Identification of a core promoter and a novel isoform of the human TSCI gene transcript and structural comparison with mouse homolog

Tuberous sclerosis complex (TSC) is an autosomal dominant disorder with loci on chromosome 9q34.12 (TSC1) and chromosome 16p13.3 (TSC2). Genes for both loci have been isolated and characterized. The promoters of both genes have not been characterized so far and little is known about the regulation of these genes. This study reports the characterization of the human TSC1 promoter region for the first time. We have identified a novel alternative isoform in the 5' untranslated region (UTR) of the TSC1 gene transcript involving exon 1. Alternative isoforms in the 5' UTR of the mouse Tsc1 gene transcript involving exon I and exon 2 have also been identified. We have identified three upstream open reading frames (uORFs) in the 5' UTR of the TSC1/Tsc1 gene. A comparative study of the 5' UTR of TSC1/Tsc1 gene has revealed that there is a high degree of similarity not only in the sequence but also in the splicing pattern of both human and mouse TSC1 genes. We have used PCR methodology to isolate approximately 1.6 kb genomic DNA 5' to the TSC1 cDNA. This sequence has directed a high level of expression of luciferase activity in both HeLa and HepG2 cells. Successive 5' and 3' deletion analysis has suggested that a -587 bp region, from position +77 to -510 from the transcription start site (TSS), contains the promoter activity. Interestingly, this region contains no consensus TATA box or CAAT box. However, a 521-bp fragment surrounding the TSS exhibits the characteristics of a CpG island which overlaps with the promoter region. The identification of the TSC1 promoter region will help in designing a suitable strategy to identify mutations in this region in patients who do not show any mutations in the coding regions. It will also help to study the regulation of the TSC1 gene and its role in tumorigenesis. (C) 2003 Elsevier B.V. All rights reserved.

Novel Algorithm for estimation of Swell Pressure of Fine Grained Soils Based on Diffuse Double Layer (DDL) Theory

Use of engineered landfills for the disposal of industrial wastes is currently a common practice. Bentonite is attracting a greater attention not only as capping and lining materials in landfills but also as buffer and backfill materials for repositories of high-level nuclear waste around the world. In the design of buffer and backfill materials, it is important to know the swelling pressures of compacted bentonite with different electrolyte solutions. The theoretical studies on swell pressure behaviour are all based on Diffuse Double Layer (DDL) theory. To establish a relation between the swell pressure and void ratio of the soil, it is necessary to calculate the mid-plane potential in the diffuse part of the interacting ionic double layers. The difficulty in these calculations is the elliptic integral involved in the relation between half space distance and mid plane potential. Several investigators circumvented this problem using indirect methods or by using cumbersome numerical techniques. In this work, a novel approach is proposed for theoretical estimations of swell pressures of fine-grained soil from the DDL theory. The proposed approach circumvents the complex computations in establishing the relationship between mid-plane potential and diffused plates’ distances in other words, between swell pressure and void ratio.

Geotechnical Characterization of Some Indian Bentonites for their Use as Buffer Material in Geological Repository

The present study examines the geotechnical properties of Indian bentonite clays for their suitability as buffer material in deep geological repository for high-level nuclear wastes. The bentonite samples are characterized for index properties, compaction, hydraulic conductivity and swelling characteristics. Evaluation of geotechnical properties of the compacted bentonite-sand admixtures, from parts of NW India reveals swelling potentials and hydraulic conductivities in the range of 55 % - 108 % and 1.2 X 10 –10 cm/s to 5.42x 10 –11 cm/s respectively. Strong correlation was observed between ESP (exchangeable sodium percentage) and liquid limit/swell potential of tested specimens. Relatively less well-defined trends emerged between ESP and swell pressure/hydraulic conductivity. The Barmer-1 bentonite despite possessing relatively lower montmorillonite content of 68 %, developed higher Atterberg limit and swell potential, and exhibited comparable swelling pressure and hydraulic conductivity as other bentonites with higher montmorillonite contents (82 to 86 %). The desirable geotechnical properties of Barmer clay as a buffer material is attributed to its large ESP (63 %) and, EMDD (1.17 Mg/m3) attained at the experimental compactive stress(5 MPa).

Scan cell reordering to minimize peak power during test cycle: A graph theoretic approach

Scan circuit is widely practiced DFT technology. The scan testing procedure consist of state initialization, test application, response capture and observation process. During the state initialization process the scan vectors are shifted into the scan cells and simultaneously the responses captured in last cycle are shifted out. During this shift operation the transitions that arise in the scan cells are propagated to the combinational circuit, which inturn create many more toggling activities in the combinational block and hence increases the dynamic power consumption. The dynamic power consumed during scan shift operation is much more higher than that of normal mode operation.

