Characterizing drought using the reliability-resilience-vulnerability concept

This study borrows the measures developed for the operation of water resources systems as a means of characterizing droughts in a given region. It is argued that the common approach of assessing drought using a univariate measure (severity or reliability) is inadequate as decision makers need assessment of the other facets considered here. It is proposed that the joint distribution of reliability, resilience, and vulnerability (referred to as RRV in a reservoir operation context), assessed using soil moisture data over the study region, be used to characterize droughts. Use is made of copulas to quantify the joint distribution between these variables. As reliability and resilience vary in a nonlinear but almost deterministic way, the joint probability distribution of only resilience and vulnerability is modeled. Recognizing the negative association between the two variables, a Plackett copula is used to formulate the joint distribution. The developed drought index, referred to as the drought management index (DMI), is able to differentiate the drought proneness of a given area when compared to other areas. An assessment of the sensitivity of the DMI to the length of the data segments used in evaluation indicates relative stability is achieved if the data segments are 5years or longer. The proposed approach is illustrated with reference to the Malaprabha River basin in India, using four adjoining Climate Prediction Center grid cells of soil moisture data that cover an area of approximately 12,000 km(2). (C) 2013 American Society of Civil Engineers.

Effect of a natural mutation in the 5 ` untranslated region on the translational control of p53 mRNA

Tumor-suppressor protein p53, the `guardian of the genome', is critical in maintaining cellular homeostasis and genomic stability. Earlier, we have reported the discovery of internal ribosome entry sites (IRESs) within the p53 mRNA that regulate the translation of the full length and its N-terminal-truncated isoform, Delta N-p53. Polypyrimidine tract-binding protein (PTB) is an IRES trans-acting factor that positively regulates the IRES activities of both p53 isoforms by relocating from nucleus to the cytoplasm during stress conditions. Here we have demonstrated the putative contact points of PTB on the p53 IRES RNA. Studies on mutations that occur naturally in the 5' untranslated region (5' UTR) in p53 mRNA were lacking. We have investigated a naturally occurring C-to-T single-nucleotide polymorphism (SNP) first reported in human melanoma tumors. This SNP is at position 119 in the 5' UTR of p53 mRNA and we demonstrate that it has consequences on the translational control of p53. Introduction of this SNP has led to decrease in cap-independent translation from p53 5' UTR in bicistronic reporter assay. Further, the effects of this SNP on cap-independent translation have been studied in the context of p53 cDNA as well. Interestingly, the 5' UTR with this SNP has shown reduced binding to PTB that can be corroborated to its weaker IRES activity. Previously, it has been shown that G2-M checkpoint, DNA-damaging stress and oncogenic insult favor IRES-mediated translation. Under similar conditions, we demonstrate that this SNP interferes with the enhancement of the IRES activity of the 5' UTR. Taken together, the results demonstrate for the first time that SNP in the 5' UTR of the p53 mRNA might have a role in translational control of this critical tumor-suppressor gene.

Microwave, infrared-microwave double resonance, and theoretical studies of C2H4 center dot center dot center dot H2S complex

In this manuscript, rotational spectra of four new isotopologues of the S-H center dot center dot center dot pi bonded C2H4 center dot center dot center dot H2S complex, i.e., C2D4 center dot center dot center dot H2S, C2D4 center dot center dot center dot D2S, C2D4 center dot center dot center dot HDS, and (CCH4)-C-13 center dot center dot center dot H2S have been reported and analyzed. All isotopologues except C2D4 center dot center dot center dot HDS show a four line pattern whereas a doubling of the transition frequencies was observed for C2D4 center dot center dot center dot HDS. These results together with our previous report on the title complex M. Goswami, P. K. Mandal, D. J. Ramdass, and E. Arunan, Chem. Phys. Lett. 393(1-3), 22-27 (2004)] confirm that both subunits (C2H4 and H2S) are involved in large amplitude motions leading to a splitting of each rotational transition to a quartet. Further, the results also confirm that the motions which are responsible for the observed splittings involve both monomers. Molecular symmetry group analysis, considering the interchange of equivalent H atoms in H2S and C2H4 could explain the observed four line pattern and their intensities in the microwave spectrum. In addition, hydride stretching fundamentals of the complex were measured using coherence-converted population transfer Fourier Transform Microwave-infrared (IR-MW double resonance) experiments in the S-H and C-H stretch regions. Changes in the tunneling splittings upon vibrational excitation are consistent with the isotopic dependence of pure rotational transitions. A complexation shift of 2.7-6.5 cm(-1) has been observed in the two fundamental S-H stretching modes of the H2S monomer in the complex. Vibrational pre-dissociation in the bound S-H stretch has been detected whereas the instrument-limited line-shapes in other S-H and C-H stretches indicate slower pre-dissociation rate. Some local perturbations in the vibrational spectra have been observed. Two combination bands have been observed corresponding to both the S-H stretching fundamentals and what appears to be the intermolecular stretching mode at 55 cm(-1). The tunneling splitting involved in the rotation of C2H4 unit has been deduced to be 1.5 GHz from the IR-MW results. In addition, ab initio barrier heights derived for different motions of the monomers support the experimental results and provide further insight into the motions causing the splitting. (C) 2013 AIP Publishing LLC.

