpositions (0.790.05), the detected structural changes differed significantly between different techniques (p<0.05). Bland-Altman difference plots showed that BZ superimposition was comparable to AC, though it presented slightly higher random error. CONCLUSIONS Superimposition of 3D datasets using surface models created from voxel data can provide accurate, precise, and reproducible results, offering also high efficiency and increased post-processing capabilities. In the present study population, the BZ superimposition was comparable to AC, with the added advantage of being applicable to scans with a smaller field of view.

Three-dimensional culture and characterization of mononuclear cells from human bone marrow

BACKGROUND AIMS The diverse phenotypic changes and clinical and economic disadvantages associated with the monolayer expansion of bone marrow-derived mesenchymal stromal cells (MSCs) have focused attention on the development of one-step intraoperative cells therapies and homing strategies. The mononuclear cell fraction of bone marrow, inclusive of discrete stem cell populations, is not well characterized, and we currently lack suitable cell culture systems in which to culture and investigate the behavior of these cells. METHODS Human bone marrow-derived mononuclear cells were cultured within fibrin for 2 weeks with or without fibroblast growth factor-2 supplementation. DNA content and cell viability of enzymatically retrieved cells were determined at days 7 and 14. Cell surface marker profiling and cell cycle analysis were performed by means of multi-color flow cytometry and a 5-ethynyl-2'-deoxyuridine incorporation assay, respectively. RESULTS Total mononuclear cell fractions, isolated from whole human bone marrow, was successfully cultured in fibrin gels for up to 14 days under static conditions. Discrete niche cell populations including MSCs, pericytes and hematopoietic stem cells were maintained in relative quiescence for 7 days in proportions similar to that in freshly isolated cells. Colony-forming unit efficiency of enzymatically retrieved MSCs was significantly higher at day 14 compared to day 0; and in accordance with previously published works, it was fibroblast growth factor-2-dependant. CONCLUSIONS Fibrin gels provide a simple, novel system in which to culture and study the complete fraction of bone marrow-derived mononuclear cells and may support the development of improved bone marrow cell-based therapies.

A two-dimensional analysis of the impact of outward FDI on performance at home: evidence from Japanese manufacturing firms

This paper empirically investigates two areas of changes in firm behavior and performance at home before and after investing abroad. The first change is dependent upon the type of foreign direct investment (FDI): horizontal FDI or vertical FDI. The second change is dependent upon the firm’s domestic activities: production activities or non-production activities. From a theoretical standpoint, the impact of outward FDIs differs not only by type, but according to the firm’s activities. By exploiting two types of firm-level data that enable us to distinguish between production and non-production activities, our paper provides a detailed picture of the intra-firm changes in behavior and performance that occur as a result of production globalization.

3-dimensional binaural sound rendering using acoustic measurements stored in the SOFA format

Several groups all over the world are researching in several ways to render 3D sounds. One way to achieve this is to use Head Related Transfer Functions (HRTFs). These measurements contain the Frequency Response of the human head and torso for each angle. Some years ago, was only possible to measure these Frequency Responses only in the horizontal plane. Nowadays, several improvements have made possible to measure and use 3D data for this purpose. The problem was that the groups didn't have a standard format file to store the data. That was a problem when a third part wanted to use some different HRTFs for 3D audio rendering. Every of them have different ways to store the data. The Spatially Oriented Format for Acoustics or SOFA was created to provide a solution to this problem. It is a format definition to unify all the previous different ways of storing any kind of acoustics data. At the moment of this project they have defined some basis for the format and some recommendations to store HRTFs. It is actually under development, so several changes could come. The SOFA[1] file format uses a numeric container called netCDF[2], specifically the Enhaced data model described in netCDF 4 that is based on HDF5[3]. The SoundScape Renderer (SSR) is a tool for real-time spatial audio reproduction providing a variety of rendering algorithms. The SSR was developed at the Quality and Usability Lab at TU Berlin and is now further developed at the Institut für Nachrichtentechnik at Universität Rostock [4]. This project is intended to be an introduction to the use of SOFA files, providing a C++ API to manipulate them and adapt the binaural renderer of the SSR for working with the SOFA format. RESUMEN. El SSR (SoundScape Renderer) es un programa que está siendo desarrollado actualmente por la Universität Rostock, y previamente por la Technische Universität Berlin. El SSR es una herramienta diseñada para la reproducción y renderización de audio 2D en tiempo real. Para ello utiliza diversos algoritmos, algunos orientados a sistemas formados por arrays de altavoces en diferentes configuraciones y otros algoritmos diseñados para cascos. El principal objetivo de este proyecto es dotar al SSR de la capacidad de renderizar sonidos binaurales en 3D. Este proyecto está centrado en el binaural renderer del SSR. Este algoritmo se basa en el uso de HRTFs (Head Related Transfer Function). Las HRTFs representan la función de transferencia del sistema formado por la cabeza y el torso del oyente. Esta función es medida desde diferentes ángulos. Con estos datos el binaural renderer puede generar audio en tiempo real simulando la posición de diferentes fuentes. Para poder incluir una base de datos con HRTFs en 3D se ha hecho uso del nuevo formato SOFA (Spatially Oriented Format for Acoustics). Este nuevo formato se encuentra en una fase bastante temprana de su desarrollo. Está pensado para servir como formato estándar para almacenar HRTFs y cualquier otro tipo de medidas acústicas, ya que actualmente cada laboratorio cuenta con su propio formato de almacenamiento y esto hace bastante difícil usar varias bases de datos diferentes en un mismo proyecto. El formato SOFA hace uso del contenedor numérico netCDF, que a su vez esta basado en un contenedor más básico llamado HRTF-5. Para poder incluir el formato SOFA en el binaural renderer del SSR se ha desarrollado una API en C++ para poder crear y leer archivos SOFA con el fin de utilizar los datos contenidos en ellos dentro del SSR.

Morphological Functions to Quantify Three-Dimensional Tomograms of Macropore Structure in a Vineyard Soil with Two Different Management Regimes

Soil tomography and morphological functions built over Minkowski functionals were used to describe the impact on pore structure of two soil management practices in a Mediterranean vineyard. Soil structure controls important physical and biological processes in soil–plant–microbial systems. Those processes are dominated by the geometry of soil pore structure, and a correct model of this geometry is critical for understanding them. Soil tomography has been shown to provide rich three-dimensional digital information on soil pore geometry. Recently, mathematical morphological techniques have been proposed as powerful tools to analyze and quantify the geometrical features of porous media. Minkowski functionals and morphological functions built over Minkowski functionals provide computationally efficient means to measure four fundamental geometrical features of three-dimensional geometrical objects, that is, volume, boundary surface, mean boundary surface curvature, and connectivity. We used the threshold and the dilation and erosion of three-dimensional images to generate morphological functions and explore the evolution of Minkowski functionals as the threshold and as the degree of dilation and erosion changes. We analyzed the three-dimensional geometry of soil pore space with X-ray computed tomography (CT) of intact soil columns from a Spanish Mediterranean vineyard by using two different management practices (conventional tillage versus permanent cover crop of resident vegetation). Our results suggested that morphological functions built over Minkowski functionals provide promising tools to characterize soil macropore structure and that the evolution of morphological features with dilation and erosion is more informative as an indicator of structure than moving threshold for both soil managements studied.