INTACTE: An Interconnect Area, Delay, and Energy Estimation Tool for Microarchitectural Explorations

Prior work on modeling interconnects has focused on optimizing the wire and repeater design for trading off energy and delay, and is largely based on low level circuit parameters. Hence these models are hard to use directly to make high level microarchitectural trade-offs in the initial exploration phase of a design. In this paper, we propose INTACTE, a tool that can be used by architects toget reasonably accurate interconnect area, delay, and power estimates based on a few architecture level parameters for the interconnect such as length, width (in number of bits), frequency, and latency for a specified technology and voltage. The tool uses well known models of interconnect delay and energy taking into account the wire pitch, repeater size, and spacing for a range of voltages and technologies.It then solves an optimization problem of finding the lowest energy interconnect design in terms of the low level circuit parameters, which meets the architectural constraintsgiven as inputs. In addition, the tool also provides the area, energy, and delay for a range of supply voltages and degrees of pipelining, which can be used for micro-architectural exploration of a chip. The delay and energy models used by the tool have been validated against low level circuit simulations. We discuss several potential applications of the tool and present an example of optimizing interconnect design in the context of clustered VLIW architectures. Copyright 2007 ACM.

Analysis of a hybrid noise control system for a duct

This letter proposes the combination of a passive muffler and an active noise control system for the control of very high‐level noise in ducts used with large industrial fans and similar equipment. The analysis of such a hybrid system is presented making use of electroacoustic analogies and the transfer matrix method. It turns out that a passive muffler upstream of the input microphone can indeed lower the acoustic pressure and, hence, the power requirement of the auxiliary source. The parameter that needs to be optimized (or maximized) for this purpose is a certain velocity ratio that can readily be evaluated in a closed form, making it more or less straightforward to synthesize the configuration of an effective passive muffler to go with the active noise control system.

“Post silicon debug of SOC designs”

Continuous advances in VLSI technology have made implementation of very complicated systems possible. Modern System-on -Chips (SoCs) have many processors, IP cores and other functional units. As a result, complete verification of whole systems before implementation is becoming infeasible; hence it is likely that these systems may have some errors after manufacturing. This increases the need to find design errors in chips after fabrication. The main challenge for post-silicon debug is the observability of the internal signals. Post-silicon debug is the problem of determining what's wrong when the fabricated chip of a new design behaves incorrectly. This problem now consumes over half of the overall verification effort on large designs, and the problem is growing worse.Traditional post-silicon debug methods concentrate on functional parts of systems and provide mechanisms to increase the observability of internal state of systems. Those methods may not be sufficient as modern SoCs have lots of blocks (processors, IP cores, etc.) which are communicating with one another and communication is another source of design errors. This tutorial will be provide an insight into various observability enhancement techniques, on chip instrumentation techniques and use of high level models to support the debug process targeting both inside blocks and communication among them. It will also cover the use of formal methods to help debug process.

Enhancing Speedup in Network Processing Applications by Exploiting Instruction Reuse with Flow Aggregation

Instruction reuse is a microarchitectural technique that improves the execution time of a program by removing redundant computations at run-time. Although this is the job of an optimizing compiler, they do not succeed many a time due to limited knowledge of run-time data. In this paper we examine instruction reuse of integer ALU and load instructions in network processing applications. Specifically, this paper attempts to answer the following questions: (1) How much of instruction reuse is inherent in network processing applications?, (2) Can reuse be improved by reducing interference in the reuse buffer?, (3) What characteristics of network applications can be exploited to improve reuse?, and (4) What is the effect of reuse on resource contention and memory accesses? We propose an aggregation scheme that combines the high-level concept of network traffic i.e. "flows" with a low level microarchitectural feature of programs i.e. repetition of instructions and data along with an architecture that exploits temporal locality in incoming packet data to improve reuse. We find that for the benchmarks considered, 1% to 50% of instructions are reused while the speedup achieved varies between 1% and 24%. As a side effect, instruction reuse reduces memory traffic and can therefore be considered as a scheme for low power.

Multi-decadal variation of the net downward shortwave radiation over south Asia: The solar dimming effect

The solar radiation flux at the earth's surface has gone through decadal changes of decreasing and increasing trends over the globe. These phenomena known as dimming and brightening, respectively, have attracted the scientific interest in relation to the changes in radiative balance and climate. Despite the interest in the solar dimming/brightening phenomenon in various parts of the world, south Asia has not attracted great scientific attention so far. The present work uses the net downward shortwave radiation (NDSWR) values derived from satellites (Modern Era Retrospective-analysis for Research and Applications, MERRA 2D) in order to examine the multi-decadal variations in the incoming solar radiation over south Asia for the period of 1979-2004. From the analysis it is seen that solar dimming continues over south Asia with a trend of -0.54 Wm(-2) yr(-1). Assuming clear skies an average decrease of -0.05 Wm(-2)yr(-1) in NDSWR was observed, which is attributed to increased aerosol emissions over the region. There is evidence that the increase in cloud optical depth plays the major role for the solar dimming over the area. The cloud optical depth (MERRA retrievals) has increased by 10.7% during the study period, with the largest increase to be detected for the high-level (atmospheric pressure P < 400 hPa) clouds (31.2%). Nevertheless, the decrease in solar radiation and the role of aerosols and clouds exhibit large monthly and seasonal variations directly affected by the local monsoon system, the anthropogenic and natural aerosol emissions. All these aspects are examined in detail aiming at shedding light into the solar dimming phenomenon over a densely populated area. (C) 2011 Elsevier Ltd. All rights reserved.

