Prevalence and analysis of t(14;18) and t(11;14) chromosomal translocations in healthy Indian population

Hematopoietic malignancies like leukemia and lymphoma are characteristically associated with various chromosomal translocations. Follicular lymphoma (FL) and mantle cell lymphoma (MCL) are two subtypes of non-Hodgkin's lymphoma which possess t(14;18) and t(11;14) translocations, respectively. The incidence of FL and MCL is higher in the western countries as compared to India. Interestingly, the associated translocations are also found in healthy individuals in western population, which is 50-80% for t(14;18), whereas t(11;14) occurs at a very low frequency. However, there are no studies to explore thes translocations in healthy Indian population, which could explain the lower incidence of FL and MCL. We employed Southern hybridization following nested PCR to detect above translocations in healthy individuals from India. Our results suggest that this assay can detect one t(14;18) translocation event in up to 10(7) normal cells where as one t(11;14) in 10(8) normal cells. According to our results, 87 out of 253 individuals carry t(14;18) indicating 34% prevalence in the population. The presence of this translocation was also detectable at the transcript level. Although, no gender-based difference was observed, an age-dependent increase in the prevalence of translocation was found in adults. However, even after studying 210 people, we could not detect any t(11;14) translocation, indicating that it is uncommon in Indian population. These results suggest that lower incidence of FL and MCL in India could be attributed to lower prevalence of these translocations in healthy individuals.

Multicarrier conduction and Boltzmann transport analysis of heavy hole mobility in HgCdTe near room temperature

Magnetotransport measurements in pulsed fields up to 15 T have been performed on mercury cadmium telluride (Hg1-xCdxTe, x similar to 0.2) bulk as well as liquid phase epitaxially grown samples to obtain the resistivity and conductivity tensors in the temperature range 220-300 K. Mobilities and densities of various carriers participating in conduction have been extracted using both conventional multicarrier fitting (MCF) and mobility spectrum analysis. The fits to experimental data, particularly at the highest magnetic fields, were substantially improved when MCF is applied to minimize errors simultaneously on both resistivity and conductivity tensors. The semiclassical Boltzmann transport equation has been solved without using adjustable parameters by incorporating the following scattering mechanisms to fit the mobility: ionized impurity, polar and nonpolar optical phonons, acoustic deformation potential, and alloy disorder. Compared to previous estimates based on the relaxation time approximation with outscattering only, polar optical scattering and ionized impurity scattering limited mobilities are shown to be larger due to the correct incorporation of the inscattering term taking into account the overlap integrals in the valence band.

Inter-helical Interactions in Membrane Proteins: Analysis Based on the Local Backbone Geometry and the Side Chain Interactions

The availability of a significant number of the Structures of helical membrane proteins has prompted us to investigate the mode of helix-helix packing. In the present study, we have considered a dataset of alpha-helical membrane proteins representing Structures solved from all the known superfamilies. We have described the geometry of all the helical residues in terms of local coordinate axis at the backbone level. Significant inter-helical interactions have been considered as contacts by weighing the number of atom-atom contacts, including all the side-chain atoms. Such a definition of local axis and the contact criterion has allowed us to investigate the inter-helical interaction in a systematic and quantitative manner. We show that a single parameter (designated as alpha), which is derived from the parameters representing the Mutual orientation of local axes, is able to accurately Capture the details of helix-helix interaction. The analysis has been carried Out by dividing the dataset into parallel, anti-parallel, and perpendicular orientation of helices. The study indicates that a specific range of alpha value is preferred for interactions among the anti-parallel helices. Such a preference is also seen among interacting residues of parallel helices, however to a lesser extent. No such preference is seen in the case of perpendicular helices, the contacts that arise mainly due to the interaction Of Surface helices with the end of the trans-membrane helices. The Study Supports the prevailing view that the anti-parallel helices are well packed. However, the interactions between helices of parallel orientation are non-trivial. The packing in alpha-helical membrane proteins, which is systematically and rigorously investigated in this study, may prove to be useful in modeling of helical membrane proteins.

Genetic analysis of structural brain connectivity using DICCCOL models of diffusion MRI in 522 twins

Genetic and environmental factors affect white matter connectivity in the normal brain, and they also influence diseases in which brain connectivity is altered. Little is known about genetic influences on brain connectivity, despite wide variations in the brain's neural pathways. Here we applied the 'DICCCOL' framework to analyze structural connectivity, in 261 twin pairs (522 participants, mean age: 21.8 y ± 2.7SD). We encoded connectivity patterns by projecting the white matter (WM) bundles of all 'DICCCOLs' as a tracemap (TM). Next we fitted an A/C/E structural equation model to estimate additive genetic (A), common environmental (C), and unique environmental/error (E) components of the observed variations in brain connectivity. We found 44 'heritable DICCCOLs' whose connectivity was genetically influenced (α2>1%); half of them showed significant heritability (α2>20%). Our analysis of genetic influences on WM structural connectivity suggests high heritability for some WM projection patterns, yielding new targets for genome-wide association studies.

