Showing papers by "Shiv Nadar University published in 2013"

Earlier springs decrease peak summer productivity in North American boreal forests

Abstract: In the northern high latitudes, alternative hypotheses with regards to how warming-related shifts in seasonality influence ecosystem productivity exist. Increased plant growth associated with a longer growing season may enhance ecosystem productivity, but shifts to earlier springs may also negatively influence soil moisture status and productivity during the peak of the growing season. Here, we analyzed nearly three decades (1982?2008) of observational records and derived products, including satellite microwave and optical imagery as well as upscaled ecosystem flux observations, to better understand how shifts in seasonality impact hydrology and productivity in the North American boreal forests. We identified a dominant adverse influence of earlier springs on peak summer forest greenness, actual evapotranspiration and productivity at interannual time scales across the drier western and central sections of the North American boreal forests. In the vast regions where this spring onset mechanism operates, ecosystem productivity gains from earlier springs during the early portion of the growing season are effectively cancelled through corresponding losses in the later portion. Our results also indicate that recent decadal shifts towards earlier springs and associated drying in the midst of the growing season over western North American boreal forests may have contributed to the reported declines in summer productivity and increases in tree mortality and fire activity. With projections of accelerated northern high-latitude warming and associated shifts to earlier springs, persistent soil moisture deficits in peak summer may be an effective mechanism for regional-scale boreal forest dieback through their strong influence on productivity, tree mortality and disturbance dynamics.

Antithyroid Drugs and Their Analogues: Synthesis, Structure, and Mechanism of Action

Abstract: Thyroid hormones are essential for the development and differentiation of all cells of the human body. They regulate protein, fat, and carbohydrate metabolism. In this Account, we discuss the synthesis, structure, and mechanism of action of thyroid hormones and their analogues.The prohormone thyroxine (T4) is synthesized on thyroglobulin by thyroid peroxidase (TPO), a heme enzyme that uses iodide and hydrogen peroxide to perform iodination and phenolic coupling reactions. The monodeiodination of T4 to 3,3′,5-triiodothyronine (T3) by selenium-containing deiodinases (ID-1, ID-2) is a key step in the activation of thyroid hormones. The type 3 deiodinase (ID-3) catalyzes the deactivation of thyroid hormone in a process that removes iodine selectively from the tyrosyl ring of T4 to produce 3,3′,5′-triiodothyronine (rT3). Several physiological and pathological stimuli influence thyroid hormone synthesis. The overproduction of thyroid hormones leads to hyperthyroidism, which is treated by antithyroid drugs that ...

Calcium-dependent permeabilization of erythrocytes by a perforin-like protein during egress of malaria parasites.

Abstract: Malaria parasites exit erythrocytes by triggering permeabilization and rupture of the host plasma membrane. Here, the authors identify a perforin-like protein that is secreted by the parasite in a calcium-dependent manner and mediates permeabilization through its insertion into the host membrane.

Li segregation induces structure and strength changes at the amorphous Si/Cu interface.

Abstract: The study of interfacial properties, especially of their change upon lithiation, is a fundamentally significant and challenging topic in designing heterogeneous nanostructured electrodes for lithium ion batteries. This issue becomes more intriguing for Si electrodes, whose ultrahigh capacity is accompanied by large volume expansion and mechanical stress, threatening with delamination of silicon from the metal current collector and failure of the electrode. Instead of inferring interfacial properties from experiments, in this work, we have combined density functional theory (DFT) and ab initio molecular dynamics (AIMD) calculations with time-of-flight secondary ion mass spectrometry (TOF-SIMS) measurements of the lithium depth profile, to study the effect of lithiation on the a-Si/Cu interface. Our results clearly demonstrate Li segregation at the lithiated a-Si/Cu interface (more than 20% compared to the bulk concentration). The segregation of Li is responsible for a small decrease (up to 16%) of the adhe...

