Developing a Cloud-Based Air Quality Monitoring Platform Using Low-Cost Sensors

Conventional air quality monitoring has been traditionally carried out in a few fixed places with expensive measuring equipment. This results in sparse spatial air quality data, which do not represent the real air quality of an entire area, e.g., when hot spots are missing. To obtain air quality data with higher spatial and temporal resolution, this research focused on developing a low-cost network of cloud-based air quality measurement platforms. These platforms should be able to measure air quality parameters including particulate matter (PM10, PM2.5, PM1) as well as gases like NO, NO2, O3, and CO, air temperature, and relative humidity. These parameters were measured every second and transmitted to a cloud server every minute on average. The platform developed during this research used one main computer to read the sensor data, process it, and store it in the cloud. Three prototypes were tested in the field: two of them at a busy traffic site in Stuttgart, Marienplatz and one at a remote site, Ötisheim, where measurements were performed near busy railroad tracks. The developed platform had around 1500 € in materials costs for one Air Quality Sensor Node and proved to be robust during the measurement phase. The notion of employing a Proportional-Integral-Derivative (PID) controller for the efficient working of a dryer that is used to reduce the negative effect of meteorological parameters such as air temperature and relative humidity on the measurement results was also pursued. This is seen as one way to improve the quality of data captured by low-cost sensors.

Single Layer Lift-Off of CSAR62 for Dense Nanostructured Patterns

Lift-off processing is a common method of pattern transfer for different nanofabrication applications. With the emergence of chemically amplified and semi-amplified resist systems, the possibilities for pattern definition via electron beam lithography has been widened. We report a reliable and simple lift-off process for dense nanostructured pattern in CSAR62. The pattern is defined in a single layer CSAR62 resist mask for gold nanostructures on silicon. The process offers a slimmed down pathway for pattern definition of dense nanostructures with varied feature size and an up to 10 nm thick gold layer. The resulting patterns from this process have been successfully used in metal assisted chemical etching applications.

POS1559-HPR PHYSIOTHERAPISTS MAKE LIMITED USE OF BEHAVIOUR CHANGE TECHNIQUES DURING PHYSICAL ACTIVITY COUNSELLING FOR PEOPLE WITH AXIAL SPONDYLOARTHRITIS

Background

The 2018 EULAR recommendations for physical activity (PA) in people with inflammatory arthritis and osteoarthritis state that PA in generally recommended dose is effective, safe and feasible (1). Based on the recommendations, the Ankylosing Spondylitis Association of Switzerland (SVMB) developed a concept for their exercise groups, consisting of guidance on exercising, regular fitness assessments and individual PA counselling by the group-leading physical therapist (PT). The use of behaviour change techniques (BCTs) during PA counselling ought to support counselees’ adherence to individual, unsupervised exercising.

Objectives

To assess the BCTs used by the PTs during their PA counselling sessions with the members of their axSpA exercise groups.

Methods

An observational cross-sectional study was performed with the first cohort of PTs (n=16) who applied the new concept and provided PA counselling, and their group members who agreed to participate. All first counselling sessions with an individual with axSpA were audiotaped, transcribed and analysed using a coding manual for BCTs (2). The manual includes 38 BCTs across the determinants ‘knowledge’ (2 BCTs), ‘awareness’ (8 BCTs), ‘social influence’ (3 BCTs), ‘attitude’ (4 BCTs)’, ‘self-efficacy’ (6 BCTs), ‘intention (6 BCTs)’, ‘action control’ (2 BCTs), ‘facilitation’ (2 BCTs), ‘maintenance’ (5 BCTs). Two raters familiar with BCTs identified the BCTs used by the PTs. They repeatedly discussed and agreed about their classifications of PTs’ phrasings to BCTs in an iterative process to achieve consistency over all counselling sessions. A BCT could be used several times within one counselling session.

Results

A total of 12 PTs (75%) who counselled 41 people with axSpA participated. All 41 PA counselling sessions, lasting between 30-55 minutes were analysed. Overall, 15 out of the 38 BCTs were identified. Across each determinant (with its number of BCTs), the most and least frequently used BCTs were as follows: 1) determinant ‘knowledge’ (1 of 2 BCTs used): ‘provide general information’ (469 times by 12 PTs); 2) ‘awareness’ (3 of 8 BCTs used): reflective listening and ‘self-monitoring of behaviour’ (328x by 12 PTs and 39x by 9 PTs respectively); 3) ‘social influence’: none of 3 BCTs used; 4) ‘attitude’ (1 of 4 BCTs used): persuasive communication (184x by 11 PTs); 5) ‘self-efficacy’ (3 of 6 BCTs used): verbal persuasion and guided practice (77x by 11 PTs and 3x by 3 PTs respectively); 6) ‘intention’ (4 of 6 BCTs used): general intention formation and develop training schedule (250x by 12 PTs and 18x by 5 PTs respectively); 7) ‘action control’ (1 of 2 BCTs used): use of cues (199x by 12 PTs), 8) ‘facilitation’: none (of 2) BCTs used; 9) ‘maintenance’ (2 of 5 BCTs used): continuous professional support and individualize regimen (137x by 12 PTs and 70x by 10 PTs respectively).

