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Supplementary Data from Clinical Validation of a Customized Multiple Signature Microarray for Breast Cancer

Purpose: Current histopathologic systems for classifying breast tumors require evaluation of multiple variables and are often associated with significant interobserver variability. Recent studies suggest that gene expression profiles may represent a promising alternative for clinical cancer classification. Here, we investigated the use of a customized microarray as a potential tool for clinical practice.Experimental Design: We fabricated custom 188-gene microarrays containing expression signatures for three breast cancer molecular subtypes [luminal/estrogen receptor (ER) positive, human epidermal growth factor receptor 2 (HER2), and “basaloid”], the Nottingham prognostic index (NPI-ES), and low histologic grade (TuM1). The reliability of these multiple-signature arrays (MSA) was tested in a prospective cohort of 165 patients with primary breast cancer.Results: The MSA-ER signature exhibited a high concordance of 90% with ER immunohistochemistry reported on diagnosis (P < 0.001). This remained unchanged at 89% (P < 0.001) when the immunohistochemistry was repeated using current laboratory standards. Expression of the HER2 signature showed a good correlation of 76% with HER2 fluorescence in situ hybridization (FISH; ratio ≥2.2; P < 0.001), which further improved to 89% when the ratio cutoff was raised to ≥5. A proportion of low-level FISH-amplified samples (ratio, 2.2-5) behaved comparably to FISH-negative samples by HER2 signature expression, HER2 quantitative reverse transcription-PCR, and HER2 immunohistochemistry. Luminal/ER+ tumors with high NPI-ES expression were associated with high NPI scores (P = 0.001), and luminal/ER+ TuM1-expressing tumors were significantly correlated with low histologic grade (P = 0.002) and improved survival outcome in an interim analysis (hazard ratio, 0.2; P = 0.019).Conclusion: The consistency of the MSA platform in an independent patient population suggests that custom microarrays could potentially function as an adjunct to standard immunohistochemistry and FISH in clinical practice.

Introduction Reflex molecular testing plays a critical role in identifying actionable targets and allocating patients to appropriate treatment. We report the clinicopathologic features and treatment outcomes of non-squamous non-small cell lung cancer (NSCLC) patients who underwent reflex testing for EGFR and ALK . Methods We analyzed the data of NSCLC patients diagnosed from 2010 to 2014 who underwent reflex testing for EGFR (from 2010) and ALK (from 2012) alterations and compared the outcome of those positive for the alterations against those who were wild-type (WT). Using multivariate cox regression, we determined the significant prognostic clinical factors that predicted for an improved survival outcome. Results EGFR mutation was more prevalent among females and never-smokers. The median OS (months) for the positive group was 24.8 versus 13.3 for the WT group (p EGFR tyrosine kinase inhibitor (TKI) treatment (all p ALK fusion was more prevalent among Malay patients (p=0.031). There were no significant survival differences in OS between positive and WT groups. Prognostic factors include gender, ethnicity, ECOG status, treatment intent, number of palliative treatment and metastatic sites (all p ALK TKI treatment (p=0.06). Conclusion This study found significant differences in demographic and clinical characteristics, and treatment outcomes between positive and WT patients for EGFR and ALK profiles, reinforcing the importance of reflex testing in patient management.