Genome-wide analysis reveals downregulation of miR-379/miR-656 cluster in human cancers

Abstract: MicroRNAs (miRNAs) are non-uniformly distributed in genomes and ~30% of the miRNAs in the human genome are clustered. In this study we have focused on the imprinted miRNA cluster miR-379/miR-656 on 14q32.31 (hereafter C14) to test their coordinated function. We have analyzed expression profile of >1000 human miRNAs in >1400 samples representing seven different human tissue types obtained from cancer patients along with matched and unmatched controls. We found 68% of the miRNAs in this cluster to be significantly downregulated in glioblastoma multiforme (GBM), 61% downregulated in kidney renal clear cell carcinoma (KIRC), 46% in breast invasive carcinoma (BRCA) and 14% in ovarian serous cystadenocarcinoma (OV). On a genome-wide scale C14 miRNAs accounted for 12-30% of the total downregulated miRNAs in different cancers. Pathway enrichment for the predicted targets of C14 miRNA was significant for cancer pathways, especially Glioma (p< 3.77x10-6, FDR<0.005). The observed downregulation was confirmed in GBM patients by real-time PCR, where 79% of C14 miRNAs (34/43) showed downregulation. In GBM samples, hypermethylation at C14 locus (p<0.003) and downregulation of MEF2, a crucial transcription factor for the cluster was observed which likely contribute to the observed downregulation of the entire miRNA cluster. We provide compelling evidence that the entire C14 miRNA cluster is a tumor suppressor locus involved in multiple cancers, especially in GBM, and points toward a general mechanism of coordinated function for clustered miRNAs. Reviewed by: Prof. Gregory J Goodall and Dr. Alexander Max Burroughs

On water: silver-catalyzed domino approach for the synthesis of benzoxazine/oxazine-fused isoquinolines and naphthyridines from o-alkynyl aldehydes.

Abstract: An operationally simple domino approach for the silver-catalyzed synthesis of oxazine/benzoxazine-fused isoquinolines 5a–q and naphthyridines 6a–v by the reaction of o-alkynyl aldehydes 3a–aa with amines having embedded nucleophiles 4a–d under mild reaction condition in water is described. The reaction shows selective C–N bond formation on the more electrophilic alkynyl carbon resulting in the formation of 6-endo-dig cyclized product. The competitive experiments show the viability of an intramolecular nucleophilic attack over an intermolecular attack of the external nucleophile. This methodology accommodates wide functional group variation, which proves to be useful for structural and biological assessment.

Seasonal variation of surface and vertical profile of aerosol properties over a tropical urban station Hyderabad, India

Abstract: [1] One year measurement of vertical profiles of volume backscatter and extinction coefficient, aerosol optical depth (AOD), mass concentration of black carbon (BC) and composite aerosol along with thermodynamic structure of the atmosphere has been carried out over an urban tropical location of Hyderabad(17.47°N, 78.58°E), India, during April 2009 to March 2010. The mean mixing layer height (MLH) exhibits large seasonality exceeding 4 km in pre-monsoon period whereas in winter it comes down to ~1.5 km with an annual mean value of 2.35 ± 1.02 km. Surface BC mass fraction (FBC) shows marked seasonal variation from winter (13 ± 1.9%), pre-monsoon (8.19 ± 2.16%), monsoon (7.3 ± 1.8%) to post-monsoon (11.8 ± 0.18%). The profiles of volume backscatter and extinction coefficients reveal presence of elevated aerosol layers from 2 to 4 km and strong oscillations during pre-monsoon (March–May) and monsoon (June–September) seasons, respectively, while in post-monsoon (October–November) and winter (December–February), the aerosols are well within the lower boundary layer and also exhibit a drastic decrease with increasing altitude. These elevated aerosol layers and vertical distribution appear to be closely linked to the thermodynamic structure of the atmosphere. The aerosol optical properties in conjunction with air mass back trajectory analysis indicate that the observed elevated aerosol layers during pre-monsoon and monsoon could contain significant fraction of coarse mode particles with a mix of dust and marine aerosols. Further analysis reveals that the aerosols within atmospheric boundary layer (ABL) dominate the column aerosol loading with ABL-AOD contributing to ~77.7 ± 17.0%, with significant seasonal variation from winter (86.2 ± 13.1%), pre-monsoon (76.6 ± 12.8%), monsoon (54.2 ± 15.6%) to post monsoon (80.8 ± 14.8%). Seasonal variation of ABL-AOD and BC mass fraction follows similar pattern in the ABL indicating that BC may be an important contributor to the ABL aerosol loading.

