bluuebunny/crossref_metadata_2025 huggingface dataset:
Direct detection ofCampylobacter jejuniin human stool samples by real-time PCR
Authors: Lin Shiyong , Wang Xinying , Zheng Haoxuan , Mao Zhengguo , Sun Yong , Jiang Bo
Published: September 2008

Our purpose was to establish a quick and accurate real-time PCR (rtPCR) method to detect Campylobacter jejuni directly from human diarrheal stool as an alternative to traditional culture methods. To determine the consistency of rtPCR and culture method, 256 clinical diarrheal stool samples and 50 normal stool samples from healthy individuals were examined, and the whole process was double-blinded. Our data showed that the sensitivity of rtPCR in pure cultures and stool was 102CFU·mL–1and 103CFU·g–1, respectively. Of the 256 diarrheal samples, 10 specimens were successfully detected by both methods, whereas two specimens were PCR positive but culture negative. No positive results were found by these two methods in 50 normal specimens. Our data suggested that rtPCR was convenient in operation and time-saving (turnaround time 3.5–4 h), so it could be used for clinical diagnostic and epidemiological purposes.
Impact of sheep urine deposition and plant species on ammonia-oxidizing bacteria in upland grassland soil
Authors: Rooney Deirdre C. , Clipson Nicholas
Published: September 2008

The effects of different concentrations of synthetic sheep urine and plant species on ammonia-oxidizing bacterial (AOB) communities in an upland grassland soil were investigated using a microcosm approach. Plant species characteristic of unimproved and improved agricultural pastures ( Agrostis capillaris and Lolium perenne , respectively) were planted in soil microcosms, and different levels of synthetic sheep urine were applied, with harvests 10 and 50 days following urine application. Shifts in the community structure of the AOB were investigated using terminal restriction fragment length polymorphism of amoA amplicons. Species richness and diversity were significantly altered by synthetic sheep urine addition and time depending on plant species type. Principal coordinate analysis revealed that AOB community structure was largely dependent on interactions between sheep urine deposition, plant species, and time after urine application, while significant changes in AOB structure were also revealed by similarity percentage analysis. The results of this study suggested that high levels of sheep urine, combined with floristic changes that are characteristic of agricultural intensification, can contribute to temporal and spatial changes in the structure of key bacterial communities in upland grassland soil. Changes in AOB community structure could potentially affect important soil processes, such as nitrification, with subsequent implications for nutrient cycling in agricultural systems.
Use of insertional mutagenesis to tag putative parasitic fitness genes in the Dutch elm disease fungus Ophiostoma novo-ulmi subsp. novo-ulmi
Authors: Plourde Karine V. , Jacobi Volker , Bernier Louis
Published: September 2008

We used insertional mutagenesis to produce genetically tagged mutants of the Dutch elm disease fungus Ophiostoma novo-ulmi subsp. novo-ulmi. We first optimized transformation of O. novo-ulmi protoplasts by the restriction enzyme mediated integration method. A concentration of 80 U of HindIII with 108 fungal protoplasts and 5 μg of plasmid DNA was the most efficient for generating a high number of O. novo-ulmi mutants carrying a single insertion in their genome. Mycelium- and yeast-like growth kinetics of 24 O. novo-ulmi mutants were evaluated in vitro. Flanking sequences were successfully recovered in 8% of the transformants analyzed. Some mutant phenotypes appeared to result from gene disruption events, whereas others likely involved modifications of noncoding regions. Several nuclear loci that control vegetative growth and could potentially impact parasitic fitness were successfully tagged.
Antioxidant, antihypertensive, and antibacterial properties of endophyticPestalotiopsisspecies from medicinal plants
Authors: Tejesvi Mysore V. , Kini Kukkundoor R. , Prakash Harishchandra S. , Subbiah Ven , Shetty Hunthrike S.
Published: September 2008