Correction of Ocular Artifacts in EEG Recordings using Empirical Mode Decomposition

EEG recordings are often contaminated with ocular artifacts such as eye blinks and eye movements. These artifacts may obscure underlying brain activity in the electroencephalogram (EEG) data and make the analysis of the data difficult. In this paper, we explore the use of empirical mode decomposition (EMD) based filtering technique to correct the eye blinks and eye movementartifacts in single channel EEG data. In this method, the single channel EEG data containing ocular artifact is segmented such that the artifact in each of the segment is considered as some type of slowly varying trend in the dataand the EMD is used to remove the trend. The filtering is done using partial reconstruction from components of the decomposition. The method is completely data dependent and hence adaptive and nonlinear. Experimental results are provided to check the applicability of the method on real EEG data and the results are quantified using power spectral density (PSD) as a measure. The method has given fairlygood results and does not make use of any preknowledge of artifacts or the EEG data used.

Reliability Analysis of Torsional MEMS Varactor

This paper discusses reliability issues in torsional MEMS varactor. Self-actuation due to high ac signals is analyzed, and solutions are proposed. The mode of failure at high actuation voltages is analyzed and established through experiments. Issues like stiction due to high voltages and effect of high residual stress are studied experimentally.

Stiff-String Basis Functions for Vibration Analysis of High Speed Rotating Beams

A new rotating beam finite element is developed in which the basis functions are obtained by the exact solution of the governing static homogenous differential equation of a stiff string, which results from an approximation in the rotating beam equation. These shape functions depend on rotation speed and element position along the beam and account for the centrifugal stiffening effect. Using this new element and the Hermite cubic finite element, a convergence study of natural frequencies is performed, and it is found that the new element converges much more rapidly than the conventional Hermite cubic element for the first two modes at higher rotation speeds. The new element is also applied for uniform and tapered rotating beams to determine the natural frequencies, and the results compare very well with the published results given in the literature.

Optimal configurations of active fiber composites based on asymptotic torsional analysis - art. no. 641413

Active Fiber Composites (AFC) possess desirable characteristics over a wide range of smart structure applications, such as vibration, shape and flow control as well as structural health monitoring. This type of material, capable of collocated actuation and sensing, call be used in smart structures with self-sensing circuits. This paper proposes four novel applications of AFC structures undergoing torsion: sensors and actuators shaped as strips and tubes; and concludes with a preliminary failure analysis. To enable this, a powerful mathematical technique, the Variational Asymptotic Method (VAM) was used to perform cross-sectional analyses of thin generally anisotropic AFC beams. The resulting closed form expressions have been utilized in the applications presented herein.

Proteomic identification of putative microRNA394 target genes in Arabidopsis thaliana identifies MLP family members critical for normal development

Expression of the F-Box protein Leaf Curling Responsiveness (LCR) is regulated by microRNA, miR394, and alterations to this interplay in Arabidopsis thaliana produce defects in leaf polarity and shoot apical meristem (SAM) organisation. Although the miR394-LCR node has been documented in Arabidopsis, the identification of proteins targeted by LCR F-box itself has proven problematic. Here, a proteomic analysis of shoot apices from plants with altered LCR levels identified a member of the Major Latex Protein (MLP) family gene as a potential LCR F-box target. Bioinformatic and molecular analyses also suggested that other MLP family members are likely to be targets for this post-translational regulation. Direct interaction between LCR F-Box and MLP423 was validated. Additional MLP members had reduction in protein accumulation, in varying degrees, mediated by LCR F-Box. Transgenic Arabidopsis lines, in which MLP28 expression was reduced through an artificial miRNA technology, displayed severe developmental defects, including changes in leaf patterning and morphology, shoot apex defects, and eventual premature death. These phenotypic characteristics resemble those of Arabidopsis plants modified to over-express LCR. Taken together, the results demonstrate that MLPs are driven to degradation by LCR, and indicate that MLP gene family is target of miR394-LCR regulatory node, representing potential targets for directly post-translational regulation mediated by LCR F-Box. In addition, MLP28 family member is associated with the LCR regulation that is critical for normal Arabidopsis development.