Conclusion

The study identified that PTs used only a limited number of BCTs. BCTs considered less effective such as providing information were widely used, whereas BCTs that are considered effective, such as specific aims or coping with barriers were much less or not at all used. This study provides an insight in real clinical practice and may help to develop counselling training for PTs. There is a need to translate theoretical BCTs into effective measures that are easy to use in clinical practice.

References

[1]Rausch Osthoff A-K et al. 2018 EULAR recommendations for physical activity. Ann Rheum Dis 2018;77:1251–1260.

[2]De Bruin M. et al. Coding manual for behavioral change techniques. Maastricht University, 2007.

Acknowledgements

We thank all participants for their collaboration

Disclosure of Interests

None declared

NanoMAX: the hard X-ray nanoprobe beamline at the MAX IV Laboratory

NanoMAX is the first hard X-ray nanoprobe beamline at the MAX IV laboratory. It utilizes the unique properties of the world's first operational multi-bend achromat storage ring to provide an intense and coherent focused beam for experiments with several methods. In this paper we present the beamline optics design in detail, show the performance figures, and give an overview of the surrounding infrastructure and the operational diffraction endstation.

Optimization of Metal-Assisted Chemical Etching for Deep Silicon Nanostructures

High-aspect ratio silicon (Si) nanostructures are important for many applications. Metal-assisted chemical etching (MACE) is a wet-chemical method used for the fabrication of nanostructured Si. Two main challenges exist with etching Si structures in the nanometer range with MACE: keeping mechanical stability at high aspect ratios and maintaining a vertical etching profile. In this work, we investigated the etching behavior of two zone plate catalyst designs in a systematic manner at four different MACE conditions as a function of mechanical stability and etching verticality. The zone plate catalyst designs served as models for Si nanostructures over a wide range of feature sizes ranging from 850 nm to 30 nm at 1:1 line-to-space ratio. The first design was a grid-like, interconnected catalyst (brick wall) and the second design was a hybrid catalyst that was partly isolated, partly interconnected (fishbone). Results showed that the brick wall design was mechanically stable up to an aspect ratio of 30:1 with vertical Si structures at most investigated conditions. The fishbone design showed higher mechanical stability thanks to the Si backbone in the design, but on the other hand required careful control of the reaction kinetics for etching verticality. The influence of MACE reaction kinetics was identified by lowering the oxidant concentration, lowering the processing temperature and by isopropanol addition. We report an optimized MACE condition to achieve an aspect ratio of at least 100:1 at room temperature processing by incorporating isopropanol in the etching solution.

Calibration Method for Particulate Matter Low-Cost Sensors Used in Ambient Air Quality Monitoring and Research

Over the last decade, manufacturers have come forth with cost-effective sensors for measuring ambient and indoor particulate matter concentration. What these sensors make up for in cost efficiency, they lack in reliability of the measured data due to their sensitivities to temperature and relative humidity. These weaknesses are especially evident when it comes to portable or mobile measurement setups. In recent years many studies have been conducted to assess the possibilities and limitations of these sensors, however mostly restricted to stationary measurements. This study reviews the published literature until 2020 on cost-effective sensors, summarizes the recommendations of experts in the field based on their experiences, and outlines the quantile-mapping methodology to calibrate low-cost sensors in mobile applications. Compared to the commonly used linear regression method, quantile mapping retains the spatial characteristics of the measurements, although a common correction factor cannot be determined. We conclude that quantile mapping can be a useful calibration methodology for mobile measurements given a well-elaborated measurement plan assures providing the necessary data.

Investigating a Low-Cost Dryer Designed for Low-Cost PM Sensors Measuring Ambient Air Quality

Air pollution in urban areas is a huge concern that demands an efficient air quality control to ensure health quality standards. The hotspots can be located by increasing spatial distribution of ambient air quality monitoring for which the low-cost sensors can be used. However, it is well-known that many factors influence their results. For low-cost Particulate Matter (PM) sensors, high relative humidity can have a significant impact on data quality. In order to eliminate or reduce the impact of high relative humidity on the results obtained from low-cost PM sensors, a low-cost dryer was developed and its effectiveness was investigated. For this purpose, a test chamber was designed, and low-cost PM sensors as well as professional reference devices were installed. A vaporizer regulated the humid conditions in the test chamber. The low-cost dryer heated the sample air with a manually adjustable intensity depending on the voltage. Different voltages were tested to find the optimum one with least energy consumption and maximum drying efficiency. The low-cost PM sensors with and without the low-cost dryer were compared. The experimental results verified that using the low-cost dryer reduced the influence of relative humidity on the low-cost PM sensor results.