Pestalotiopsis species were most dominant endophytic species isolated from four medicinal plants including Terminalia arjuna , Terminalia chebula , Azadirachta indica , and Holarrhena antidysenterica . Thirty Pestalotiopsis species isolated from different parts of the medicinal plants were selected for the study. The antioxidant and antihypertensive properties of Pestalotiopsis isolates were determined by measuring 1,1-diphenyl-2-picrylhydrazyl inhibitory activity, lipid peroxidation, and angiotensin-converting enzyme inhibition activity. Pestalotiopsis isolates of T. arjuna origin exhibited maximum radical scavenging activity compared with the others. The IC50values of Pestalotiopsis extracts for 1,1-diphenyl-2-picrylhydrazyl scavenging activity ranged from 14 to 27 μg/mL compared with 15 and 6 μg/mL for butylated hydroxytoluene and ascorbic acid, respectively. The DNA damage study was also done for three isolates, TC-315, TA-37, and TA-60; TA-37 gave 80% protection. The IC50values of Pestalotiopsis extracts for lipid peroxidation ranged between 30 and 35.5 μg/mL, while for the positive control butylated hydroxytoluene, it was 26 μg/mL. Out of 32 fungal extracts screened for antihypertensive assay, five (TA-37, TA-60, TA-102, TA-103, and TC-320) showed >60% inhibition of angiotensin-converting enzyme. The IC50values for five extracts ranged from 21 to 37 μg/mL and was 20 μg/mL for captopril used as a positive control. The antibacterial activity was measured by the microplate-based turbidity measurement method. Four Pestalotiopsis extracts (TA-04, TA-37, TA-60, and TA-102) showed >75% inhibition against five bacterial strains including Bacillus subtilis , Escherichia coli , Pseudomonas fluorescens , Xanthomonas axonopodis pv. malvacearum, and Staphylococcus aureus . The antioxidant, antibacterial, and antihypertensive activities demonstrated the potential of Pestalotiopsis extracts as therapeutic targets.
COMPUTATIONAL CHARACTERIZATION OF THE ELUSIVE C-CLUSTER OF CARBON MONOXIDE DEHYDROGENASE
Authors: CAO ZEXING , MO YIRONG
Published: September 2008

Structural features of the C-cluster of carbon monoxide dehydrogenases at different redox states have been investigated by the density functional theory. The key species involved in the oxidation of CO at clusters C , Cox, Cred1, Cred2, and Cint, have been specified. Computational results indicate that the CO -induced transformation of the [Ni–4Fe–5S] cluster C into the [Ni–4Fe–4S] cluster is facile energetically, and such structural conversion at the active site may reconcile different reported crystal structures of cluster C. The coordination of CO to the Ni site of the reduced C-cluster (Cred1) will enhance its electron accommodation ability and makes Fe1 more accessible to other substrates, which lends support to the assumption that Cred1is a ready state for CO oxidation. On the basis of calculations, the possible catalytic cycle for the oxidation of CO at cluster C was proposed.
DFT STUDIES ON THE STABILITY OF THE TRANS AND CIS ISOMERS IN THE SQUARE PLANAR PALLADIUM(II) COMPLEXES Pd(I)(PPh3)(η3-XCHC(Ph)CHR) (X = CMe3, CO2Me, P(O)(OMe)2, AND SO2H; R = H, Me)
Authors: XUE LIQIN , JIA GUOCHEN , LIN ZHENYANG
Published: September 2008

The relative stability of the trans and cis isomers in the square planar palladium(II) complexes Pd ( I )( PPh 3)(η3- XCHC ( Ph ) CHR ) ( X = H , Me , CMe 3, CO 2 Me , P ( O )( OMe )2, and SO 2 H ; R = H , Me ) was investigated with the aid of the B3LYP density functional theory calculations. We examined how the substituents X, with different electronic properties, of the η3-allyl ligands affect the relative stability of the trans and cis isomers. Through the investigation, we were able to explain the trans/cis relative stability derived from the experimentally measured trans/cis isomer ratios in the palladium(II) complexes.
EXCITON BINDING ENERGY OF ELECTRONIC POLYMERS: A FIRST PRINCIPLES STUDY
Authors: ZHU LINGYUN , YI YUANPING , CHEN LIPING , SHUAI ZHIGANG
Published: September 2008