Integrative functional genomics analysis of sustained polyploidy phenotypes in breast cancer cells identifies an oncogenic profile for GINS2

Aneuploidy is among the most obvious differences between normal and cancer cells. However, mechanisms contributing to development and maintenance of aneuploid cell growth are diverse and incompletely understood. Functional genomics analyses have shown that aneuploidy in cancer cells is correlated with diffuse gene expression signatures and that aneuploidy can arise by a variety of mechanisms, including cytokinesis failures, DNA endoreplication and possibly through polyploid intermediate states. Here, we used a novel cell spot microarray technique to identify genes with a loss-of-function effect inducing polyploidy and/or allowing maintenance of polyploid cell growth of breast cancer cells. Integrative genomics profiling of candidate genes highlighted GINS2 as a potential oncogene frequently overexpressed in clinical breast cancers as well as in several other cancer types. Multivariate analysis indicated GINS2 to be an independent prognostic factor for breast cancer outcome (p = 0.001). Suppression of GINS2 expression effectively inhibited breast cancer cell growth and induced polyploidy. In addition, protein level detection of nuclear GINS2 accurately distinguished actively proliferating cancer cells suggesting potential use as an operational biomarker.

Analysis of continuous beams—a three dimensional elasticity solution

A three dimensional elasticity solution for the analysis of beams continuous over an infinite number of equally spaced supports has been given. The beam has been subjected to normal tractions on its two opposite faces and these loads are identical over each span. The other two faces are traction free. Numerical results have been given for different cases when the beam is loaded on its bottom face. The results obtained have been compared with the results of two dimensional elasticity solution.

Raman spectrum of guanidinium aluminium sulphate hexahydrate

The Raman spectrum of guanidinium aluminium sulphate hexahydrate also known as ‘GASH’ which is a ferro-electric crystal and has strong hydrogen bonds has been recorded. 38 Raman lines have been identified in the spectra of GASH. The O-H stretching mode is found to be very much influenced by the hydrogen bond and they appear over a widely extended region from 2240–3600 cm.−1 It can therefore be concluded that all the O-H bonds are hydrogen bonded and some of them are quite strong. The Raman lines due to the N-H vibrations appear with the normal frequency shifts indicating thereby that N-H bonds are not hydrogen bonded. These conclusions are fully supported by the results obtained from the X-ray crystal structure analysis of GASH. The principal vibrations of the Al-(OH2)6 groups have also been identified.

Elastic stress analysis of jointed half-planes

Using a Fourier-integral approach, the problem of stress analysis in a composite plane consisting of two half-planes of different elastic properties rigidly joined along their boundaries has been solved. The analysis is done for a force acting in one of the half-planes for both cases when the force acts parallel and perpendicular to the interface. As a particular case, the interface stresses are evaluated when the interface is smooth. Some properties of the normal stress at the interface are discussed both for plane stress and plane strain conditions.

Effect of vibration on heat transfer from a horizontal cylinder to a normal air stream

The effect of vibration on heat transfer from a horizontal copper cylinder, 0.344 in. in diameter and 6 in. long, was investigated. The cylinder was placed normal to an air stream and was sinusoidally vibrated in a direction perpendicular to the direction of the air stream. The flow velocity varied from 19 ft/s to 92 ft/s; the double amplitude of vibration from 0.75 cm to 3.2 cm, and the frequency of vibration from 200 to 2800 cycles/min. A transient technique was used to determine the heat transfer coefficients. The experimental data in the absence of vibration is expressed by NNu = 0.226 NRe0.6 in the range 2500 < NRe < 15 000. By imposing vibrational velocities as high as 20 per cent of the flow velocity, no appreciable change in the heat transfer coefficient was observed. An analysis using the resultant of the vibration and the flow velocity explains the observed phenomenon.

Open Access to Scientific Publications – An Analysis of the Barriers to Change?

One of the effects of the Internet is that the dissemination of scientific publications in a few years has migrated to electronic formats. The basic business practices between libraries and publishers for selling and buying the content, however, have not changed much. In protest against the high subscription prices of mainstream publishers, scientists have started Open Access (OA) journals and e-print repositories, which distribute scientific information freely. Despite widespread agreement among academics that OA would be the optimal distribution mode for publicly financed research results, such channels still constitute only a marginal phenomenon in the global scholarly communication system. This paper discusses, in view of the experiences of the last ten years, the many barriers hindering a rapid proliferation of Open Access. The discussion is structured according to the main OA channels; peer-reviewed journals for primary publishing, subject- specific and institutional repositories for secondary parallel publishing. It also discusses the types of barriers, which can be classified as consisting of the legal framework, the information technology infrastructure, business models, indexing services and standards, the academic reward system, marketing, and critical mass.