Relation between charge carrier mobility and lifetime in organic photovoltaics

Abstract: 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.

New Group IV chemical motifs for improved dielectric permittivity of polyethylene.

Abstract: An enhanced dielectric permittivity of polyethylene and related polymers, while not overly sacrificing their excellent insulating properties, is highly desirable for various electrical energy storage applications. In this computational study, we use density functional theory (DFT) in combination with modified group additivity based high throughput techniques to identify promising chemical motifs that can increase the dielectric permittivity of polyethylene. We consider isolated polyethylene chains and allow the CH2 units in the backbone to be replaced by a number of Group IV halides (viz., SiF2, SiCl2, GeF2, GeCl2, SnF2, or SnCl2 units) in a systematic, progressive, and exhaustive manner. The dielectric permittivity of the chemically modified polyethylene chains is determined by employing DFT computations in combination with the effective medium theory for a limited set of compositions and configurations. The underlying chemical trends in the DFT data are first rationalized in terms of various tabulated a...

Electrochemical and oxygen reduction properties of pristine and nitrogen-doped few layered graphene nanoflakes (FLGs)

Abstract: Vertically aligned few layered graphene (FLGs) nanoflakes were synthesized by microwave plasma deposition for various time durations ranging from 30 to 600 s to yield graphene films of varying morphology, microstructure and areal/edge density. Their intrinsic electrochemical properties were explored using Fe(CN)6 3−/4− and Ru(NH3)6 3+/2+ redox species. All the FLG electrodes demonstrate fast electron transfer kinetics with near ideal ΔEp values of 60–65 mV. Using a relationship between electron transfer rate and edge plane density, an estimation of the edge plane density was carried out which revealed a moderation of edge plane density with increase in growth time. The pristine FLGs also possess excellent electrocatalytic activity towards oxygen reduction reaction (ORR) in alkaline solutions. This ORR activity can be further enhanced by exposing the pristine FLGs to nitrogen electron cyclotron resonance plasma. The metal free N-doped FLGs exhibit much higher electrocatalytic activity towards ORR than pristine FLGs with higher durability and selectivity than Pt-based catalysts. The excellent electrochemical performance of N-doped FLGs is explained in terms of enhanced edge plane exposure, high content of pyridinic nitrogen and an increase in the electronic density of states.

Growth behavior, electronic structure, and vibrational properties of Si n Y anion clusters ( n = 4–20): Metal atom as linker and endohedral dopant

Abstract: We report results of ab initio calculations on Y-doped anion Si${}_{n}$ clusters with $n$ $=$ 4--20. Our results suggest two growth behaviors in the intermediate range of $n$ $=$ 8 and 20: (1) There is the formation of linked clusters in which a metal atom links two subclusters and (2) where silicon atoms form a cage structure and the metal atom is inside the cage to produce endohedral cages of silicon clusters. The cluster structures have been identified by comparing the calculated spectra of the electronic states with the photoemission spectra on anion clusters. Our results suggest that in some cases a higher energy isomer may be present in experiments. We report the calculations of the infrared and Raman spectra as well as the dipole moments, electron affinity, and polarizability that could provide other ways of identifying the growth behavior in these clusters.

Access to Higher Education in India: An Exploration of Its Antecedents *

Abstract: Deficits in participation of marginalized groups in Higher Education (HE) have attracted significant policy and research attention. Recent studies have explored the role of socioreligious affiliation and other factors in determining participation in HE. It is also shown that appropriate measures of ‘deficits’ in participation should inform the nature and scope of affirmative action for marginalized groups. Using appropriate measures of participation, this paper explores if the role of socio-religious background and other factors has changed over a period of time. This dynamics of participation in HE is analyzed by using three rounds of NSS data for the period 1999-2010.