Metal-Assisted Chemical Etching and Electroless Deposition for Fabrication of Hard X-ray Pd/Si Zone Plates

Zone plates are diffractive optics commonly used in X-ray microscopes. Here, we present a wet-chemical approach for fabricating high aspect ratio Pd/Si zone plate optics aimed at the hard X-ray regime. A Si zone plate mold is fabricated via metal-assisted chemical etching (MACE) and further metalized with Pd via electroless deposition (ELD). MACE results in vertical Si zones with high aspect ratios. The observed MACE rate with our zone plate design is 700 nm/min. The ELD metallization yields a Pd density of 10.7 g/cm 3 , a value slightly lower than the theoretical density of 12 g/cm 3 . Fabricated zone plates have a grid design, 1:1 line-to-space-ratio, 30 nm outermost zone width, and an aspect ratio of 30:1. At 9 keV X-ray energy, the zone plate device shows a first order diffraction efficiency of 1.9%, measured at the MAX IV NanoMAX beamline. With this work, the possibility is opened to fabricate X-ray zone plates with low-cost etching and metallization methods.

Ptychographic characterization of a coherent nanofocused X-ray beam

The NanoMAX hard X-ray nanoprobe is the first beamline to take full advantage of the diffraction-limited storage ring at the MAX IV synchrotron and delivers a high coherent photon flux for applications in diffraction and imaging. Here, we characterize its coherent and focused beam using ptychographic analysis. We derive beam profiles in the energy range 6-22 keV and estimate the coherent flux based on a probe mode decomposition approach.

Stability investigation of a cryo soft x-ray microscope by fiber interferometry

We present a stability investigation of the Stockholm laboratory cryo soft x-ray microscope. The microscope operates at a wavelength of 2.48 nm and can image biological samples at liquid-nitrogen temperatures in order to mitigate radiation damage. We measured the stability of the two most critical components, sample holder and optics holder, in vacuo and at cryo temperatures at both short and long time scales with a fiber interferometer. Results revealed vibrations in the kHz range, originating mainly from a turbo pump, as well as long term drifts in connection with temperature fluctuations. With improvements in the microscope, earlier stability issues vanished and close-to diffraction-limited imaging could be achieved. Moreover, our investigation shows that fiber interferometers are a powerful tool in order to investigate position-sensitive setups at the nanometer level.

Reaction control of metal-assisted chemical etching for silicon-based zone plate nanostructures

Metal-assisted chemical etching (MACE) reaction parameters were investigated for the fabrication of specially designed silicon-based X-ray zone plate nanostructures using a gold catalyst pattern and etching solutions composed of HF and H₂O₂. Etching depth, zone verticality and zone roughness were studied as a function of etching solution composition, temperature and processing time. Homogeneous, vertical etching with increasing depth is observed at increasing H₂O₂ concentrations and elevated processing temperatures, implying a balance in the hole injection and silica dissolution kinetics at the gold–silicon interface. The etching depth decreases and zone roughness increases at the highest investigated H₂O₂ concentration and temperature. Possible reasons for these observations are discussed based on reaction chemistry and zone plate design. Optimum MACE conditions are found at HF : H₂O₂ concentrations of 4.7 M : 0.68 M and room temperature with an etching rate of ≈0.7 μm min⁻¹, which is about an order of magnitude higher than previous reports. Moreover, our results show that a grid catalyst design is important for successful fabrication of vertical high aspect ratio silicon nanostructures.

Specially designed X-ray zone plates with high aspect-ratios have been fabricated via metal-assisted chemical etching, by controlling the reaction kinetics.

Moiré method for nanometer instability investigation of scanning hard x-ray microscopes

We present a Moiré method that can be used to investigate positional instabilities in a scanning hard x-ray microscope with nanometer precision. The development of diffraction-limited storage rings offering highly-brilliant synchrotron radiation and improvements of nanofocusing x-ray optics paves the way towards 3D nanotomography with 10 nm resolution or below. However, this trend demands improved designs of x-ray microscope instruments which should offer few-nm beam stabilities with respect to the sample. Our technique can measure the position of optics and sample stage relative to each other in the two directions perpendicular to the beam propagation in a scanning x-ray microscope using simple optical components and visible light. The usefulness of the method was proven by measuring short and long term instabilities of a zone-plate-optics-based prototype microscope. We think it can become an important tool for the characterization of scanning x-ray microscopes, especially prior to experiments with an actual x-ray beam.