Spindle cell lipoma is an uncommon variant of lipoma and usually occurs as a solitary, subcutaneous, and well circumscribed lesion in the posterior neck, shoulders, and back of older men. Primary renal lipomas are rarely reported. Spindle cell lipoma in the kidney has not been previously described in the literature.A 60-year-old Chinese man suffered graft failure 10 years after living related donor kidney transplantation. During cancer surveillance, he was found to have a mass in the renal allograft, which increased in size and was suspicious for renal cell carcinoma on computerized tomographic scan. The patient underwent renal graft explantation. Grossly, the kidney was atrophic, containing a 6.5 cm yellowish solid lesion without hemorrhage and necrosis in the renal sinus fat. Microscopically, the lesion was composed of variably sized adipocytes and cellular areas of bland spindle cells with no cytologic atypia. There were prominent slender blood vessels within the lesion, along with focal myxoid change as well as scattered mast cells and inflammatory cells. Lipoblasts were not identified. The spindle cells were positive for CD34 and negative for Melan-A, HMB45, S100, and SMA. Pax-2 stain was nonspecific. MDM2 amplification by means of fluorescence in situ hybridization (FISH) and overexpression by immunohistochemistry were negative. The Ki-67 proliferation index was 1%. Interphase FISH revealed loss of 13q and 16q in the tumor.Renal spindle cell lipoma is a rare benign tumor. Angiomyolipoma and well differentiated liposarcoma are the main differential diagnoses. Immunohistochemistry and cytogenetic techniques are helpful in differentiating it from malignant entities.

Effect of Cu and powder mixing with Cu-free (Nd, Dy)-Fe-B jet-milled powder on the magnetic properties of sintered magnets was investigated. The coercivity of a magnet prepared from the Cu-free (Nd, Dy)-Fe-B powder was about 10 kOe even though the alloy powder already contained some Dy (3.5 wt%). When small copper powder was blended, however, the coercivity of the magnet increased almost 100%, exhibiting about 20 kOe. On the contrary, the coercivity enhancement was moderate, about 4 kOe, when dysprosium content in the sintered magnet was simply increased to 4.9 wt% by the addition of small 3 powder.

In order to increase the coercivity of (Nd, Dy)-Fe-B sintered magnets without much reduction of remanence, small amount of Dy compounds such as and was mixed with (Nd, Dy)-Fe-B powder. After mixing, the coercivity of (Nd, Dy)-Fe-B sintered magnets apparently increased with the increase of Dy compound in the mixture. Addition of was more effective than for the improvement of coercivity. Reduction of the remanence by the addition of Dy compound, however, was larger than expected mostly due to unresolved coarse Dy compound in the magnet. EPMA analysis revealed that Dy was diffused throughout the grains in the magnet mixed with whereas Dy was rather concentrated around grain boundaries in the magnet mixed with .

Multiple myeloma is clinically heterogeneous and risk stratification is vital for prognostication and informing treatment decisions. As bortezomib is able to overcome several high-risk features of myeloma, the validity of conventional risk-stratification and prognostication systems needs to be reevaluated. We study the survival data of 261 previously untreated myeloma patients managed at our institution, where bortezomib became available from 2004 for the treatment of relapse disease. Patient and disease characteristics, and survival data were evaluated overall, and with respect to bortezomib exposure. Overall, the international staging system (ISS), metaphase karyotyping and interphase fluorescence in situ hybridization (FISH) were discerning of survival outcomes, where the median for the entire cohort was 5.2 years. However, when stratified by bortezomib exposure, only metaphase karyotyping was still discriminating of long-term prognosis. The presence of an abnormal nonhyperdiploid karyotype overrides all other clinical and laboratory parameters in predicting for a worse outcome on multivariate analysis (median survival 2.6 years, P = 0.001), suggesting that bortezomib used at relapse is better able to overcome adverse risk related to high tumor burden (as measured by the ISS) than adverse cytogenetics on conventional karyotyping. Metaphase karyotyping provides additional prognostic information on tumor kinetics where the presence of a normal diploid karyotype in the absence of any high-risk FISH markers correlated with superior survival and could act as a surrogate for lower plasma cell proliferation.

