A Comparative Kinetic and Thermodynamic Perspective of the sigma-Competition Model in Escherichia coli

Transcription is the most fundamental step in gene expression in any living organism. Various environmental cues help in the maturation of core RNA polymerase (RNAP; alpha(2)beta beta'omega) with different sigma-factors, leading to the directed recruitment of RNAP to different promoter DNA sequences. Thus it is essential to determine the sigma-factors that affect the preferential partitioning of core RNAP among various a-actors, and the role of sigma-switching in transcriptional gene regulation. Further, the macromolecular assembly of holo RNAP takes place in an extremely crowded environment within a cell, and thus far the kinetics and thermodynamics of this molecular recognition process have not been well addressed. In this study we used a site-directed bioaffinity immobilization method to evaluate the relative binding affinities of three different Escherichia coli sigma-factors to the same core RNAP with variations in temperature and ionic strength while emulating the crowded cellular milieu. Our data indicate that the interaction of core RNAP-sigma is susceptible to changes in external stimuli such as osmolytic and thermal stress, and the degree of susceptibility varies among different sigma-factors. This allows for a reversible sigma-switching from housekeeping factors to alternate sigma-factors when the organism senses a change in its physiological conditions.

QUAD: quality assessment of documents

We propose a set of metrics that evaluate the uniformity, sharpness, continuity, noise, stroke width variance,pulse width ratio, transient pixels density, entropy and variance of components to quantify the quality of a document image. The measures are intended to be used in any optical character recognition (OCR) engine to a priori estimate the expected performance of the OCR. The suggested measures have been evaluated on many document images, which have different scripts. The quality of a document image is manually annotated by users to create a ground truth. The idea is to correlate the values of the measures with the user annotated data. If the measure calculated matches the annotated description,then the metric is accepted; else it is rejected. In the set of metrics proposed, some of them are accepted and the rest are rejected. We have defined metrics that are easily estimatable. The metrics proposed in this paper are based on the feedback of homely grown OCR engines for Indic (Tamil and Kannada) languages. The metrics are independent of the scripts, and depend only on the quality and age of the paper and the printing. Experiments and results for each proposed metric are discussed. Actual recognition of the printed text is not performed to evaluate the proposed metrics. Sometimes, a document image containing broken characters results in good document image as per the evaluated metrics, which is part of the unsolved challenges. The proposed measures work on gray scale document images and fail to provide reliable information on binarized document image.

Water treatment potential in relation to phytoplankton dynamics in tropical sewage-fed urban water bodies

Urban water bodies frequently receive untreated sewage and water levels in such water bodies are maintained by daily inputs of sewage. They function as “variable-zone” anaerobic-aerobic lagoons suffering several macrophyte, biotic and abiotic stresses. We have studied two such lakes in Bangalore (Bellandur-360 ha and Varthur-220 ha) to understand whether such an occurrence could be made beneficial (maintaining water levels as well as treatment). Such hypertrophic water body receives sewage at 180-250mg/L and is discharged at 25-80mg/L COD/BOD in different seasons. In an earlier study we reported macrophyte altering the purification function of the water body. In this paper we studied the impact of phytoplankton dynamics and macrophyte cover on the functions such as organic load removal. Algal community analysis, algal biomass, macrophyte cover, water quality, nutrient status was studied seasonally during 2009-2010. Oxygen deficiency and sometimes anoxia, recorded from surface samples resulted in high quantities of NH4+-N (30-40mg/L) and phosphate (0.5-4mg/L)-characteristics of anoxic hypertrophic urban lakes. The productiveness favoured high phytoplanktonic community characterized by small cells (<10μm; Chlorella sp. - highest numbers). The lake could be clearly demarcated into an initial anaerobic zone (40% area), a facultative zone (20%) and an aerobic zone (40%) based on redox values and GIS/bathymetry. During summer the lake is covered by floating macrophytes converting the lake into an anoxic/anaerobic water pool subduing the water purification function as well as aesthetics. When macrophytes are controlled such sewage fed water bodies can be used for treating urban wastewater while also maintaining water sustainability in these semi-arid ecosystems. This paper reports the community dynamics of phytoplankton, their function and competition with macrophytes.