Density Functional Calculations of the Structural and Electronic Properties of (Y2O3)n0,±1 Clusters with n = 1–10

Abstract: We report results of ab initio calculations on yttrium oxide clusters using a plane wave pseudopotential method within density functional theory. (Y2O3)n clusters in the size range n = 1–10 prefer compact and symmetric globular configurations where preference for an octahedron unit of Y6O8 is seen. The evolution of the atomic structures shows similarity with that of the local structure in the bulk cubic (C-Y2O3) phase. The maximum coordinations of Y and O atoms are 6 and 4, respectively. The addition (removal) of an electron to (from) the lowest energy configurations of the neutral clusters induces significant changes for some of the cluster sizes. Sequential addition of a Y2O3 unit to the (Y2O3)n cluster leads to an increase in the binding energy. However, the HOMO–LUMO gap, ionization potential, and electron affinity do not show any systematic variation in these clusters with increasing size. The bonding characteristics have been studied using charge density and Bader charge analysis. The charge transfe...

Cationic vacancies and anomalous spectral-weight transfer in Ti1-xTaxO2 thin films studied via polarization-dependent near-edge x-ray absorption fine structure spectroscopy

Abstract: We report the electronic structures of Ta-doped anatase TiO 2 thin films grown by pulsed laser deposition (PLD) with varying magnetization using a combination of first-principles calculations and near-edge x-ray absorption fine structure (NEXAFS) spectroscopy. The roles of Ta doping and Ti vacancies are clarified, and the observed room-temperature ferromagnetism is attributed to the localized magnetic moments at Ti vacancy sites ferromagnetically ordered by electron charge carriers. O K -edge spectra exhibit significant polarization dependence which is discussed and supported by first-principles calculations in relation to both the crystal symmetry and the formation of defects. In particular, anomalous spectral-weight transfer across the entire O K edge for the ferromagnetic thin film is associated exclusively with the occurrence of Ti vacancies and strong correlation effects, which result in the enhancement of the direct interaction between oxygen sites and of the anisotropy of the e g - p σ hybridizations in the out-of-plane component. Our results show that O K -edge NEXAFS spectra can provide reliable experimental probes capable of revealing cationic defects that are intimately related to the ferromagnetism in transition metal oxides.

Word shape descriptor-based document image indexing: a new DBH-based approach

Abstract: In this paper, we propose a novel feature representation for binary patterns by exploiting the object shape information. Initial evaluation of the representation is performed for Bengali and Gujarati script character classification. The extension of the representation for word images is presented subsequently. The proposed feature representation in combination with distance-based hashing is applied for defining novel word image-based document image indexing and retrieval framework. The concept of hierarchical hashing is utilized to reduce the retrieval time complexity. In addition, with the objective of reduction in the size of hashing data structure, the concept of multi-probe hashing is extended for binary mapping functions. The exhaustive experimental evaluation of the proposed framework on a collection of documents belonging to Devanagari, Bengali and English scripts has yielded encouraging results.

Nanoscale phase domain structure and associated device performance of organic solar cells based on a diketopyrrolopyrrole polymer