Purpose: Current histopathologic systems for classifying breast tumors require evaluation of multiple variables and are often associated with significant interobserver variability. Recent studies suggest that gene expression profiles may represent a promising alternative for clinical cancer classification. Here, we investigated the use of a customized microarray as a potential tool for clinical practice. Experimental Design: We fabricated custom 188-gene microarrays containing expression signatures for three breast cancer molecular subtypes [luminal/estrogen receptor (ER) positive, human epidermal growth factor receptor 2 (HER2), and “basaloid”], the Nottingham prognostic index (NPI-ES), and low histologic grade (TuM1). The reliability of these multiple-signature arrays (MSA) was tested in a prospective cohort of 165 patients with primary breast cancer. Results: The MSA-ER signature exhibited a high concordance of 90% with ER immunohistochemistry reported on diagnosis (P < 0.001). This remained unchanged at 89% (P < 0.001) when the immunohistochemistry was repeated using current laboratory standards. Expression of the HER2 signature showed a good correlation of 76% with HER2 fluorescence in situ hybridization (FISH; ratio ≥2.2; P < 0.001), which further improved to 89% when the ratio cutoff was raised to ≥5. A proportion of low-level FISH-amplified samples (ratio, 2.2-5) behaved comparably to FISH-negative samples by HER2 signature expression, HER2 quantitative reverse transcription-PCR, and HER2 immunohistochemistry. Luminal/ER+ tumors with high NPI-ES expression were associated with high NPI scores (P = 0.001), and luminal/ER+ TuM1-expressing tumors were significantly correlated with low histologic grade (P = 0.002) and improved survival outcome in an interim analysis (hazard ratio, 0.2; P = 0.019). Conclusion: The consistency of the MSA platform in an independent patient population suggests that custom microarrays could potentially function as an adjunct to standard immunohistochemistry and FISH in clinical practice.

Crude palm oil (CPO) is one of the vegetable oils that have potential for use as fuels for diesel engines. CPO is renewable, and is safe and easy to handle. However, at room temperature (30–32°C) CPO has a viscosity about 10 times higher than that of diesel. To lower CPO’s viscosity to the level of diesel’s viscosity, a heating temperature of at least 92 °C is needed. At this temperature, there is a concern that the close-fitting parts of the injection system might be affected. This study focused on finding out the effects of preheating of fuel on the injection system utilising a modified method of friction test, which involves injecting fuel outside the combustion chamber during motoring. Results show that preheating of CPO lowered CPO’s viscosity and provided smooth fuel flow, but did not affect the injection system, even heating up to 100 °C. Nevertheless, heating up to such a high temperature offered no benefits in terms of engine performance. However, heating is necessary for smooth flow and to avoid fuel filter clogging. Both can be achieved by heating CPO to 60 °C. Combustion analyses comparisons between CPO and diesel found that CPO produced a higher peak pressure of 6%, a shorter ignition delay of 2.6°, a lower maximum heat release rate and a longer combustion period. Over the entire load range, CPO combustion produced average CO and NO emissions that were 9.2 and 29.3% higher, respectively, compared with those from diesel combustion.

A blighted ovum diagnosed initially by ultrasound was determined to be a partial hydatidiform mole with a 69,XXY,t(2;6)(p12;q24)der(6)t(2;6)(p12;q24)pat karyotype by cytogenetic analysis. The triploid state arose through dispermy in which both spermatozoa carried rearranged chromosomes, one carrying a balanced translocation through alternate segregation and the other an unbalanced derivative chromosome 6 through adjacent 1 segregation. Segregation analysis of 7,000 spermatozoa from the father was performed with a three-color fluorescence in situ hybridization (FISH) protocol using alpha-satellite 6, telomeric 2p, and telomeric 6q probes. Segregation frequencies of normal and balanced products (alternate segregation), adjacent 1, adjacent 2, and 3:1 were 49.9%, 42.4%, 2.5%, and 4.2%, respectively. The high percentage of alternate segregation is consistent with the knowledge of their preferential outcome. However, the high incidence of adjacent 1 sperm highlights the abnormality risk. Alternate and adjacent 1 segregations (92.3%) accounted for the observed rearranged chromosomes in the triploid. The most viable imbalanced combination would be the one carrying the der(6) chromosome, but since the unbalanced segment comprises 3.6% of the haploid autosomal length (HAL), no risk of a viable imbalanced offspring is indicated. However, an increased likelihood of recurrent miscarriages is likely, and this is confirmed by the couple's two earlier miscarriages. Sperm segregation patterns of translocation carriers determined by FISH can help in ascertaining expected and unexpected karyotypes. The high frequency of adjacent 1 products shows that the presence of the additional derivative chromosome in the partial mole, though rare in occurrence, should be less surprising.