G-Quadruplex Structures Formed at the HOX11 Breakpoint Region Contribute to Its Fragility during t(10;14) Translocation in T-Cell Leukemia

The t(10;14) translocation involving the HOX11 gene is found in several T-cell leukemia patients. Previous efforts to determine the causes of HOX11 fragility were not successful. The role of non-B DNA structures is increasingly becoming an important cause of genomic instability. In the present study, bioinformatics analysis revealed two G-quadruplex-forming motifs at the HOX11 breakpoint cluster. Gel shift assays showed formation of both intra- and intermolecular G-quadruplexes, the latter being more predominant. The structure formation was dependent on four stretches of guanines, as revealed by mutagenesis. Circular dichroism analysis identified parallel conformations for both quadruplexes. The non-B DNA structure could block polymerization during replication on a plasmid, resulting in consistent K K+-dependent pause sites, which were abolished upon mutation of G-motifs, thereby demonstrating the role of the stretches of guanines even on double-stranded DNA. Extrachromosomal assays showed that the G-quadruplex motifs could block transcription, leading to reduced expression of green fluorescent protein (GFP) within cells. More importantly, sodium bisulfite modification assay showed the single-stranded character at regions I and II of HOX11 in the genome. Thus, our findings suggest the occurrence of G-quadruplex structures at the HOX11 breakpoint region, which could explain its fragility during the t(10;14) translocation.

C-H center dot center dot center dot O-nitrate synthon assisted molecular assembly of hydrogen bonded Ni(II) and Cu(II) complexes

Two Schiff base metal complexes Cu-SPETNNO3 (1) and Ni-SPETNNO3 (2) SPETN=2,2-propane,1,3-diylbis(nitrilomethyldyne)pyridyl,phenolate] ] with hydrogen bonding groups have been synthesized and characterized by single-crystal X-ray diffraction. In both of the compounds nitrates occupy a crystallographic general position. In 1 the lattice nitrates are on the 2(1) screw axis while in 2 they are at the crystallographic inversion center. C-HOnitrate synthons (formed by the nitrate anions and peripheral hydrogen bonding groups of the metal complexes) are non-covalent building blocks in molecular-assembly and packing of the cationic Schiff base metal complexes (M=Ni2+, Cu2+), resulting in 2-D hydrogen bonded networks. The CuCu non-bonding contact in 1 is 3.268 angstrom while the Ni-Ni bonding distance in 2 is 3.437 angstrom.

Rack Level Modeling of Air Flow Through Perforated Tile in a Data Center

Effective air flow distribution through perforated tiles is required to efficiently cool servers in a raised floor data center. We present detailed computational fluid dynamics (CFD) modeling of air flow through a perforated tile and its entrance to the adjacent server rack. The realistic geometrical details of the perforated tile, as well as of the rack are included in the model. Generally, models for air flow through perforated tiles specify a step pressure loss across the tile surface, or porous jump model based on the tile porosity. An improvement to this includes a momentum source specification above the tile to simulate the acceleration of the air flow through the pores, or body force model. In both of these models, geometrical details of tile such as pore locations and shapes are not included. More details increase the grid size as well as the computational time. However, the grid refinement can be controlled to achieve balance between the accuracy and computational time. We compared the results from CFD using geometrical resolution with the porous jump and body force model solution as well as with the measured flow field using particle image velocimetry (PIV) experiments. We observe that including tile geometrical details gives better results as compared to elimination of tile geometrical details and specifying physical models across and above the tile surface. A modification to the body force model is also suggested and improved results were achieved.

