Loss of frugivore seed dispersal services under climate change

The capacity of species to track shifting climates into the future will strongly influence outcomes for biodiversity under a rapidly changing climate. However, we know remarkably little about the dispersal abilities of most species and how these may be influenced by climate change. Here we show that climate change is projected to substantially reduce the seed dispersal services provided by frugivorous vertebrates in rainforests across the Australian Wet Tropics. Our model projections show reductions in both median and long-distance seed dispersal, which may markedly reduce the capacity of many rainforest plant species to track shifts in suitable habitat under climate change. However, our analyses suggest that active management to maintain the abundances of a small set of important frugivores under climate change could markedly reduce the projected loss of seed dispersal services and facilitate shifting distributions of rainforest plant species.

Socio-cultural protection of endemic trees in humanised landscape

Culturally protected forest patches or sacred groves have been the integral part of many traditional societies. This age old tradition is a classic instance of community driven nature conservation sheltering native biodiversity and supporting various ecosystem functions particularly hydrology. The current work in Central Western Ghats of Karnataka, India, highlights that even small sacred groves amidst humanised landscapes serve as tiny islands of biodiversity, especially of rare and endemic species. Temporal analysis of landuse dynamics reveals the changing pattern of the studied landscape. There is fast reduction of forest cover (15.14-11.02 %) in last 20 years to meet up the demand of agricultural land and plantation programs. A thorough survey and assessment of woody endemic species distribution in the 25 km(2) study area documented presence of 19 endemic species. The distribution of these species is highly skewed towards the culturally protected patches in comparison to other land use elements. It is found that, among the 19 woody endemic species, those with greater ecological amplitude are widely distributed in the studied landscape in groves as well as other land use forms whereas, natural population of the sensitive endemics are very much restricted in the sacred grove fragments. The recent degradation in the sacred grove system is perhaps, due to weakening of traditional belief systems and associated laxity in grove protection leading to biotic disturbances. Revitalisation of traditional practices related to conservation of sacred groves can go a long way in strengthening natural ecological systems of fragile humid tropical landscape.

Photoluminescence, thermoluminescence and EPR studies of solvothermally derived Ni2+ doped Y(OH)(3) and Y2O3 multi-particle-chain microrods

Rod like structures of hexagonal Y(OH)(3):Ni2+ and cubic Y2O3:Ni2+ phosphors have been successfully synthesized by solvothermal method. X-ray diffraction studies of as-formed product shows hexagonal phase, whereas the product heat treated at 700 degrees C shows pure cubic phase. Scanning electron micrographs (SEM) of Y(OH)(3):Ni2+ show hexagonal rods while Y2O3:Ni2+ rods were found to consist of many nanoparticles stacked together forming multi-particle-chains. EPR studies suggest that the site symmetry around Ni2+ ions is predominantly octahedral. PL spectra show emission in blue, green and red regions due to the T-3(1)(P-3)->(3)A(2)(F-3), T-1(2)(D-1)->(3)A(2)(F-3) and T-1(2)(D-1)-> T-3(2)(F-3) transitions of Ni2+ ions, respectively. TL studies were carried out for Y(OH)(3):Ni2+ and Y2O3:Ni2+ phosphor upon gamma-dose for 1-6 kGy. A single well resolved glow peaks at 195 and 230 degrees C were recorded for Y(OH)(3):Ni2+ and Y2O3:Ni2+, respectively. The glow peak intensity increases linearly up to 4 kGy and 5 kGy for Y(OH)(3):Ni2+ and Y2O3:Ni2+, respectively. The kinetic parameters such as activation energy (E), frequency factor (s) and order of kinetics (b) were estimated by different methods. The phosphor follows simple glow peak structure, linear response with gamma dose, low fading and simple trap distribution, suggesting that it is quite suitable for radiation dosimetry. (C) 2014 Elsevier B.V. All rights reserved.