Exciton binding energy (E b ) is a key factor for the polymer electronics as well as for the fundamental polymer physics, which has been controversial since long time. Light-emitting polymer requires a large E b so that the charge recombination dominates. But, the photovoltaic polymers need small E b to allow efficient charge separation. First-principles Density Functional Theory (DFT) is employed to calculate E b for polydiacetylene (PDA), trans-polyacetylene (PA), polythiophene (PT), poly(2,5-thienylenevinylene) (PTV), and poly(p-phenylene vinylene) (PPV). We find that the hybrid B3LYP, B972, PBE1PBE, and B1B95 functionals with 20–25% amount of exact HF exchange can give reasonable results and predict E b is around 0.1–0.6 eV for these π-conjugated polymers.
STRUCTURE AND STABILITY OF HYDROGEN POOR CLOSO-${\rm B}_{n}{\rm H}_{n-x}^{-/0/+}$ (n = 5 - 12)
Authors: QIN XIAO-FANG , WU HAI-SHUN , JIAO HAIJUN
Published: September 2008

Structures and stabilities of hydrogen poor closo-[Formula: see text], closo- B n H n-2, and closo-[Formula: see text] (n = 5 - 12) have been investigated at the B3LYP/6-311+G** density functional level of theory. It is found that [Formula: see text], B 5 H 3, [Formula: see text], and [Formula: see text] have open instead of the expected closo structures, and the other isomers have the same structural pattern as closo-[Formula: see text]. Energetic analysis identifies closo-[Formula: see text] (n = 7, 9), closo- B n H n-2 (n = 7, 11), and closo-[Formula: see text] (n = 6, 8, 10) as the most stable clusters. The CO affinities of the most stable closo- B n H n-1 CO -, closo- B n H n-2( CO )2, and closo-[Formula: see text] (n = 5 - 12) have been computed.
CATALYTIC REACTION MECHANISM OF HUMAN PHOTORECEPTOR RETINOL DEHYDROGENASE: A THEORETICAL STUDY
Authors: YAO YUAN , HAN WEI-WEI , ZHOU YI-HAN , LUO QUAN , LI ZE-SHENG
Published: September 2008

Human photoreceptor retinol dehydrogenase (hRDH8) catalyzes the reduction of all-trans-retinal to all-trans-retinol with NADPH as a rate-limiting step in the visual cycle. Based on the docking results of the substrate to the 3D structure of hRDH8 which is generated by homology modeling method, three quantum chemical calculation models with different sizes were used to investigate the catalytic reaction mechanism of hRDH8 with the aid of density functional theory. The calculations indicate that hRDH8 employs a general acid/base mechanism that a proton is transferred to the keto oxygen of the substrate after the pro-S hydride of NADPH transfer to keto carbon of the substrate. The H-transfer order is converse to that in the proposed mechanism of 17ß-hydroxysteroid dehydrogenase 1, which is highly related to the hRDH8 sequence. Tyr155 always provides the proton to the keto oxygen of the substrate whether unprotonated Lys159 is considered or not in the calculation models. However, protonated Lys159 changes the initial mechanism and replaces Tyr155 to provide the proton to the keto oxygen of the substrate. Moreover, protonated Lys159 can also decrease very effectively the Gibbs free energy barrier to make the reaction indeed energetically feasible. The role of Lys159 in hRDH8 is different from that in 17ß-hydroxysteroid dehydrogenase 1. The solvent effect calculations indicate that the reaction is more feasible energetically in the protein electrostatic environment than in the gas phase.
THEORETICAL STUDIES ON THE LASER-DRIVEN MANY-ELECTRON DYNAMICS OF FINITE-SIZE BORON-NITRIDE NANOTUBES
Authors: SUN JIN , LIANG WAN-ZHEN , LIU YU
Published: September 2008