Eigen-profiles of spatio-temporal fragments for adaptive region-based tracking

We propose a novel space-time descriptor for region-based tracking which is very concise and efficient. The regions represented by covariance matrices within a temporal fragment, are used to estimate this space-time descriptor which we call the Eigenprofiles(EP). EP so obtained is used in estimating the Covariance Matrix of features over spatio-temporal fragments. The Second Order Statistics of spatio-temporal fragments form our target model which can be adapted for variations across the video. The model being concise also allows the use of multiple spatially overlapping fragments to represent the target. We demonstrate good tracking results on very challenging datasets, shot under insufficient illumination conditions.

Computational Study of the Migration of Rhenium from One Enantioface of an Olefin to the Other Facilitated by (C-H)center dot center dot center dot Re Interactions

The migration of a metal atom in a metal olefin complex from one pi face of the olefin to the opposite pi face has been rarely documented. Gladysz and co-workers showed that such a movement is indeed possible in monosubstituted chiral Re olefin complexes, resulting in diastereomerization. Interestingly, this isomerization occurred without dissociation, and on the basis of kinetic isotope effects, the involvement of a trans C-H bond was indicated. Either oxidative addition or an agostic interaction of the vinylic C-H(D) bond with the metal could account for the experimentally observed kinetic isotope effect. In this study we compute the free energy of activation for the migration of Re from one enantioface of the olefin to the other through various pathways. On the basis of DFT calculations at the B3LYP level we show that a trans (C-H)center dot center dot center dot Re interaction and trans C-H oxidative addition provide a nondissociative path for the diastereomerization. The trans (C-H)center dot center dot center dot Re interaction path is computed to be more favorable by 2.3 kcal mol(-1) than the oxidative addition path. While direct experimental evidence was not able to discount the migration of the metal through the formation of a eta(2)-arene complex (conducted tour mechanism), computational results at the B3LYP level show that it is energetically more expensive. Surprisingly, a similar analysis carried out at the M06 level computes a lower energy path for the conducted tour mechanism and is not consistent with the experimental isotope effects observed. Metal-(C-H) interactions and oxidative additions of the metal into C-H bonds are closely separated in energy and might contribute to unusual fluxional processes such as this diastereomerization.

Achievable rate region of gaussian broadcast channel with finite input alphabet and quantized output

In this paper, we study the achievable rate region of two-user Gaussian broadcast channel (GBC) when the messages to be transmitted to both the users take values from finite signal sets and the received signal is quantized at both the users. We refer to this channel as quantized broadcast channel (QBC). We first observe that the capacity region defined for a GBC does not carry over as such to QBC. Also, we show that the optimal decoding scheme for GBC (i.e., high SNR user doing successive decoding and low SNR user decoding its message alone) is not optimal for QBC. We then propose an achievable rate region for QBC based on two different schemes. We present achievable rate region results for the case of uniform quantization at the receivers. We find that rotation of one of the user's input alphabet with respect to the other user's alphabet marginally enlarges the achievable rate region of QBC when almost equal powers are allotted to both the users.

Co-evolution of specific amino acid in sigma 1.2 region and nucleotide base in the discriminator to act as sensors of small molecule effectors of transcription initiation in mycobacteria

The transcription from rrn and a number of other promoters is regulated by initiating ribonucleotides (iNTPs) and guanosine tetra/penta phosphate (p)ppGpp], either by strengthening or by weakening of the RNA polymerase (RNAP)-promoter interactions during initiation. Studies in Escherichia coli revealed the importance of a sequence termed discriminator, located between -10 and the transcription start site of the responsive promoters in this mode of regulation. Instability of the open complex at these promoters is attributed to the lack of stabilizing interactions between the suboptimal discriminator and the 1.2 region of sigma 70 (Sig70) in RNAP holoenzyme. We demonstrate a different pattern of interaction between the promoters and sigma A (SigA) of Mycobacterium tuberculosis to execute similar regulation. Instead of cytosine and methionine, thymine at three nucleotides downstream to -10 element and leucine 232 in SigA are found to be essential for iNTPs and pppGpp mediated response at the rrn and gyr promoters of the organism. The specificity of the interaction is substantiated by mutational replacements, either in the discriminator or in SigA, which abolish the nucleotide mediated regulation in vitro or in vivo. Specific yet distinct bases and the amino acids appear to have co-evolved' to retain the discriminator-sigma 1.2 region regulatory switch operated by iNTPs/pppGpp during the transcription initiation in different bacteria.