Interferometric characterization of rotation stages for X-ray nanotomography

The field of three-dimensional multi-modal X-ray nanoimaging relies not only on high-brilliance X-rays but also on high-precision mechanics and position metrology. Currently available state-of-the-art linear and rotary drives can provide 3D position accuracy within tens to hundreds of nm, which is often insufficient for high resolution imaging with nanofocused X-ray beams. Motion errors are especially troublesome in the case of rotation drives and their correction is more complicated and relies on the metrology grade reference objects. Here we present a method which allows the characterisation and correction of the radial and angular errors of the rotary drives without the need for a highly accurate metrology object. The method is based on multi-probe error separation using fiber-laser interferometry and uses a standard cylindrical sample holder as a reference. The obtained runout and shape measurements are then used to perform the position corrections using additional drives. We demonstrate the results of the characterization for a piezo-driven small rotation stage. The error separation allowed us to measure the axis runout to be approximately ±1.25 μm, and with active runout compensation this could be reduced down to ±42 nm.

Perfect X-ray focusing via fitting corrective glasses to aberrated optics

Due to their short wavelength, X-rays can in principle be focused down to a few nanometres and below. At the same time, it is this short wavelength that puts stringent requirements on X-ray optics and their metrology. Both are limited by today's technology. In this work, we present accurate at wavelength measurements of residual aberrations of a refractive X-ray lens using ptychography to manufacture a corrective phase plate. Together with the fitted phase plate the optics shows diffraction-limited performance, generating a nearly Gaussian beam profile with a Strehl ratio above 0.8. This scheme can be applied to any other focusing optics, thus solving the X-ray optical problem at synchrotron radiation sources and X-ray free-electron lasers.

Ce K edge XAS of ceria-based redox materials under realistic conditions for the two-step solar thermochemical dissociation of water and/or CO2

X-ray absorption spectroscopy was used to characterise ceria-based materials under realistic conditions present in a reactor for solar thermochemical two-step water and carbon dioxide splitting.

3D simulation of the image formation in soft x-ray microscopes

In water-window soft x-ray microscopy the studied object is typically larger than the depth of focus and the sample illumination is often partially coherent. This blurs out-of-focus features and may introduce considerable fringing. Understanding the influence of these phenomena on the image formation is therefore important when interpreting experimental data. Here we present a wave-propagation model operating in 3D for simulating the image formation of thick objects in partially coherent soft x-ray microscopes. The model is compared with present simulation methods as well as with experiments. The results show that our model predicts the image formation of transmission soft x-ray microscopes more accurately than previous models.

Ronchi test for characterization of X-ray nanofocusing optics and beamlines

A Ronchi interferometer for hard X-rays is reported in order to characterize the performance of the nanofocusing optics as well as the beamline stability. Characteristic interference fringes yield qualitative data on present aberrations in the optics. Moreover, the visibility of the fringes on the detector gives information on the degree of spatial coherence in the beamline. This enables the possibility to detect sources of instabilities in the beamline like vibrations of components or temperature drift. Examples are shown for two different nanofocusing hard X-ray optics: a compound refractive lens and a zone plate.

Thermochemical CO2 splitting via redox cycling of ceria reticulated foam structures with dual-scale porosities

Efficient radiation heat transfer and rapid chemical kinetics for solar thermochemical CO₂ splitting utilizing dual-scale ceria foam structures.

Damage investigation on tungsten and diamond diffractive optics at a hard x-ray free-electron laser

Focusing hard x-ray free-electron laser radiation with extremely high fluence sets stringent demands on the x-ray optics. Any material placed in an intense x-ray beam is at risk of being damaged. Therefore, it is crucial to find the damage thresholds for focusing optics. In this paper we report experimental results of exposing tungsten and diamond diffractive optics to a prefocused 8.2 keV free-electron laser beam in order to find damage threshold fluence levels. Tungsten nanostructures were damaged at fluence levels above 500 mJ/cm(2). The damage was of mechanical character, caused by thermal stress variations. Diamond nanostructures were affected at a fluence of 59 000 mJ/cm(2). For fluence levels above this, a significant graphitization process was initiated. Scanning Electron Microscopy (SEM) and µ-Raman analysis were used to analyze exposed nanostructures.

Ronchi test for characterization of nanofocusing optics at a hard x-ray free-electron laser

We demonstrate the use of the classical Ronchi test to characterize aberrations in focusing optics at a hard x-ray free-electron laser. A grating is placed close to the focus and the interference between the different orders after the grating is observed in the far field. Any aberrations in the beam or the optics will distort the interference fringes. The method is simple to implement and can provide single-shot information about the focusing quality. We used the Ronchi test to measure the aberrations in a nanofocusing Fresnel zone plate at the Linac Coherent Light Source at 8.194 keV.

High average brightness water window source for short-exposure cryomicroscopy

Laboratory water window cryomicroscopy has recently demonstrated similar image quality as synchrotron-based microscopy but still with much longer exposure times, prohibiting the spread to a wider scientific community. Here we demonstrate high-resolution laboratory water window imaging of cryofrozen cells with 10 s range exposure times. The major improvement is the operation of a λ=2.48 nm, 2 kHz liquid nitrogen jet laser plasma source with high spatial and temporal stability at high average brightness >1.5×10(12) ph/(s×sr×μm(2)×line), i.e., close to that of early synchrotrons. Thus, this source enables not only biological x-ray microscopy in the home laboratory but potentially other applications previously only accessible at synchrotron facilities.