We present a theoretical study on the electronic dynamics of finite-size Boron-Nitride Nanotubes (BNNTs) driven by the linearly polarized (LP) and circularly polarized (CP) intense laser fields. The many-electron dynamics is described by propagating the reduced one-electron density matrix in real-time domain. The high harmonic generation (HHG) spectra and the time evolution of charge density during harmonic generation are demonstrated. Comparison is made with Carbon Nanotubes (CNTs). The selection rules (SRs) for HHG of finite-size nanotubes are established. One of the important consequences of our results is that HHG of finite-size nanotubes are dependent not only on the molecular point-groups but also on the strength of inter chain interactions. The characteristic difference in nonlinear optical properties between finite and infinitely extended zigzag and armchair BNNTs is significant. Another important consequence is that the laser pulse can drive the electrons to move along or normal to tube axis and produce a charge current on the tube wall.
A VALENCE BOND APPROACH BASED ON LEWIS STRUCTURES
Authors: CHEN ZHENHUA , SONG JINSHUAI , SONG LINGCHUN , WU WEI
Published: September 2008

In this paper, a valence bond method based on Lewis structures, called LVB, is presented. The method uses a Slater determinant expansion of doubly occupied orbitals for describing a Lewis structure, where two orbital sets, semi-localized orbitals, called bond orbitals, and localized hybrid atomic orbitals (HAOs), are employed. The levels of LVB method are fashioned as LVBS, LVBSD, etc. LVBS involves only the single bond orbital replacements with HAOs, while LVBSD involves also double replacements, and so on. Tests of three examples, methane, methylene, and benzene, show that the LVB method at both of LVBS and LVBSD levels gives results that match those of the VBSCF method very well, even though the form of LVB wave function is much compact.
VIBRATIONALLY AVERAGED POTENTIAL ENERGY SURFACES AND PREDICTED INFRARED SPECTRA OF THE He–18O13C18O AND He–16O13C16O COMPLEXES
Authors: CUI YALI , RAN HONG , XIE DAIQIAN
Published: September 2008

Vibrationally averaged potential energy surfaces for isotopic He–CO 2 complexes ( He –18 O 13 C 18 O and He –16 O 13 C 16 O ) are presented. Based on the latest ab initio potential of He –16 O 12 C 16 O (Ran H, Xie D, J Chem Phys128:124323, 2008.) including the Q3 normal mode for the v3 antisymmetric stretching vibration of the CO 2 molecule, the averaged potentials for both He –18 O 13 C 18 O and He –16 O 13 C 16 O are obtained by integrating the potential energy surfaces over the Q3 normal mode. The averaged potentials have T-shaped global minima and two equivalent linear local minima. The radial discrete variable representation/angular finite basis representation method and Lanczos algorithm are employed to calculate the related rovibrational energy levels. The calculated band origin shifts of He –18 O 13 C 18 O and He –16 O 13 C 16 O are 0.1066 and 0.0914 cm-1, respectively, which agree very well with the observed values of 0.1123 and 0.0929 cm-1. The calculated rovibrational transitions of He –18 O 13 C 18 O and He –16 O 13 C 16 O are also in very good agreement with the available experimental spectra.
INTRAMOLECULAR CHARGE TRANSFER AND PHOTOISOMERIZATION OF THE DCM STYRENE DYE: A THEORETICAL STUDY
Authors: XU XUEFEI , ZHANG RUIQIN , CAO ZEXING , ZHANG QIANER
Published: September 2008