When good neighbors don't need fences: temporal landscape partitioning among baboon social groups

Intraspecific competition is a key factor shaping space-use strategies and movement decisions in many species, yet how and when neighbors utilize shared areas while exhibiting active avoidance of one another is largely unknown. Here, we investigated temporal landscape partitioning in a population of wild baboons (Papio cynocephalus). We used global positioning system (GPS) collars to synchronously record the hourly locations of five baboon social groups for similar to 900 days, and we used behavioral, demographic, and life history data to measure factors affecting use of overlap areas. Annual home ranges of neighboring groups overlapped substantially, as predicted (baboons are considered non-territorial), but home ranges overlapped less when space use was assessed over shorter time scales. Moreover, neighboring groups were in close spatial proximity to one another on fewer days than predicted by a null model, suggesting an avoidance-based spacing pattern. At all time scales examined (monthly, biweekly, and weekly), time spent in overlap areas was greater during time periods when groups fed on evenly dispersed, low-quality foods. The percent of fertile females in social groups was negatively correlated with time spent in overlap areas only during weekly time intervals. This suggests that broad temporal changes in ecological resources are a major predictor of how intensively overlap areas are used, and groups modify these ecologically driven spacing patterns at short time scales based on female reproductive status. Together, these findings offer insight into the economics of territoriality by highlighting the dynamics of spacing patterns at differing time scales.

Biogeochemical facsimile of the organic matter quality and trophic status of a micro-tidal tropical estuary

Seasonal studies were carried out from 21 stations, comprising of three zones, of Cochin Estuary, to assess the organic matter quality and trophic status. The hydographical parameters showed significant seasonal variations and nutrients and chlorophylls were generally higher during the monsoon season. However, chemical contamination along with the seasonal limitations of light and nitrogen imposed restrictions on the primary production and as a result, mesotrophic conditions generally prevailed in the water column. The nutrient stoichometries and delta C-13 values of surficial sediments indicated significant allochthonous contribution of organic matter. Irrespective of the higher content of total organic matter, the labile organic matter was very low. Dominance of carbohydrates over lipids and proteins indicated the lower nutritive aspect of the organic matter, and their aged and refractory nature. This, along with higher amount of phytodetritus and the low algal contribution to the biopolymeric carbon corroborated the dominance of allochthonous organic matter and the heterotrophic nature. The spatial and seasonal variations of labile organic components could effectively substantiate the observed shift in the productivity pattern. An alternative ratio, lipids to tannins and lignins, was proposed to ascertain the relative contribution of allochthonous organic matter in the estuary. This study confirmed the efficiency of an integrated biogeochemical approach to establish zones with distinct benthic trophic status associated with different degrees of natural and anthropogenic input. Nevertheless, our results also suggest that the biochemical composition alone could lead to erroneous conclusions in the case of regions that receive enormous amounts of anthropogenic inputs.

The role of tusks, musth and body size in male-male competition among Asian elephants, Elephas maximus

The evolution of sexually dimorphic, elaborate male traits that are seemingly maladaptive may be driven by sexual selection (male-male competition and or female mate choice). Tusk possession in the Asian elephant is sexually dimorphic and exaggerated but its role in male-male competition has not yet been determined. We examined the role of the tusks in establishing dominance along with two other known male-male signals, namely, body size and musth (a temporary physiologically heightened sexual state) in an Asian elephant population in northeastern India with equal proportions of tusked and tuskless males. We observed 116 agonistic interactions with clear dominance outcomes between adult (>15 years) males during 458 field days in the dry season months of 2008-2011. A generalized linear mixed-effects model was used to predict the probability of winning as a function of body size, tusk possession and musth status relative to the opponent. A hierarchy of the three male-male signals emerged from this analysis, with musth overriding body size and body size overriding tusk possession. In this elephant population tusk possession thus plays a relatively minor role in male-male competition. An important implication of musth and body size being stronger determinants of dominance than tusk possession is that it could facilitate rapid evolution of tuskless males in the population under artificial selection against tusked individuals, which are poached for ivory. (C) 2013 The Association for the Study of Animal Behaviour. Published by Elsevier Ltd. All rights reserved.