Explosives Sensing by Using Electron-Rich Supramolecular Polymers: Role of Intermolecular Hydrogen Bonding in Significant Enhancement of Sensitivity

We demonstrate here that supramolecular interactions enhance the sensitivity towards detection of electron-deficient nitro-aromatic compounds (NACs) over discrete analogues. NACs are the most commonly used explosive ingredients and are common constituents of many unexploded landmines used during World WarII. In this study, we have synthesised a series of pyrene-based polycarboxylic acids along with their corresponding discrete esters. Due to the electron richness and the fluorescent behaviour of the pyrene moiety, all the compounds act as sensors for electron-deficient NACs through a fluorescence quenching mechanism. A Stern-Volmer quenching constant determination revealed that the carboxylic acids are more sensitive than the corresponding esters towards NACs in solution. The high sensitivity of the acids was attributed to supramolecular polymer formation through hydrogen bonding in the case of the acids, and the enhancement mechanism is based on an exciton energy migration upon excitation along the hydrogen-bond backbone. The presence of intermolecular hydrogen bonding in the acids in solution was established by solvent-dependent fluorescence studies and dynamic light scattering (DLS) experiments. In addition, the importance of intermolecular hydrogen bonds in solid-state sensing was further explored by scanning tunnelling microscopy (STM) experiments at the liquid-solid interface, in which structures of self-assembled monolayer of the acids and the corresponding esters were compared. The sensitivity tests revealed that these supramolecular sensors can even detect picric acid and trinitrotoluene in solution at levels as low as parts per trillion (ppt), which is much below the recommended permissible level of these constituents in drinking water.

Mining Unit Tests for Discovery and Migration of Math APIs

Today's programming languages are supported by powerful third-party APIs. For a given application domain, it is common to have many competing APIs that provide similar functionality. Programmer productivity therefore depends heavily on the programmer's ability to discover suitable APIs both during an initial coding phase, as well as during software maintenance. The aim of this work is to support the discovery and migration of math APIs. Math APIs are at the heart of many application domains ranging from machine learning to scientific computations. Our approach, called MATHFINDER, combines executable specifications of mathematical computations with unit tests (operational specifications) of API methods. Given a math expression, MATHFINDER synthesizes pseudo-code comprised of API methods to compute the expression by mining unit tests of the API methods. We present a sequential version of our unit test mining algorithm and also design a more scalable data-parallel version. We perform extensive evaluation of MATHFINDER (1) for API discovery, where math algorithms are to be implemented from scratch and (2) for API migration, where client programs utilizing a math API are to be migrated to another API. We evaluated the precision and recall of MATHFINDER on a diverse collection of math expressions, culled from algorithms used in a wide range of application areas such as control systems and structural dynamics. In a user study to evaluate the productivity gains obtained by using MATHFINDER for API discovery, the programmers who used MATHFINDER finished their programming tasks twice as fast as their counterparts who used the usual techniques like web and code search, IDE code completion, and manual inspection of library documentation. For the problem of API migration, as a case study, we used MATHFINDER to migrate Weka, a popular machine learning library. Overall, our evaluation shows that MATHFINDER is easy to use, provides highly precise results across several math APIs and application domains even with a small number of unit tests per method, and scales to large collections of unit tests.

Enriching the annotation of Mycobacterium tuberculosis H37Rv proteome using remote homology detection approaches: Insights into structure and function

The availability of the genome sequence of Mycobacterium tuberculosis H37Rv has encouraged determination of large numbers of protein structures and detailed definition of the biological information encoded therein; yet, the functions of many proteins in M. tuberculosis remain unknown. The emergence of multidrug resistant strains makes it a priority to exploit recent advances in homology recognition and structure prediction to re-analyse its gene products. Here we report the structural and functional characterization of gene products encoded in the M. tuberculosis genome, with the help of sensitive profile-based remote homology search and fold recognition algorithms resulting in an enhanced annotation of the proteome where 95% of the M. tuberculosis proteins were identified wholly or partly with information on structure or function. New information includes association of 244 proteins with 205 domain families and a separate set of new association of folds to 64 proteins. Extending structural information across uncharacterized protein families represented in the M. tuberculosis proteome, by determining superfamily relationships between families of known and unknown structures, has contributed to an enhancement in the knowledge of structural content. In retrospect, such superfamily relationships have facilitated recognition of probable structure and/or function for several uncharacterized protein families, eventually aiding recognition of probable functions for homologous proteins corresponding to such families. Gene products unique to mycobacteria for which no functions could be identified are 183. Of these 18 were determined to be M. tuberculosis specific. Such pathogen-specific proteins are speculated to harbour virulence factors required for pathogenesis. A re-annotated proteome of M. tuberculosis, with greater completeness of annotated proteins and domain assigned regions, provides a valuable basis for experimental endeavours designed to obtain a better understanding of pathogenesis and to accelerate the process of drug target discovery. (C) 2014 Elsevier Ltd. All rights reserved.