Abstract: We investigate the blend morphology and performance of bulk heterojunction organic photovoltaic devices comprising the donor polymer, pDPP-TNT (poly{3,6-dithiophene-2-yl-2,5-di(2-octyldodecyl)-pyrrolo[3,4-c]pyrrole-1,4-dione-alt-naphthalene}) and the fullerene acceptor, [70]PCBM ([6,6]-phenyl C71-butyric acid methyl ester). The blend morphology is heavily dependent upon the solvent system used in the fabrication of thin films. Thin films spin-coated from chloroform possess a cobblestone-like morphology, consisting of thick, round-shaped [70]PCBM-rich mounds separated by thin polymer-rich valleys. The size of the [70]PCBM domains is found to depend on the overall film thickness. Thin films spin-coated from a chloroform : dichlorobenzene mixed solvent system are smooth and consist of a network of pDPP-TNT nanofibers embedded in a [70]PCBM-rich matrix. Rinsing the films in hexane selectively removes [70]PCBM and allows for analysis of domain size and purity. It also provides a means for investigating exciton dissociation efficiency through relative photoluminescence yield measurements. Devices fabricated from chloroform solutions show much poorer performance than the devices fabricated from the mixed solvent system; this disparity in performance is seen to be more pronounced with increasing film thickness. The primary cause for the improved performance of devices fabricated from mixed solvents is attributed to the greater donor–acceptor interfacial area and resulting greater capacity for charge carrier generation.

Polarization-dependent manipulation of optical properties in a tripod system

Abstract: We analyze the dependence of the transmission profiles of an atom in a tripod configuration on the polarizations of the coupling and the probe beams and use room-temperature metastable helium (${}^{4}$He*) as a model system. We show that, by rotating the orthogonally polarized coupling-probe beams with respect to an applied small magnetic field, one can manipulate the detuned peaks due to electromagnetically induced transparency [Kumar, Laupr\^etre, Ghosh, Bretenaker, and Goldfarb, Phys. Rev. A 84, 023811 (2011)] and the central peak arising because of ground-state coherent population oscillations [Laupr\^etre, Kumar, Berger, Faoro, Ghosh, Bretenaker, and Goldfarb, Phys. Rev. A 85, 051805(R) (2012)] observed earlier separately. Our experimental results match well with our numerical simulation using the Floquet method.

Band Gap Tunable N-Type Molecules for Organic Field Effect Transistors

Abstract: A series of four novel n-type molecules has been synthesized. Unlike previous approaches, the end group of these molecules was fixed and the molecular core was varied. The resulting materials were thoroughly analyzed. Electronic properties were derived from photoemission spectroscopy, optical properties were derived with the help of optical spectroscopy, and the structure of thin films on Au(111) was derived by scanning tunneling microscopy (STM). In addition, prototypical organic field-effect transistors (OFETs) (forming n-channels in OFETs) have been fabricated and tested. The correlation between the device performance of the respective OFETs (i.e., electron mobility) and their electronic as well as structural properties was investigated. It turned out that a combination of beneficial electronic and structural properties provides the best results. These findings are important for the design of new materials for future device applications.

The atom in a molecule as a mereological construct in chemistry

Abstract: In this paper I discuss some consequences and manifestations of a mereology of structured wholes in chemistry, with particular reference to the concept of atoms in molecules.

Structural and electrical properties of Ag grid/poly(3,4-ethylenedioxythiophene): poly(styrene sulfonate) coatings for diode application through advanced printing technology.

Abstract: This paper is focused on printed techniques for the fabrication of hybrid structure of silver (Ag) grid/poly(3,4-ethylenedioxythiophene): Poly(styrenesulfonate) (PEDOT:PSS) on polyethylene terepthalate (PET) as a flexible substrate. Ag grid has been printed on PET substrate by using gravure offset printing process, followed by PEDOT:PSS thin film deposition on Ag grid through electrohydrodynamic atomization (EHDA) technique. The important parameters for achieving uniform hybrid structure of Ag grid/PEDOT:PSS through printed techniques have been clearly discussed. Field emission scanning electron microscope studies revealed the uniformity of printed Ag grid with homogeneous deposition of PEDOT:PSS on Ag grid. The optical properties of Ag grid/PEDOT:PSS were measured by UV-visible spectroscopy, which showed nearly 80-82% of transparency in the visible region and it was nearly same as PEDOT:PSS thin film on PET substrate. Current-voltage (I-V) analysis of fabricated hybrid device by using printed Ag grid/PEDOT:PSS as a bottom electrode showed good rectifying behavior with possible interfacial mechanisms. Capacitance-voltage (C-V) analysis was carried over different frequencies. These results suggest that fabrication of hybrid structure through printed techniques will play a significant role in mass production of printed electronic devices for commercial application by using flexible substrate.