Subchannel allocation and power control in femtocells to provide quality of service

Femtocells are a new concept which improves the coverage and capacity of a cellular system. We consider the problem of channel allocation and power control to different users within a Femtocell. Knowing the channels available, the channel states and the rate requirements of different users the Femtocell base station (FBS), allocates the channels to different users to satisfy their requirements. Also, the Femtocell should use minimal power so as to cause least interference to its neighboring Femtocells and outside users. We develop efficient, low complexity algorithms which can be used online by the Femtocell. The users may want to transmit data or voice. We compare our algorithms with the optimal solutions.

Modification of Extended Open Frameworks with Fluorescent Tags for Sensing Explosives: Competition between Size Selectivity and Electron Deficiency

Three new electron-rich metal-organic frameworks (MOF-1-MOF-3) have been synthesized by employing ligands bearing aromatic tags. The key role of the chosen aromatic tags is to enhance the -electron density of the luminescent MOFs. Single-crystal X-ray structures have revealed that these MOFs form three-dimensional porous networks with the aromatic tags projecting inwardly into the pores. These highly luminescent electron-rich MOFs have been successfully utilized for the detection of explosive nitroaromatic compounds (NACs) on the basis of fluorescence quenching. Although all of the prepared MOFs can serve as sensors for NACs, MOF-1 and MOF-2 exhibit superior sensitivity towards 4-nitrotoluene (4-NT) and 2,4-dinitrotoluene (DNT) compared to 2,4,6-trinitrotoluene (TNT) and 1,3,5-trinitrobenzene (TNB). MOF-3, on the other hand, shows an order of sensitivity in accordance with the electron deficiencies of the substrates. To understand such anomalous behavior, we have thoroughly analyzed both the steady-state and time-resolved fluorescence quenching associated with these interactions. Determination of static Stern-Volmer constants (K-S) as well as collisional constants (K-C) has revealed that MOF-1 and MOF-2 have higher K-S values with 4-NT than with TNT, whereas for MOF-3 the reverse order is observed. This apparently anomalous phenomenon was well corroborated by theoretical calculations. Moreover, recyclability and sensitivity studies have revealed that these MOFs can be reused several times and that their sensitivities towards TNT solution are at the parts per billion (ppb) level.

High-quality ZnO nanorod based flexible devices for electronic and biological applications

Vertically aligned zinc oxide nanorods (ZnO NRs) were synthesized on kapton flexible sheets using a simple and cost-effective three-step process (electrochemical seeding, annealing under ambient conditions, and chemical solution growth). Scanning electron microscopy studies reveal that ZnO NRs grown on seed-layers, developed by electrochemical deposition at a negative potential of 1.5 V over a duration of 2.5 min and annealed at 200 degrees C for 2 h, consist of uniform morphology and good chemical stoichiometry. Transmission electron microscopy analyses show that the as-grown ZnO NRs have single crystalline hexagonal structure with a preferential growth direction of < 001 >. Highly flexible p-n junction diodes fabricated by using p-type conductive polymer exhibited excellent diode characteristics even under the fold state.

