JK1 (FAM134B) gene and colorectal cancer : a pilot study on the gene copy number alterations and correlations with clinicopathological parameters

AIMS The aims of the study are to characterize changes in JK-1 (FAM134B) at the DNA level in colorectal adenocarcinoma and adenoma and exploring the possible correlations with clinical and pathological features. METHOD JK-1 gene DNA copy number changes were studied in 211 colorectal carcinomas, 32 colorectal adenoma and 20 colorectal non-cancer colorectal tissue samples by real-time quantitative polymerase chain reaction. The results were correlated with clinical and pathological parameters. RESULTS Colorectal adenomas were more likely to be amplified than deleted with regard to JK-1 (FAM134B) DNA copy number change. The copy number level of JK-1 (FAM134B) DNA in colorectal adenocarcinomas was significantly lower in comparison to colorectal adenomas. Changes in JK-1 (FAM134B) DNA copy number were associated with histological subtypes, and cancer stage. Lower copy numbers were associated with higher tumor stage, lymph node stage and overall pathological stage of cancer. Conversely, higher DNA copy numbers were detected more often in the mucinous adenocarcinoma. CONCLUSIONS This is the first study showing significant correlations of the JK-1 (FAM134B) gene copy number alterations with clinical and pathological features in a large cohort of pre-invasive and invasive colorectal malignancies. The changes in DNA copy number associated with progression of colorectal malignancies reflect that JK-1 (FAM134B) gene could play a role in controlling some steps in development of the invasive phenotypes.

Large arrays and networks of carbon nanotubes : morphology control by process parameters

Large arrays and networks of carbon nanotubes, both single- and multi-walled, feature many superior properties which offer excellent opportunities for various modern applications ranging from nanoelectronics, supercapacitors, photovoltaic cells, energy storage and conversation devices, to gas- and biosensors, nanomechanical and biomedical devices etc. At present, arrays and networks of carbon nanotubes are mainly fabricated from the pre-fabricated separated nanotubes by solution-based techniques. However, the intrinsic structure of the nanotubes (mainly, the level of the structural defects) which are required for the best performance in the nanotube-based applications, are often damaged during the array/network fabrication by surfactants, chemicals, and sonication involved in the process. As a result, the performance of the functional devices may be significantly degraded. In contrast, directly synthesized nanotube arrays/networks can preclude the adverse effects of the solution-based process and largely preserve the excellent properties of the pristine nanotubes. Owing to its advantages of scale-up production and precise positioning of the grown nanotubes, catalytic and catalyst-free chemical vapor depositions (CVD), as well as plasma-enhanced chemical vapor deposition (PECVD) are the methods most promising for the direct synthesis of the nanotubes.

Correlation between BRAF mutation and the clinicopathological parameters in papillary thyroid carcinoma with particular reference to follicular variant

Mutation of the BRAF gene is common in thyroid cancer. Follicular variant of papillary thyroid carcinoma is a variant of papillary thyroid carcinoma that has created continuous diagnostic controversies among pathologists. The aims of this study are to (1) investigate whether follicular variant of papillary thyroid carcinoma has a different pattern of BRAF mutation than conventional papillary thyroid carcinoma in a large cohort of patients with typical features of follicular variant of papillary thyroid carcinoma and (2) to study the relationship of clinicopathological features of papillary thyroid carcinomas with BRAF mutation. Tissue blocks from 76 patients with diagnostic features of papillary thyroid carcinomas (40 with conventional type and 36 with follicular variant) were included in the study. From these, DNA was extracted and BRAF V600E mutations were detected by polymerase chain reaction followed by restriction enzyme digestion and sequencing of exon 15. Analysis of the data indicated that BRAF V600E mutation is significantly more common in conventional papillary thyroid carcinoma (58% versus 31%, P = .022). Furthermore, the mutation was often noted in female patients (P = .017), in high-stage cancers (P = .034), and in tumors with mild lymphocytic thyroiditis (P = .006). We concluded that follicular variant of papillary thyroid carcinoma differs from conventional papillary thyroid carcinoma in the rate of BRAF mutation. The results of this study add further information indicating that mutations in BRAF play a role in thyroid cancer development and progression.

Relation between charge carrier mobility and lifetime in organic photovoltaics

The relationship between charge carrier lifetime and mobility in a bulk heterojunction based organic solar cell, utilizing diketopyrrolopyrole- naphthalene co-polymer and PC71BM in the photoactive blend layer, is investigated using the photoinduced charge extraction by linearly increasing voltage technique. Light intensity, delay time, and temperature dependent experiments are used to quantify the charge carrier mobility and density as well as the temperature dependence of both. From the saturation of photoinduced current at high laser intensities, it is shown that Langevin-type bimolecular recombination is present in the studied system. The charge carrier lifetime, especially in Langevin systems, is discussed to be an ambiguous and unreliable parameter to determine the performance of organic solar cells, because of the dependence of charge carrier lifetime on charge carrier density, mobility, and type of recombination. It is revealed that the relation between charge mobility (μ) and lifetime (τ) is inversely proportional, where the μτ product is independent of temperature. The results indicate that in photovoltaic systems with Langevin type bimolecular recombination, the strategies to increase the charge lifetime might not be beneficial because of an accompanying reduction in charge carrier mobility. Instead, the focus on non-Langevin mechanisms of recombination is crucial, because this allows an increase in the charge extraction rate by improving the carrier lifetime, density, and mobility simultaneously. © 2013 AIP Publishing LLC.