The results of a program of experiments set up to explore the post-failure behaviour of box section beams subjected to pure bending are presented. Rectangular and trapezoidal cross-section beams were loaded up to and beyond collapse in a four-point bending configuration. Load–deflection graphs were recorded and the details of the observed plastic collapse mechanisms were noted. Experimental collapse curves are compared with those derived from theoretical models of plastic collapse mechanisms based upon rigid–plastic theory.

Four intact human head-neck complexes were fixed between T1 and T2. Reflective target markers were inserted into the exposed cervical vertebra to document the 3D kinematics of the cervical spine and head. A dynamic pulse was delivered to the specimen using a mini-sled pendulum apparatus. Each specimen was examined in five different orientations and with two different pulses, for a total of tens trials. Cervical spine motion was recorded from two high-speed cine cameras. 3D reconstruction of the markers was computed using a triangulation software routine. Preliminary analysis of camera images show that the system is sufficient for high-speed analysis.

Variable structure control and adaptive control are two advanced control strategies for robot manipulator. However, the advantages and disadvantages of these two control strategies are not clear to engineers new in this field. This paper presents a comparative study of these two strategies on the Adept One SCARA robot. Four situations, namely the ideal situation, the situation where there is payload, the situation where there is joint friction and the situation where there is external disturbance are studied. Simulation studies reveal clearly the advantages and disadvantages of both schemes. >

A method for the numerical solution of the singular integral equations related to a vertical jet problem is developed. A jet flow from an aperture on the bottom of a large vessel fully filled with liquid, under gravity, has been studied. The problem has been programmed and run on a computer, and the computed results are shown.

The Riemann-Hilbert method in the upper half-plane is used to find a set of integral equations for the surface of a steady gravity wave of arbitrary amplitude in water of arbitrary depth over a smooth bottom. Numerical solutions are found by an iterative method. Values of parameters are tabulated and shown graphically. Agreement with the work of other authors is found to be very good.

We consider steady, plane, irrotational and incompressible flow in an infinite channel between two horizontal planes. The flow is formed by two equal but opposite uniform streams approaching from infinity and meeting over a horizontal slot, whence they emerge as a vertical jet under gravity. Conformal mapping is used, and the Riemann-Hilbert solution is obtained for a mixed boundary value problem in the upper half-plane. Numerical methods are introduced, and the problem programmed and run on a digital computer; results are obtained and some difficulties of the computing are discussed.

A thin-foil electron metallographic and electron diffraction study was made of hydrides in Zr-2.5wt%Nb alloy nuclear reactor pressure tubing containing 7–300 ppm by weight hydrogen. At the higher hydrogen contents and for slow cooling rates from above the solvus temperature, there was an increasing tendency to form the equilibrium δ-hydride (ZrH1.66) rather than the metastable γ-hydride (ZrH). The γ- and δ-hydrides differed in morphology; the γ-hydrides were either acicular or of flake form, whereas the δ-hydrides were larger and more blocky in appearance. The large δ-hydrides often formed in a radial through-wall orientation which could lead to through-wall cracks in the pressure tubes.

In this paper, we consider steady, supercritical, plane, incompressible and irrotational flow in a channel with an obstacle of polygonal shape placed on the bottom. The solution is based on the combined use of a conformal mapping and the Riemann-Hilbert solution of a mixed boundary-value problem in the upper half plane. Numerical methods are introduced, and numerical solutions for some symmetric examples are presented. Numerical checks are applied showing good agreement. A comparison with the solution of the corresponding linearised problem shows that there are large differences, and contrary behaviour of the shape of the free surface as the Froude number is varied.