Structures and properties of the low-lying states in 4-(dicyanomethylene)-2-methyl-6-(p-dimethylaminostyryl)-4H-pyran (DCM) have been investigated theoretically. Calculations show that the dimethylamino and dimethylanilino twisted conformations of DCM on the potential energy surface of the first excited state ( S 1) have relatively high stabilities and remarkable intramolecular charge transfers (ICT). Both structures can serve as candidates for the red-shifted emissive state in polar solvent. In particular, the dimethylanilino twisted ICT state has been predicted to have a dipole moment increment of 20 Debye with respect to the ground state by CASSCF calculations, in good agreement with the suggested experimental values. The optimized geometry of the S 1 state exhibits a long central CC bond of 1.458 Å, which makes the trans–cis isomerization quite facile through intramolecular rotation around the central CC bond on the S 1 potential surface. The S 1 state is a precursor to the formation of the ICT emissive state and photoinduced trans–cis isomerization. The S 1/ S 0 crossing in polar solvent and avoid-crossing in the gas phase as well as in non-polar solvent are involved in the trans–cis isomerization process. The presence of an early S 1/ S 0 crossing in the strong polar solvent reduces the isomerization efficiency.
SIZE EFFECT OF ENCASED ATOM ON ABSORPTION AND NONLINEAR OPTICAL PROPERTIES OF EMBEDDED METALLOFULLERENES M@C82 (M = Sc, Y, La)
Authors: HU HUI , CHENG WEN-DAN , HUANG SHU-PING , XIE ZHI , ZHANG HAO
Published: September 2008

The linear absorption spectra and third-order nonlinear optical properties of M@ C 82 (M = Sc , Y , La ) nanostructural materials, whose configurations were optimized at the unrestricted open shell UB3LYP level, are simulated by the sum-over-states combined with the time-dependent UB3LYP methods. The obtained results show that the electronic absorption bands have redshifts, and the values of third-order nonlinear optical polarizabilities and two-photon absorption cross sections increase for M@ C 82 fullerenes (M = Sc , Y , La ) as the atomic radius of encased metal M increase in the order of Sc → Y → La . It is indicated that the electron-donating ability from the encased M atom to cage C 82 decreases or the electron-accepting ability from C 82 to M atom increases as the atomic radius of M increases, which results in third-order nonlinear optical response enhancement in the order of Sc @ C 82 < Y @ C 82 < La @ C 82. This gives a clue to design the nanostructural materials of encased fullerenes having a large nonlinear optical response.
GEOMETRIES AND ENERGY SEPARATIONS OF ELECTRONIC STATES OF In3N, InN3, AND THEIR IONS
Authors: CAO ZHIJI , BALASUBRAMANIAN KRISHNAN
Published: September 2008

Spectroscopic properties of the low-lying electronic states of In 3 N , InN 3, and their ions are computed by the complete active-space self-consistent field (CASSCF) followed by multireference singles + doubles configuration interaction (MRSDCI) calculations. Our results predict that the spectra of In 3 N / InN 3 are substantially different from those of Ga 3 As / GaAs 3 and Al 3 P / AlP 3 tetramers. The ground state of In 3 N is a closed-shell 1 A ′1 state with a planar D 3h symmetry, whereas the ground state of InN 3 is a 1Σ+ state of linear In – N – N – N structure. The equilibrium geometries, vibrational frequencies, atomization energies, adiabatic ionization potentials, electron affinities, and other properties are discussed.
POSE SCALING: GEOMETRICAL ASSESSMENT OF LIGAND BINDING POSES
Authors: ZHONG SHIJUN , MACKERELL ALEXANDER D.
Published: September 2008

A descriptor, the pose scaling factor, is proposed to quantitatively evaluate the geometrical match between a ligand and a target binding site. The pose scaling factor can be used to readily rank results of target-based in silico database screening or docking on large numbers of compounds. Such an approach will be of utility in the development and refinement of docking algorithms.
SPIN DENSITY OF SPIN-FREE VALENCE BOND WAVE FUNCTIONS AND ITS IMPLEMENTATION IN VB2000
Authors: LI JIABO , DUKE BRIAN J. , KLAPÖTKE THOMAS M. , MCWEENY ROY
Published: September 2008

The expressions for computing the spin density of spin-free valence bond wave functions are derived based on the bonded tableaux approach. The new expressions, although similar to the original forms given by Cooper and McWeeny in the 1960s, are simpler and thus easier for coding. The new formulation was implemented in VB2000, an ab initio valence bond program based on algebrant algorithm and group function theory. The spin density calculation for multi-group VB wave functions is also briefly discussed. As examples of applications, the spin densities of allyl radical and diazide anion [Formula: see text] were computed at different VB levels.
HYPERFINE COUPLING CONSTANTS OF FLUORINATED BENZENE RADICAL CATIONS: A DFT B3LYP AND MP2 STUDY
Authors: XIAO HONG-YAN , LIU YA-JUN , FANG WEI-HAI , LIU RUO-ZHUANG , SHIOTANI MASARU
Published: September 2008