Belief propagation for minimum weight many-to-one matchings in the random complete graph

In a complete bipartite graph with vertex sets of cardinalities n and n', assign random weights from exponential distribution with mean 1, independently to each edge. We show that, as n -> infinity, with n' = n/alpha] for any fixed alpha > 1, the minimum weight of many-to-one matchings converges to a constant (depending on alpha). Many-to-one matching arises as an optimization step in an algorithm for genome sequencing and as a measure of distance between finite sets. We prove that a belief propagation (BP) algorithm converges asymptotically to the optimal solution. We use the objective method of Aldous to prove our results. We build on previous works on minimum weight matching and minimum weight edge cover problems to extend the objective method and to further the applicability of belief propagation to random combinatorial optimization problems.

Novel Functions of (p)ppGpp and Cyclic di-GMP in Mycobacterial Physiology Revealed by Phenotype Microarray Analysis of Wild-Type and Isogenic Strains of Mycobacterium smegmatis

The bacterial second messengers (p)ppGpp and bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) regulate important functions, such as transcription, virulence, biofilm formation, and quorum sensing. In mycobacteria, they regulate long-term survival during starvation, pathogenicity, and dormancy. Recently, a Pseudomonas aeruginosa strain lacking (p) ppGpp was shown to be sensitive to multiple classes of antibiotics and defective in biofilm formation. We were interested to find out whether Mycobacterium smegmatis strains lacking the gene for either (p)ppGpp synthesis (Delta rel(Msm)) or c-di-GMP synthesis (Delta dcpA) would display similar phenotypes. We used phenotype microarray technology to compare the growth of the wild-type and the knockout strains in the presence of several antibiotics. Surprisingly, the Delta rel(Msm) and Delta dcpA strains showed enhanced survival in the presence of many antibiotics, but they were defective in biofilm formation. These strains also displayed altered surface properties, like impaired sliding motility, rough colony morphology, and increased aggregation in liquid cultures. Biofilm formation and surface properties are associated with the presence of glycopeptidolipids (GPLs) in the cell walls of M. smegmatis. Thin-layer chromatography analysis of various cell wall fractions revealed that the levels of GPLs and polar lipids were reduced in the knockout strains. As a result, the cell walls of the knockout strains were significantly more hydrophobic than those of the wild type and the complemented strains. We hypothesize that reduced levels of GPLs and polar lipids may contribute to the antibiotic resistance shown by the knockout strains. Altogether, our data suggest that (p)ppGpp and c-di-GMP may be involved in the metabolism of glycopeptidolipids and polar lipids in M. smegmatis.

A cis-Regulatory Mutation in Troponin-I of Drosophila Reveals the Importance of Proper Stoichiometry of Structural Proteins During Muscle Assembly

Rapid and high wing-beat frequencies achieved during insect flight are powered by the indirect flight muscles, the largest group of muscles present in the thorax. Any anomaly during the assembly and/or structural impairment of the indirect flight muscles gives rise to a flightless phenotype. Multiple mutagenesis screens in Drosophila melanogaster for defective flight behavior have led to the isolation and characterization of mutations that have been instrumental in the identification of many proteins and residues that are important for muscle assembly, function, and disease. In this article, we present a molecular-genetic characterization of a flightless mutation, flightless-H (fliH), originally designated as heldup-a (hdp-a). We show that fliH is a cis-regulatory mutation of the wings up A (wupA) gene, which codes for the troponin-I protein, one of the troponin complex proteins, involved in regulation of muscle contraction. The mutation leads to reduced levels of troponin-I transcript and protein. In addition to this, there is also coordinated reduction in transcript and protein levels of other structural protein isoforms that are part of the troponin complex. The altered transcript and protein stoichiometry ultimately culminates in unregulated acto-myosin interactions and a hypercontraction muscle phenotype. Our results shed new insights into the importance of maintaining the stoichiometry of structural proteins during muscle assembly for proper function with implications for the identification of mutations and disease phenotypes in other species, including humans.