Trends in aerosol optical depth over Indian region: Potential causes and impact indicators

The first regional synthesis of long-term (back to similar to 25 years at some stations) primary data (from direct measurement) on aerosol optical depth from the ARFINET (network of aerosol observatories established under the Aerosol Radiative Forcing over India (ARFI) project of Indian Space Research Organization over Indian subcontinent) have revealed a statistically significant increasing trend with a significant seasonal variability. Examining the current values of turbidity coefficients with those reported similar to 50 years ago reveals the phenomenal nature of the increase in aerosol loading. Seasonally, the rate of increase is consistently high during the dry months (December to March) over the entire region whereas the trends are rather inconsistent and weak during the premonsoon (April to May) and summer monsoon period (June to September). The trends in the spectral variation of aerosol optical depth (AOD) reveal the significance of anthropogenic activities on the increasing trend in AOD. Examining these with climate variables such as seasonal and regional rainfall, it is seen that the dry season depicts a decreasing trend in the total number of rainy days over the Indian region. The insignificant trend in AOD observed over the Indo-Gangetic Plain, a regional hot spot of aerosols, during the premonsoon and summer monsoon season is mainly attributed to the competing effects of dust transport and wet removal of aerosols by the monsoon rain. Contributions of different aerosol chemical species to the total dust, simulated using Goddard Chemistry Aerosol Radiation and Transport model over the ARFINET stations, showed an increasing trend for all the anthropogenic components and a decreasing trend for dust, consistent with the inference deduced from trend in Angstrom exponent.

A Donor-Acceptor-Donor Structured Organic Conductor with S center dot center dot center dot S Chalcogen Bonding

A novel thiophene derivative 7,9-di(thiophen-2-yl)-8H-cyclopentaa]acenaphthylen-8-one (DTCPA) is shown to exhibit high electrical conductivity (1.97 x 10(-2) +/- 0.0018 S/cm at RT) in the crystalline state. The material shows two orders of increase in conductivity from normal solid to single crystalline state. The crystal structure has S center dot center dot center dot S chalcogen bonding, C-H center dot center dot center dot O hydrogen bonding, and pi center dot center dot center dot pi stacking as the major intermolecular interactions. The nature and strength of the S center dot center dot center dot S interactions in this structure have been evaluated by theoretical charge density analysis, and its contribution to the crystal packing quantified by Hirshfeld surface analysis. Further, thermal and morphological characterizations have been carried out, and the second harmonic generation (SHG) efficiency has been measured using the Kurtz-Perry method.

The N-terminal region containing the zinc finger domain of tobacco streak virus coat protein is essential for the formation of virus-like particles

Tobacco streak virus (TSV), a member of the genus Ilarvirus (family Bromoviridae), has a tripartite genome and forms quasi-isometric virions. All three viral capsids, encapsidating RNA 1, RNA 2 or RNA 3 and subgenomic RNA 4, are constituted of a single species of coat protein (CP). Formation of virus-like particles (VLPs) could be observed when the TSV CP gene was cloned and the recombinant CP (rCP) was expressed in E. coli. TSV VLPs were found to be stabilized by Zn2+ ions and could be disassembled in the presence of 500 mM CaCl2. Mutational analysis corroborated previous studies that showed that an N-terminal arginine-rich motif was crucial for RNA binding; however, the results presented here demonstrate that the presence of RNA is not a prerequisite for assembly of TSV VLPs. Instead, the N-terminal region containing the zinc finger domain preceding the arginine-rich motif is essential for assembly of these VLPs.

Topological analysis of electron density and the electrostatic properties of isoniazid: an experimental and theoretical study

Isoniazid (isonicotinohydrazide) is an important first-line antitubercular drug that targets the InhA enzyme which synthesizes the critical component of the mycobacterial cell wall. An experimental charge-density analysis of isoniazid has been performed to understand its structural and electronic properties in the solid state. A high-resolution single-crystal X-ray intensity data has been collected at 90 K. An aspherical multipole refinement was carried out to explore the topological and electrostatic properties of the isoniazid molecule. The experimental results were compared with the theoretical charge-density calculations performed using CRYSTAL09 with the B3LYP/6-31G** method. A topological analysis of the electron density reveals that the Laplacian of electron density of the N-N bond is significantly less negative, which indicates that the charges at the b.c.p. (bond-critical point) of the bond are least accumulated, and so the bond is considered to be weak. As expected, a strong negative electrostatic potential region is present in the vicinity of the O1, N1 and N3 atoms, which are the reactive locations of the molecule. The C-H center dot center dot center dot N, C-H center dot center dot center dot O and N-H center dot center dot center dot N types of intermolecular hydrogen-bonding interactions stabilize the crystal structure. The topological analysis of the electron density on hydrogen bonding shows the strength of intermolecular interactions.