Identification of differentially expressed genes in rice during its early phases of interaction with Magnaporthe oryzae

Abstract: Rice blast caused by Magnaporthe oryzae is one of the most destructive diseases causing extensive yield loss throughout the world. The present study deals with identification of stress responsive genes in susceptible rice cultivar HR 12 after challenge with M. oryzae. Transcript profiling using the Affymetrix 57 K GeneChip revealed a total of 72 differentially expressed genes whose expression level was significantly altered under diseased condition. Molecular function enrichment analysis suggested that the differentially regulated genes were mainly related to protein degradation and modification, cell signalling and stressrelated mechanisms. Our study reveals that majority of the genes of protein degradation and modification, transport, signalling and transcription factors are repressed at the initial stages of interaction. The host genes that were induced in response to pathogen infection included hormonal signalling, cell wall defense and transcription factors belonging to the WRKY super family. This study would be helpful in identification of early induced genes in pathogen associated molecular patterns (PAMP)-Triggered Immunity.

Trapping of Light in Nonlinear 1-D Photonic Crystal

Abstract: Theoretical studies on the group velocity of light wave in 1-D polystyrene/SiO2 nonlinear photonic crystal is investigated. The speed of light wave through these multilayered structures is calculated in the absence as well as in the presence of a high intensity controlling wave by using the transfer matrix method. This letter shows that we can trap a light wave inside the nonlinear 1-D photonic crystal by switching off the controlling wave.

Molecular details of ligand selectivity determinants in a promiscuous β-glucan periplasmic binding protein

Abstract: Background: Members of the periplasmic binding protein (PBP) superfamily utilize a highly conserved inter-domain ligand binding site that adapts to specifically bind a chemically diverse range of ligands. This paradigm of PBP ligand binding specificity was recently altered when the structure of the Thermotoga maritima cellobiose-binding protein (tmCBP) was solved. The tmCBP binding site is bipartite, comprising a canonical solvent-excluded region (subsite one), adjacent to a solvent-filled cavity (subsite two) where specific and semi-specific ligand recognition occur, respectively. Results: A molecular level understanding of binding pocket adaptation mechanisms that simultaneously allow both ligand specificity at subsite one and promiscuity at subsite two has potentially important implications in ligand binding and drug design studies. We sought to investigate the determinants of ligand binding selectivity in tmCBP through biophysical characterization of tmCBP in the presence of varying β-glucan oligosaccharides. Crystal structures show that whilst the amino acids that comprise both the tmCBP subsite one and subsite two binding sites remain fixed in conformation regardless of which ligands are present, the rich hydrogen bonding potential of water molecules may facilitate the ordering and the plasticity of this unique PBP binding site. Conclusions: The identification of the roles these water molecules play in ligand recognition suggests potential mechanisms that can be utilized to adapt a single ligand binding site to recognize multiple distinct ligands.

Hybrid feature selection and peptide binding affinity prediction using an EDA based algorithm

Abstract: Protein function prediction is an important problem in functional genomics. Typically, protein sequences are represented by feature vectors. A major problem of protein datasets that increase the complexity of classification models is their large number of features. The process of drug discovery often involves the use of quantitative structure-activity relationship (QSAR) models to identify chemical structures that could have good inhibitory effects on specific targets and have low toxicity (non-specific activity). QSAR models are regression or classification models used in the chemical and biological sciences. Because of high dimensionality problems, a feature selection problem is imminent. In this study, we thus employ a hybrid Estimation of Distribution Algorithm (EDA) based filter-wrapper methodology to simultaneously extract informative feature subsets and build robust QSAR models. The performance of the algorithm was tested on the benchmark classification challenge datasets obtained from the CoePRa competition platform, developed in 2006. Our results clearly demonstrate the efficacy of a hybrid EDA filter-wrapper algorithm in comparison to the results reported earlier.