Compact x-ray microscope for the water window based on a high brightness laser plasma source

We present a laser plasma based x-ray microscope for the water window employing a high-average power laser system for plasma generation. At 90 W laser power a brightness of 7.4 x 10(11) photons/(s x sr x μm(2)) was measured for the nitrogen Lyα line emission at 2.478 nm. Using a multilayer condenser mirror with 0.3 % reflectivity 10(6) photons/(μm(2) x s) were obtained in the object plane. Microscopy performed at a laser power of 60 W resolves 40 nm lines with an exposure time of 60 s. The exposure time can be further reduced to 20 s by the use of new multilayer condenser optics and operating the laser at its full power of 130 W.

Laboratory cryo soft X-ray microscopy

Lens-based water-window X-ray microscopy allows two- and three-dimensional (2D and 3D) imaging of intact unstained cells in their near-native state with unprecedented contrast and resolution. Cryofixation is essential to avoid radiation damage to the sample. Present cryo X-ray microscopes rely on synchrotron radiation sources, thereby limiting the accessibility for a wider community of biologists. In the present paper we demonstrate water-window cryo X-ray microscopy with a laboratory-source-based arrangement. The microscope relies on a λ=2.48-nm liquid-jet high-brightness laser-plasma source, normal-incidence multilayer condenser optics, 30-nm zone-plate optics, and a cryo sample chamber. We demonstrate 2D imaging of test patterns, and intact unstained yeast, protozoan parasites and mammalian cells. Overview 3D information is obtained by stereo imaging while complete 3D microscopy is provided by full tomographic reconstruction. The laboratory microscope image quality approaches that of the synchrotron microscopes, but with longer exposure times. The experimental image quality is analyzed from a numerical wave-propagation model of the imaging system and a path to reach synchrotron-like exposure times in laboratory microscopy is outlined.

Laboratory soft-x-ray microscope for cryotomography of biological specimens

Soft-x-ray cryotomography allows quantitative and high-resolution three-dimensional imaging of intact unstained cells. To date, the method relies on synchrotron-radiation sources, which limits accessibility for researchers. Here we present a laboratory water-window microscope for cryotomography. It is based on a λ=2.48 nm liquid-jet laser-plasma source, a normal-incidence multilayer condenser, a 30 nm zone-plate objective, and a cryotilt sample holder. We demonstrate high-resolution imaging, as well as quantitative tomographic imaging, of frozen intact cells. The reconstructed tomogram of the intracellular local absorption coefficient shows details down to ∼100 nm.

Numerical model for tomographic image formation in transmission x-ray microscopy

We present a numerical image-formation model for investigating the influence of partial coherence, sample thickness and depth-of-focus on the accuracy of tomographic reconstructions in transmission x-ray microscopes. The model combines wave propagation through the object by finite difference techniques with Fourier methods. We include a ray-tracing model to analyse the origin of detrimental stray light in zone plate-based x-ray microscopes. These models allow optimization of x-ray microscopy systems for quantitative tomographic imaging of thick objects. Results show that both the depth-of-focus and the reconstructed local absorption coefficient are highly dependent on the degree of coherence of the optical system.

Prediction of Metastasis in Node-Negative, Hormone Receptor Positive, Tamoxifen Adjuvant Treated Primary Breast Cancer Patients Using Ki-67 (IHC) and RT-PCR Based 14-Gene Prognostic Signature

Background: Risk estimation based on the recommendations of St. Gallen Consensus commonly decides for additional cytostatic therapy in node-negative (N-), hormone receptor positive (HR+) primary breast cancer patients. High proliferative activity in the HR+ subtype confers a 19-fold relative risk of relapse compared with HR+ tumors of low proliferative activity. Furthermore immunohistochemically determined Ki-67 is characterized as a Luminal B marker that identifies a high risk subgroup in HR+, N- breast cancer patients.Aim of this investigation was to compare risk estimation using Ki-67 (%) with the results of a RT-PCR based multi-gene prognostic signature. Methods: Tumor tissues of totally 321 unselected primary breast cancer patients were formalin fixed and routinely processed for immunohistochemical determination and scored for protein expression of ER, PgR and Ki-67. HER2 was determined using dd-PCR. Content of both hormone receptors and proliferation activity were evaluated counting positively coloured nuclei from at least 100 tumor cells. The median follow up was 61 months. To calculate the cut off for high proliferation Ki-67 values were subjected to a log rank CART analysis. High proliferation was defined by Ki-67 of 19% and more. With this cut off it was possible to distinguish significantly various patient cohorts (N-, pT1, postmenopausal) into two different risk groups regarding metastasis free survival. The definition of low risk was low proliferation and HER2 negativity, of high risk high proliferation or HER2 positivity. The risk for metastasis of 16 new primary breast cancer patients was estimated based on two surrogate risk groups and the multi-gene prognostic signature. Results: Tamoxifen adjuvant treated HR+, HER2-, low proliferating (Ki-67 <19%), N- low risk patients (N= 68) and HR+, HER2-, high proliferating/HR+, HER2+, N- high risk patients (N= 84) showed a recurrence rate of 2.94% and 27.4%, respectively (P< .000). In the ongoing observation study all 5 low proliferating HER2- tumors had a low risk gene prognostic signature. From 11 high proliferating HER2- patients one patient had a low risk gene signature (9%), 3 patients a moderate risk gene signature (27%) and 7 patients a high risk gene signature (64%). Conclusion: Despite the small number of patients investigated up to now (N= 16) the preliminary results appear to show that low proliferative activity is associated with a low risk gene prognostic signature, whereas high proliferation means only in part a high risk gene prognostic signature.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 6025.