Experimental determination and theoretical correlation for the solubilities of dicarboxylic acid esters in supercritical carbon dioxide

The synthesis of high molecular weight esters such as bis (2-ethylhexyl) sebacate is of significance for its use as a lubricant. This ester is synthesized by the transesterification of dimethyl sebacate with 2-ethylhexanol. Therefore, the solubilities of bis (2-ethylhexyl) sebacate and dimethyl sebacate were determined at 308-328 K at pressures of 10-18 MPa in supercritical carbon dioxide. The solubility of dimethyl sebacate was always higher than bis (2-ethylhexyl) sebacate at a given temperature and pressure. The Mendez-Teja model was used to verify the self-consistency of data. Further, a new semi-empirical model with three parameters was developed using the solution theory coupled with Wilson activity coefficient. This model was used to correlate the experimental data of this work and solubilities of many high molecular weight esters reported in the literature. (C) 2015 Elsevier B.V. All rights reserved.

Joint Strength and Wall Deformation Characteristics of a Single-Cell Geocell Subjected to Uniaxial Compression

Geocells are three-dimensional expandable panels with a wide range of applications in geotechnical engineering. A geocell is made up of many internally connected single cells. The current study discusses the joint strength and the wall deformation characteristics of a single cell when it is subjected to uniaxial compression. The study helps to understand the causes for the failure of the single cell in a cellular confinement system. Experimental studies were conducted on single cells with cell pockets filled up with three different infill materials, namely silty clay, sand, and the aggregates. The results of the experimental study revealed that the deformation of the geocell wall decreases with the increase in the friction angle of the infill material. Experimental results were also validated using numerical simulations carried out using Lagrangian analysis software. The experiment and the numerical results were found to be in good agreement with each other. A simple analytical model based on the theory of thin cylinders is also proposed to calculate the accumulated strain of the geocell wall. This model operates under a simple elastic solution framework. The proposed model slightly overestimates the strains as compared with experimental and numerical values. (C) 2014 American Society of Civil Engineers.

SUPPORTING ENVIRONMENTALLY-BENIGN DESIGN ELUCIDATING ENVIRONMENTAL IMPACT PROPAGATION IN CONCEPTUAL DESIGN PHASE BY SAPPHIRE MODEL OF CAUSALITY

Conceptual Design Phase is the most critical for design decisions and their impact on the Environment. It is also a phase of many `unknowns' making it flexible and allowing exploration of many solutions. Thus, it is a challenge to determine the most Environmentally-benign Solution or Concept to be translated in to a `good' product. The SAPPhIRE Model captures the various levels of abstractions present in Conceptual Design by Outcomes and defines a Solution-variant as a set of verifiable and quantifiable Outcomes. The Causality explains the propagation of Environmental Impact across Outcomes at varying levels of abstraction, suggesting that the Environmental Impact of an Outcome at a certain level can be represented as a collation of Environmental Impact information of all the Outcomes at each of its subsequent lower levels of abstraction. Thus a ball-park impact value can be associated with the higher-levels of abstraction, thereby supporting design decisions taken earlier on in Conceptual Design directing towards Environmentally-benign Design.

Lifshitz transition and modulation of electronic and transport properties of bilayer graphene by sliding and applied normal compressive strain

Using density functional theory (DFT) we investigate the changes in electronic and transport properties of graphene bilayer caused by sliding one of the layers. Change in stacking pattern breaks the lattice symmetry, which results in Lifshitz transition together with the modulation of the electronic structure. Going from AA to AB stacking by sliding along armchair direction leads to a drastic transition in electronic structure from linear to parabolic dispersion. Our transport calculations show a significant change in the overall transmission value for large sliding distances along zigzag direction. The increase in interlayer coupling with normal compressive strain increases the overlapping of conduction and valence band, which leads to further shift in the Dirac points and an enhancement in the Lifshitz transition. The ability to tune the topology of band structure by sliding and/or applying normal compressive strain will open doors for controlled tuning of many physical phenomenon such as Landau levels and quantum Hall effect in graphene. (C) 2015 Elsevier Ltd. All rights reserved.