On the quality of hydrogenated amorphous silicon deposited by sputtering

Amorphous hydrogenated silicon (a-Si:H) is well-known material in the global semiconductor industry. The quality of the a-Si:H films is generally decided by silicon and hydrogen bonding configuration (Si-H-x, x=1,2) and hydrogen concentration (C-H). These quality aspects are correlated with the plasma parameters like ion density (N-i) and electron temperature (T-e) of DC, Pulsed DC (PDC) and RF plasmas during the sputter-deposition of a-Si:H thin films. It was found that the N-i and T-e play a major role in deciding Si-H-x bonding configuration and the C-H value in a-Si:H films. We observed a trend in the variation of Si-H and Si-H-2 bonding configurations, and C-H in the films deposited by DC, Pulsed DC and RF reactive sputtering techniques. Ion density and electron energy are higher in RF plasma followed by PDC and DC plasma. Electrons with two different energies were observed in all the plasmas. At a particular hydrogen partial pressure, RF deposited films have higher C-H followed by PDC and then DC deposited films. The maximum energy that can be acquired by the ions was found to be higher in RF plasma. Floating potential (V-f) is more negative in DC plasma, whereas, plasma potential (V-p) is found to be more positive in RF plasma. (C) 2014 Elsevier Ltd. All rights reserved.

High quality oxide-free metallic nanoparticles: a strategy for synthesis through laser ablation in aqueous medium

The paper explores the synthesis of oxide-free nanoparticles of Ag and Cu through laser ablation of pure targets under aqueous medium and tuning the quality and size through addition of Polyvinylpyrrolidone (PVP) in the medium. The size distribution of nanoparticles reduces from 37 +/- 30 nm and 13 +/- 5 nm to 32 +/- 12 nm and 4 +/- 1 nm for Ag and Cu with changes in PVP concentration from 0.00 to 0.02 M, respectively. Irregular shaped particles of Ag with Ag2O phase and a Cu-Cu2O core-shell particles form without the addition of PVP, while oxide layer is absent with 0.02 M of PVP. The recent understanding of the mechanism of particle formation during laser ablation under liquid medium allows us to rationalize our observation.

Low Complexity Power and Scheduling Policies for Wireless Networks to Provide Quality of Service

We consider optimal power allocation policies for a single server, multiuser system. The power is consumed in transmission of data only. The transmission channel may experience multipath fading. We obtain very efficient, low computational complexity algorithms which minimize power and ensure stability of the data queues. We also obtain policies when the users may have mean delay constraints. If the power required is a linear function of rate then we exploit linearity and obtain linear programs with low complexity.

Continuous synthesis of high quality CdSe quantum dots in supercritical fluids

We demonstrate in here a powerful scalable technology to synthesize continuously high quality CdSe quantum dots (QDs) in supercritical hexane. Using a low cost, highly thermally stable Cd-precursor, cadmium deoxycholate, the continuous synthesis is performed in 400 mu m ID stainless steel capillaries resulting in CdSe QDs having sharp full-width-at-half-maxima (23 nm) and high photoluminescence quantum yields (45-55%). Transmission electron microscopy images show narrow particles sizes distribution (sigma <= 5%) with well-defined crystal lattices. Using two different synthesis temperatures (250 degrees C and 310 degrees C), it was possible to obtain zinc blende and wurtzite crystal structures of CdSe QDs, respectively. This synthetic approach allows achieving substantial production rates up to 200 mg of QDs per hour depending on the targeted size, and could be easily scaled to gram per hour.

High Quality Photometric Reconstruction using a Depth Camera

In this paper we present a depth-guided photometric 3D reconstruction method that works solely with a depth camera like the Kinect. Existing methods that fuse depth with normal estimates use an external RGB camera to obtain photometric information and treat the depth camera as a black box that provides a low quality depth estimate. Our contribution to such methods are two fold. Firstly, instead of using an extra RGB camera, we use the infra-red (IR) camera of the depth camera system itself to directly obtain high resolution photometric information. We believe that ours is the first method to use an IR depth camera system in this manner. Secondly, photometric methods applied to complex objects result in numerous holes in the reconstructed surface due to shadows and self-occlusions. To mitigate this problem, we develop a simple and effective multiview reconstruction approach that fuses depth and normal information from multiple viewpoints to build a complete, consistent and accurate 3D surface representation. We demonstrate the efficacy of our method to generate high quality 3D surface reconstructions for some complex 3D figurines.