The EPR spectra of a series of fluorinated benzene radical cations were first-time assigned by MP2//B3LYP quantum chemical calculations. Most of the calculated values are in agreement with the experimentally observed ones. The hyperfine structures of some cations with near-degenerated states were well assigned with the help of extra QCISD calculations.
THEORETICAL STUDY OF GLYCINE CONFORMERS
Authors: KE HONG-WEI , RAO LI , XU XIN , YAN YI-JING
Published: September 2008

Glycine conformers were investigated with three density functional theory (DFT) methods (B3LYP, PBE1PBE, X3LYP), and the second order Møller–Plesset perturbation theory (MP2) combined with basis sets of 6-31+G*, aug-cc-pVDZ, and aug-cc-pVTZ. Solvation effects were considered by using polarizable continuum model. Results from B3LYP and X3LYP were in generally good agreement with those of MP2, while PBE1PBE was shown to be inferior for the description of conformational potential energy surfaces. Conformers Ip, IIp, IIn, IIIp, IIIn, and IVn were all found to be low-lying states within 2.0 kcal/mol, with Ip being the global minimum in gas phase. Solvation effects can significantly change the nature of the conformational surfaces of glycine. A proper description of conformational equilibrium demands for a good treatment of both long-range and short-range solute–solvent interactions.
A STATE-TO-STATE QUANTUM DYNAMICAL STUDY OF THE H + HBr REACTION
Authors: FU BINA , ZHOU YONG , ZHANG DONG H.
Published: September 2008

The time-dependent wave packet method was used to calculate the state-to-state differential cross sections for abstraction and exchange processes in the title reaction on the Kurosaki–Takayanagi potential energy surface [Kurosaki Y, Takayanagi T, J Chem Phys119:7838, 2003], with the reactant HBr initially in the ground rovibrational state. It is found that the trend in the product distributions is similar for abstraction and exchange processes, but the differential cross sections are very different. For the exchange reaction, the product is mainly scattered in the backward hemisphere for collision energy up to 2.0 eV, although forward scattering gradually shows up in high collision energies. While for abstraction reaction, the differential cross section changes substantially with the collision energy, moving from predominantly backward peaked at low collision energy to predominantly forward peaked at high collision energy. The rovibrational state resolved differential cross section at collision energy of 2.0 eV exhibits two peaks for the abstraction reaction, one is around the angle of 50°, and the other at 0°. It is found that the peaks around 50°, are below the corresponding maximum j' lines provided by the kinematic constraint model, while the forward-scattered peaks straddle both sides of the kinematic limit, and are likely contributed from both the direct and the migratory reaction mechanisms as proposed by Zare and coworkers.
Vital effects and beyond: a modelling perspective on developing palaeoceanographical proxy relationships in foraminifera
Authors: Zeebe Richard E. , Bijma Jelle , Hönisch Bärbel , Sanyal Abhijit , Spero Howard J. , Wolf-Gladrow Dieter A.
Published: September 2008

This paper mainly reviews our recent work on the biology and geochemistry of foraminifera with respect to their use as palaeoceanographic proxies. Our approach to proxy validation and development is described, primarily from a modeler's point of view. The approach is based on complementary steps in understanding the inorganic chemistry, inorganic isotope fractionation, and biological controls that determine palaeo-tracer signals in organisms used in climate reconstructions. Integration of laboratory experiments, field and culture studies, theoretical considerations and numerical modelling holds the key to the method's success. We describe effects of life-processes in foraminifera on stable carbon, oxygen, and boron isotopes as well as Mg incorporation into foraminiferal calcite shells. Stable boron isotopes will be used to illustrate our approach. We show that a mechanism-based understanding is often required before primary climate signals can be extracted from the geologic record because the signals can be heavily overprinted by secondary, non-climate related phenomena. Moreover, for some of the proxies, fundamental knowledge on the thermodynamic, inorganic basis is still lacking. One example is stable boron isotopes, a palaeo-
p
H proxy, for which the boron isotope fractionation between the dissolved boron compounds in seawater was not precisely known until recently. Attempts to overcome such hurdles are described and implications of our work for palaeoceanographic reconstructions are discussed.
Foraminifer test preservation and diagenesis: comparison of high latitude Eocene sites
Authors: Pearson Paul N. , Burgess Catherine E.
Published: September 2008