Data-resolution based optimization of the data-collection strategy for near infrared diffuse optical tomography

Purpose: To optimize the data-collection strategy for diffuse optical tomography and to obtain a set of independent measurements among the total measurements using the model based data-resolution matrix characteristics. Methods: The data-resolution matrix is computed based on the sensitivity matrix and the regularization scheme used in the reconstruction procedure by matching the predicted data with the actual one. The diagonal values of data-resolution matrix show the importance of a particular measurement and the magnitude of off-diagonal entries shows the dependence among measurements. Based on the closeness of diagonal value magnitude to off-diagonal entries, the independent measurements choice is made. The reconstruction results obtained using all measurements were compared to the ones obtained using only independent measurements in both numerical and experimental phantom cases. The traditional singular value analysis was also performed to compare the results obtained using the proposed method. Results: The results indicate that choosing only independent measurements based on data-resolution matrix characteristics for the image reconstruction does not compromise the reconstructed image quality significantly, in turn reduces the data-collection time associated with the procedure. When the same number of measurements (equivalent to independent ones) are chosen at random, the reconstruction results were having poor quality with major boundary artifacts. The number of independent measurements obtained using data-resolution matrix analysis is much higher compared to that obtained using the singular value analysis. Conclusions: The data-resolution matrix analysis is able to provide the high level of optimization needed for effective data-collection in diffuse optical imaging. The analysis itself is independent of noise characteristics in the data, resulting in an universal framework to characterize and optimize a given data-collection strategy. (C) 2012 American Association of Physicists in Medicine. http://dx.doi.org/10.1118/1.4736820]

ZnO/Poly(3,4-ethylenedioxythiophene) Poly(styrenesulfonate) Based Ultraviolet and Visible Photodetectors: Role of Defects

Here, we report the ZnO/poly(3,4-ethylenedioxythiophene) poly(styrenesulfonate) (PEDOT:PSS) based photodetectors that can response to ultraviolet as well as visible light. The temporal response of the heterostructures for various excitations in the ultraviolet (UV) and visible range are performed. The time constants are found to be excitation-dependent, the response to visible light is better as compared to UV. The reason behind the better response to UV light is the high level of defects present in ZnO as confirmed by the photoluminescence (PL) measurements. This is corroborated by the time resolved fluorescence (TRF) measurements which provides sufficient information behind the slow response time under the UV excitations. The possible explanation being the non-radiative recombinations occurring due to the traps or impurities present in the film which slows down the photoresponse.

Characterization and iodide adsorption behaviour of HDPY+ modified bentonite

Owing to its favourable physical, chemical and rheological properties, densely compacted bentonite or bentonite-sand mix is considered as a suitable buffer material in deep geological repositories to store high level nuclear waste. Iodine-129 is one of the significant nuclides in the high level waste owing to its long half life and poor sorption onto most geologic media. Bentonite by virtue of negatively charged surface has negligible affinity to retain iodide ions. As organo-bentonites are known to retain iodide ions, the present study characterizes hexadecylpyridinium chloride (HDPyCl.H2O) treated bentonite from Barmer India (referred as HDPy+B) for physico-chemical properties, engineering properties and the iodide adsorption behavior of the organo clay. Batch experiments revealed that HDPy+ ions are largely retained (94 % retention) via cation exchange; the ion-exchange process neutralizes the negative surface charge and bridges clay particles leading to reduction in Atterberg limits, clay content and sediment volume. The organo clay retains iodide by Coulombic attraction (at primary sites) and anion exchange (at secondary sites). The free-energy change (Delta G (o) = -25.5 kJ/mol) value indicated that iodide retention by organo clay is favored physical adsorption process. Iodide adsorption capacity of organo clay decreased significantly (85-100 %) on dilution with 50-80 % bentonite. On the other hand, dilution of bentonite with 50 % organo clay caused 58 % reduction in swell potential and 21 % reduction in swell pressure.

Shola habitats on sky islands: status of research on montane forests and grasslands in southern India

The Shola habitat on the high elevation sky islands of the Western Ghats in southern India is a unique habitat. Although this habitat hosts a disproportionately high level of endemism and is threatened by anthropogenic modifications, it has received little research attention. We compiled publications of research conducted in this habitat from scientific databases and the grey literature to examine trends in publication. For a quantitative summary, all publications were classified according to the taxa of research and the broad topic of research. We identified 279 publications from 1964 and found an almost threefold increase in the number of publications and diversity of research topics studied over the last decade. Studies on flora, birds and mammals have been numerous (62% of the studies examined), but certain taxa like fish (1%) have been ignored. Most studies (65%) are descriptive, focusing on diversity, distribution trends and management suggestions, while surprisingly few have concentrated on climate change, ecological restoration and invasive species, all major threats to this landscape. We have identified some key gaps in research and conservation focus that future studies could address. We also suggest that initiatives like edited volumes and special journal sections, along with the use of creative commons licensed data-sharing portals, can be used to usher unpublished work into the public domain.