Application of GIS in understanding and communicating interaction between environmental parameters and sewer blockages

Sewer main chokes (blockages) are a key performance indicator for Australian water utilities. Blockages caused by tree roots often result in wastewater overflow posing an environmental and health risk and also requiring service interruptions to repair asset. The purpose of the research project outlined in this paper was to understand the role of environmental parameters, in particular soil type and tree density, in determining the propensity of a sewer to become blocked. The paper demonstrates the application of spatial analysis to inform and communicate the results of the analysis. GIS was used to explore the relationship between tree density and previously recorded sewer blockages for a Melbourne utility. Initial results from the research reveal a relationship between increased tree densities and occurrence of sewer blockages. An improved understanding of the influence of environmental parameters on the inherent risk of sewer blockage will enable asset managers to identify those assets requiring proactive management in order to minimise service interruptions, repairs and environmental impacts.

Online estimation of Allan variance parameters

A new online method is presented for estimation of the angular randomwalk and rate randomwalk coefficients of inertial measurement unit gyros and accelerometers. In the online method, a state-space model is proposed, and recursive parameter estimators are proposed for quantities previously measured from offline data techniques such as the Allan variance method. The Allan variance method has large offline computational effort and data storage requirements. The technique proposed here requires no data storage and computational effort of approximately 100 calculations per data sample.

Reduced complexity on-line estimation of hidden Markov model parameters

In this paper we propose and study low complexity algorithms for on-line estimation of hidden Markov model (HMM) parameters. The estimates approach the true model parameters as the measurement noise approaches zero, but otherwise give improved estimates, albeit with bias. On a nite data set in the high noise case, the bias may not be signi cantly more severe than for a higher complexity asymptotically optimal scheme. Our algorithms require O(N3) calculations per time instant, where N is the number of states. Previous algorithms based on earlier hidden Markov model signal processing methods, including the expectation-maximumisation (EM) algorithm require O(N4) calculations per time instant.

On-line estimation of Allan variance parameters

A new online method is presented for estimation of the angular random walk and rate random walk coefficients of IMU (inertial measurement unit) gyros and accelerometers. The online method proposes a state space model and proposes parameter estimators for quantities previously measured from off-line data techniques such as the Allan variance graph. Allan variance graphs have large off-line computational effort and data storage requirements. The technique proposed here requires no data storage and computational effort of O(100) calculations per data sample.

Porosity: Establishing the relationship between drying parameters and dried food quality [SpringerBriefs in Food, Health, and Nutrition]

The preservation technique of drying offers a significant increase in the shelf life of food materials, along with the modification of quality attributes due to simultaneous heat and mass transfer. Variations in porosity are just one of the microstructural changes that take place during the drying of most food materials. Some studies found that there may be a relationship between porosity and the properties of dried foods. However, no conclusive relationship has yet been established in the literature. This paper presents an overview of the factors that influence porosity, as well as the effects of porosity on dried food quality attributes. The effect of heat and mass transfer on porosity is also discussed along with porosity development in various drying methods. After an extensive review of the literature concerning the study of porosity, it emerges that a relationship between process parameters, food qualities, and sample properties can be established. Therefore, we propose a hypothesis of relationships between process parameters, product quality attributes, and porosity.

Melanoma cell colony expansion parameters revealed by approximate Bayesian computation

In vitro studies and mathematical models are now being widely used to study the underlying mechanisms driving the expansion of cell colonies. This can improve our understanding of cancer formation and progression. Although much progress has been made in terms of developing and analysing mathematical models, far less progress has been made in terms of understanding how to estimate model parameters using experimental in vitro image-based data. To address this issue, a new approximate Bayesian computation (ABC) algorithm is proposed to estimate key parameters governing the expansion of melanoma cell (MM127) colonies, including cell diffusivity, D, cell proliferation rate, λ, and cell-to-cell adhesion, q, in two experimental scenarios, namely with and without a chemical treatment to suppress cell proliferation. Even when little prior biological knowledge about the parameters is assumed, all parameters are precisely inferred with a small posterior coefficient of variation, approximately 2–12%. The ABC analyses reveal that the posterior distributions of D and q depend on the experimental elapsed time, whereas the posterior distribution of λ does not. The posterior mean values of D and q are in the ranges 226–268 µm2h−1, 311–351 µm2h−1 and 0.23–0.39, 0.32–0.61 for the experimental periods of 0–24 h and 24–48 h, respectively. Furthermore, we found that the posterior distribution of q also depends on the initial cell density, whereas the posterior distributions of D and λ do not. The ABC approach also enables information from the two experiments to be combined, resulting in greater precision for all estimates of D and λ.