Gene Expression Profiling for Therapy Prediction in a Breast Cancer Neoadjuvant Therapy Study Applying Docetaxel/Epirubicin/Cyclophosphamide

Background: Gene expression profiling is a powerful tool to identify markers associated with clinical and therapy outcome of cancer patients. Prediction of the response to neoadjuvant regimens remains a persistent challenge. Aim of this ongoing study is the development of a gene set predicting the response of the tumor to a taxane- anthracycline based neoadjuvant chemotherapy.Material and Methods: Microarray expression profiling was performed on biopsy samples from patients before treatment using Human Genome Survey microarrays (HGSM). The protocol for a phase II study was elaborated for the treatment of breast cancer patients suffering from a primary tumor 1.5 cm or inflammatory breast cancer with Docetaxel/Epirubicin/Cyclophosphamide (TEC) prior to surgical treatment. The study was approved by the local ethical committee and all patients signed an informed consent.Results: Overall 80 patients have been enrolled in the presented study. High quality gene expression data were available from 58 patients. Of these patients 21 responded to the TEC regimen (pCR or MIB1 expressing cells in the residual tumor <= 5% and decrease of Mib1-expression >= 20%). Based on the gene-expression profile we were able to identify a preliminary gene set of 150 genes which allows us to separate responding tumors from the non responding ones based on their gene expression profile. A comparable separation of the groups could not achieved by established tumor markers, e.g. ER, PgR, HER2, uPA etc. which are measured simultaneously on the HGSM. Among the genes distinguishing the two groups several genes normally expressed in mononuclear blood cells were identified, pointing to the presence of tumor infiltrating leukocytes, predominantly in the tumors responding the TEC regimen. The presence of these cells has already been verified in a subset of the samples.Conclusion: We identified a gene set which allows to select patients who will benefit from neoadjuvant chemotherapy. Furthermore at least in the so far investigated samples tumor infiltrating leukocytes are significantly more often found in tumors which respond to a taxane- anthracycline based neoadjuvant chemotherapy.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 2039.

Sub-25-nm laboratory x-ray microscopy using a compound Fresnel zone plate

Improving the resolution in x-ray microscopes is of high priority to enable future applications in nanoscience. However, high-resolution zone-plate optics often have low efficiency, which makes implementation in laboratory microscopes difficult. We present a laboratory x-ray microscope based on a compound zone plate. The compound zone plate utilizes multiple diffraction orders to achieve high resolution while maintaining reasonable efficiency. We analyze the illumination conditions necessary for this type of optics in order to suppress stray light and demonstrate microscopic imaging resolving 25 nm features.

High-resolution computed tomography with a compact soft x-ray microscope

Computed tomography based on high-resolution soft x-ray microscopy utilizes the natural contrast for biological specimens provided by the water window (lambda = 2.4 - 4.4 nm) and the high resolving power of zone plate objectives. It is capable of revealing the 3D structure of biological specimens at sub-visible-microscopic resolution. To date, the technique has only been available at synchrotron-based microscopes, which limits the researchers access. In the present paper we demonstrate high-resolution soft x-ray tomography with a laboratory zone-plate-based soft x-ray microscope. The specimen, a diatom mounted on a glass capillary, was reconstructed from a tilt series of 53 images covering 180 degrees using a filtered back projection algorithm. The resolution of the tomogram was estimated to a half period of 140 nm using a differential-phase-residual method. Cryo-fixation, increased source brightness and extended-depth-of-focus objectives are important for pushing the resolution of compact systems for biological samples.

Compact Zernike phase contrast x-ray microscopy using a single-element optic

We demonstrate Zernike phase contrast in a compact soft x-ray microscope using a single-element optic. The optic is a combined imaging zone plate and a Zernike phase plate and does not require any additional alignment or components. Contrast is increased and inversed in an image of a test object using the Zernike zone plate. This type of optic may be implemented into any existing x-ray microscope where phase contrast is of interest.