A glucose-centric perspective of hyperglycemia

Digestion of food in the intestines converts the compacted storage carbohydrates, starch and glycogen, to glucose. After each meal, a flux of glucose (>200 g) passes through the blood pool (4-6 g) in a short period of 2 h, keeping its concentration ideally in the range of 80-120 mg/100 mL. Tissue-specific glucose transporters (GLUTs) aid in the distribution of glucose to all tissues. The balance glucose after meeting the immediate energy needs is converted into glycogen and stored in liver (up to 100 g) and skeletal muscle (up to 300 g) for later use. High blood glucose gives the signal for increased release of insulin from pancreas. Insulin binds to insulin receptor on the plasma membrane and activates its autophosphorylation. This initiates the post-insulin-receptor signal cascade that accelerates synthesis of glycogen and triglyceride. Parallel control by phos-dephos and redox regulation of proteins exists for some of these steps. A major action of insulin is to inhibit gluconeogensis in the liver decreasing glucose output into blood. Cases with failed control of blood glucose have alarmingly increased since 1960 coinciding with changed life-styles and large scale food processing. Many of these turned out to be resistant to insulin, usually accompanied by dysfunctional glycogen storage. Glucose has an extended stay in blood at 8 mM and above and then indiscriminately adds on to surface protein-amino groups. Fructose in common sugar is 10-fold more active. This random glycation process interferes with the functions of many proteins (e.g., hemoglobin, eye lens proteins) and causes progressive damage to heart, kidneys, eyes and nerves. Some compounds are known to act as insulin mimics. Vanadium-peroxide complexes act at post-receptor level but are toxic. The fungus-derived 2,5-dihydroxybenzoquinone derivative is the first one known to act on the insulin receptor. The safe herbal products in use for centuries for glucose control have multiple active principles and targets. Some are effective in slowing formation of glucose in intestines by inhibiting alpha-glucosidases (e.g., salacia/saptarangi). Knowledge gained from French lilac on active guanidine group helped developing Metformin (1,1-dimethylbiguanide) one of the popular drugs in use. One strategy of keeping sugar content in diets in check is to use artificial sweeteners with no calories, no glucose or fructose and no effect on blood glucose (e.g., steviol, erythrytol). However, the three commonly used non-caloric artificial sweetener's, saccharin, sucralose and aspartame later developed glucose intolerance, the very condition they are expected to evade. Ideal way of keeping blood glucose under 6 mM and HbAlc, the glycation marker of hemoglobin, under 7% in blood is to correct the defects in signals that allow glucose flow into glycogen, still a difficult task with drugs and diets.

Nonlinear Constitutive Behavior Of Ferroelectric Materials

The ferroelectric specimen is considered as an aggregation of many randomly oriented domains. According to this mechanism, a multi-domain mechanical model is developed in this paper. Each domain is represented by one element. The applied stress and electric field are taken to be the stress and electric field in the formula of the driving force of domain switching for each element in the specimen. It means that the macroscopic switching criterion is used for calculating the volume fraction of domain switching for each element. By using the hardening relation between the driving force of domain switching and the volume fraction of domain switching calibrated, the volume fraction of domain switching for each element is calculated. Substituting the stress and electric field and the volume fraction of domain switching into the constitutive equation of ferroelectric material, one can easily get the strain and electric displacement for each element. The macroscopic behavior of the ferroelectric specimen is then directly calculated by volume averaging. Meanwhile, the nonlinear finite element analysis for the ferroelectric specimen is carried out. In the finite element simulation, the volume fraction of domain switching for each element is calculated by using the same method mentioned above. The interaction between different elements is taken into account in the finite element simulation and the local stress and electric field for each element is obtained. The macroscopic behavior of the specimen is then calculated by volume averaging. The computation results involve the electric butterfly shaped curves of axial strain versus the axial electric field and the hysteresis loops of electric displacement versus the electric field for ferroelectric specimens under the uniaxial coupled stress and electric field loading. The present theoretical prediction agrees reasonably with the experimental results.