Theoretical development of a high-resolution differential-interference-contrast optic for x-ray microscopy

In this paper, the theoretical background and development of a differential-interference contrast (DIC) x-ray optic is presented. The single-element optic is capable of high-resolution phase contrast imaging and is compatible with compact sources. It is shown that an understanding of the coherence requirements in this type of imaging is imperative and is explained in detail. The optic is capable of a wavefront separation equal to the resolution of the optic which places only minor constraints on the object illumination.

A 9 keV electron-impact liquid-gallium-jet x-ray source

We demonstrate a high-brightness compact 9 keV electron-impact microfocus x-ray source based on a liquid-gallium-jet anode. A approximately 30 W, 50 kV electron gun is focused onto the approximately 20 ms, 30 mum diameter liquid-gallium-jet anode to produce an approximately 10 microm full width at half maximum x-ray spot. The peak spectral brightness is >2 x 10(10) photons(s mm(2) mrad(2)x0.1% BW). Calculation and experiments show potential for increasing this brightness by approximately three orders of magnitude, making the source suitable for laboratory-scale x-ray crystallography and hard x-ray microscopy.

Simulation of partially coherent image formation in a compact soft X-ray microscope

In this paper, we describe a numerical method of simulating two-dimensional images in a compact soft X-ray microscope using partially coherent illumination considerations. The work was motivated by recent test object images obtained by the latest generation in-house compact soft X-ray microscope, which showed diffraction-like artifacts not observed previously. The numerical model approximates the condenser zone plate as a secondary incoherent source represented by individually coherent but mutually incoherent source points, each giving rise to a separate image. A final image is obtained by adding up all the individual source point contributions. The results are compared with the microscope images and show qualitative agreement, indicating that the observed effects are caused by partially coherent illumination.

Semi-quantitative gene expression profiling for therapy prediction in a breast cancer neoadjuvant therapy study applying docetaxel/epirubicin/cyclophosphamide

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Background: More than 28000 curated human genes can be analyzed semi-quantitatively using a chemiluminescent detection technology and 60mer oligonucleotides on a Human Genome Survey Microarray (HGSM, Applied Biosytems). Methods: HGSM expression profiling was performed on biopsy samplesfrom a setting of patients under neoadjuvant treatment. The protocol for a phase II study was elaborated for the treatment of breast cancer patients suffering from a primary tumor > 1,5 cm or inflammatory breast cancer with Docetaxel / Epirubicin/Cyclophosphamide (TEC) prior to surgical treatment. The study was approved by the local ethical committee and 80 patients will be included into the study after written informed consent. 40 patients have been already included in the ongoing study. In this prospective study a biopsy from the tumor is taken before chemotherapy. Therefore, success of treatment is detectable directly at the operated residual tumor. Our results demonstrate a low rate of false-positives (1.2%), a high specificity and quantification accuracy of HGSM system. Comparison of data from HGSM and RT-PCR obtained on mRNA from fresh frozen tissue resulted a Pearson-correlation of 0.92 to 0.63 for the breast cancer genes. Results: Tumour response (pCR, pPR) of more than 70 % can be achieved using neoadjuvant TEC- regimen. 25 % of pCR in this study is comparable with data of other published neoadjuvant trails. First expression profiling results are obtainable showing that a subset of 148 genes indicates patients with complete remission (pCR, no detectable tumor at end of chemotherapy), partial remission (pPR) and progressive disease (pPD). Remarkable, that the expression profile clearly separated pCR and pPD tumors whereas pPR tumors presented with a closer relationship to pPD tumors than to pCR tumors but displayed small specific subprofiles. A comparable separation of the groups could not achieved by established tumor markers, e.g. ER, PgR, HER2, uPA etc. which are measured simultaneously on the HGSM. Conclusions: HGSM expression profiling is promising to have the potential to figure out genes that are related to cancer progression and chemotherapy resistance, especially in PST.

No significant financial relationships to disclose.

Laboratory arrangement for soft x-ray zone plate efficiency measurements

We demonstrate a laboratory-scale arrangement for rapid and accurate measurements of the absolute and local efficiency of soft x-ray micro zone plates in the water window. This in-house instrument is based on a single-line lambda = 2.88 nm liquid-jet laser-plasma source. Measurements are performed by a simultaneous comparison of first diffraction-order photon flux with the flux in a calibrated reference signal. This arrangement eliminates existing source emission fluctuations. The performance of the method is demonstrated by the result from measurements of two approximately 55 microm diameter nickel micro zone plates, showing a groove efficiency of 12.9% +/- 1.1% and 11.7% +/- 1.0%. Furthermore, we show that spatially resolved efficiency mapping is an effective tool for a detailed characterization of local zone plate properties. Thus, this laboratory-scale instrument allows rapid feedback to the fabrication process which is important for future improvements.

Whole genome expression analysis for biologic rational pathway modeling: application in cancer prognosis and therapy prediction

Using semi-quantitative microarray technology, almost every one of the approximately 30 000 human genes can be analyzed simultaneously with a low rate of false-positives, a high specificity, and a high quantification accuracy. This is supported by data from comparative studies of microarrays and reverse-transcription PCR for established cancer genes including those for epidermal growth factor receptor (EGFR), human epidermal growth factor receptor-2 (HER2/ERBB2), estrogen receptor (ESR1), progesterone receptor (PGR), urokinase-type plasminogen activator (PLAU), and plasminogen activator inhibitor-1 (SERPINE1). As such, semi-quantitative expression data provide an almost completely comprehensive background of biological knowledge that can be applied to cancer diagnostics. In clinical terms, expression profiling may be able to provide significant information regarding (i) the identification of high-risk patients requiring aggressive chemotherapy; (ii) the pathway control of therapy predictive parameters (e.g. ESR1 and HER2); (iii) the discovery of targets for biologically rational therapeutics (e.g. capecitabine and trastuzumab); (iv) additional support for decisions about switching therapy; (v) target discovery; and (vi) the prediction of the course of new therapies in clinical trials. In conclusion, whole genome expression analysis might be able to determine important genes related to cancer progression and adjuvant chemotherapy resistance, especially in the context of new approaches involving primary systemic chemotherapy. In this review, we will survey the current progress in whole genome expression analyses for cancer prognosis and prediction. Special emphasis is given to the approach of combining biostatistical analysis of expression data with knowledge of biochemical and genetic pathways.

Medical Uses of Cosmetic Colored Contact Lenses

PURPOSE

To explore the clinical issues surrounding the use of hand-painted contact lenses for medical indications and to assess patient satisfaction with the use of these lenses for an unsightly eye.

METHODS

A questionnaire was sent to all patients visiting the contact lens department of Western Eye Hospital for a colored contact lens fitting during a 1-year period. The questionnaire related to patient satisfaction with the lenses and aspects of wear.

RESULTS

Replies were received from 25 of a total of 33 patients. The average wearing time was 11.3 hours per day. Most (88%) patients wore lenses for cosmetic reasons, and 12% wore lenses for cosmetic and refractive purposes. Satisfaction was 76% regarding lens comfort and 88% regarding lens color.

CONCLUSIONS

Provided lens care is satisfactory and the patient does not have unreasonable expectations, a tinted contact lens can be a useful device. In view of the cost implication, this is a valuable service provided by the hospital.

Therapy prediction in a breast cancer primary systemic chemotherapy (PST) study applying docetaxel/epirubicin/cyclophosphamide (TEC) by gene expression profiling

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Background: Currently there are no tests to assist in selecting the optimal PST regimen for breast cancer patients. Primary study goals of this prospective, single-armed multicentric investigation are pathologically confirmed tumor response and the rate of breast conserving therapy (BCT). Secondary goals are to find histopathologic and gene profiling patterns best correlating with tumor remission in a taxane- anthracycline based neoadjuvant setting as well as to evaluate cytostatic toxicity and quality of life. Methods: In this phase II study of totally 40 eligible patients with invasive breast cancer Human Genome Survey Microarray (HGSM) expression profiling is performed on jet-biopsy sample basis. The protocol was elaborated for the treatment of patients suffering from a primary tumor with 6 cycles of TEC (3-weekly) prior to the surgical treatment. The selection of predictor genes was done with BRB-ArrayTools Version 3.3 using a model based on the Compound Covariate Predictor, Diagonal Linear Discriminant Analysis, Nearest Neighbor Classification, and Support Vector Machines with linear kernel.We estimated the prediction error of each model using leave-one-out cross-validation (LOOCV) as described by Simon R. 2000 random permutations were used. Clustering was done using Cluster 3.0 and Java TreeView 1.0.12. Results: Tumor response (pCR, pPR) of more than 70% can be achieved using neoadjuvant TEC-regimen. 22% pCR (ypT0; ypN0) and 90% BCT in this study are comparable with data of other published PST trials. Preliminary expression profiling results reveal a subset of 148 genes that classifies all patients with a complete remission (pCR), in one cluster with a very closely related gene expression pattern (n=5; PPV = 100%). Furthermore 10 patients defined as responders due to selected MIB1-expression based criteria (expressing cells in the residual tumor ≤ 5% and a Δ MIB1-expression ≥ 20%) can be correctly classified in 9 of 10 cases. Comparable separation of the groups could not be achieved by established tumor factors. Conclusions: HGSM expression profiling is promising to have the potential to figure out genes that are related to chemotherapy response, especially in PST.

No significant financial relationships to disclose.