Foraminifer tests are prone to diagenetic recrystallization on a micron scale that can affect their geochemical composition, hence it is important to identify fossil material that is well-preserved. Here we illustrate the textures of tests from several high-latitude Eocene sites using a combination of Reflected Light Microscopy and high-resolution Scanning Electron Microscopy. The sites are Ocean Drilling Program (ODP) Site 647 in the Labrador Sea (53°N), ODP Site 689 at Maud Rise in the Weddell Sea (64°S), ODP Site 1135 (Kerguelen Plateau
c
. 59°S) and outcrop samples from Hampden Beach, New Zealand (palaeolatitude
c
. 55°S). The foraminifera studied from Site 647 and Hampden Beach have glassy, transparent tests that show only minor signs of diagenetic alteration, whereas the foraminifera from Sites 690 and 1135 are opaque and recrystallized. We associate the better state of foraminifer preservation at the former sites with the high clay content of the sediments. Our observations suggest that Site 647 and Hampden Beach may be useful for the establishment of high-latitude sea-surface temperatures and hence global temperature gradients in the Eocene.
The influences of growth rates on planktic foraminifers as proxies for palaeostudies – a review
Authors: Schmidt D. N. , Elliott T. , Kasemann S. A.
Published: September 2008

Size dependent changes in element concentrations in planktic foraminifers have long been recognized to influence their reliability as an archive for climate change. Traditionally, these changes have been interpreted as changes in element partitioning during the ontogeny of the organism with faster growth rates in the earlier part of the development. These changes, in the light of new culture experiments, can also be interpreted as changes in growth rate throughout the entire life of the organism, with larger, faster-growing specimens discriminating less efficiently against trace element incorporation into the calcite shell. Growth rates of foraminifera are influenced by the environment and hence change geographically and temporally at various scales, e.g. glacial-interglacial or rapid millennial events such as the Younger Dryas. These changes in growth rate can account for some changes in element to calcium ratio between glacial and interglacials, which were previously linked to changes in seawater element ratios.
Undecidability of the unification and admissibility problems for modal and description logics
Authors: Wolter Frank , Zakharyaschev Michael
Published: September 2008

We show that the unification problem “is there a substitution instance of a given formula that is provable in a given logic?” is undecidable for basic modal logics K and K4 extended with the universal modality. It follows that the admissibility problem for inference rules is undecidable for these logics as well. These are the first examples of standard decidable modal logics for which the unification and admissibility problems are undecidable. We also prove undecidability of the unification and admissibility problems for K and K4 with at least two modal operators and nominals (instead of the universal modality), thereby showing that these problems are undecidable for basic hybrid logics. Recently, unification has been introduced as an important reasoning service for description logics. The undecidability proof for K with nominals can be used to show the undecidability of unification for Boolean description logics with nominals (such as ALCO and SHIQO). The undecidability proof for K with the universal modality can be used to show that the unification problem relative to role boxes is undecidable for Boolean description logics with transitive roles, inverse roles, and role hierarchies (such as SHI and SHIQ).
Open answer set programming with guarded programs
Authors: Heymans Stijn , Nieuwenborgh Davy Van , Vermeir Dirk
Published: September 2008

Open answer set programming (OASP) is an extension of answer set programming where one may ground a program with an arbitrary superset of the program's constants. We define a fixed-point logic (FPL) extension of Clark's completion such that open answer sets correspond to models of FPL formulas and identify a syntactic subclass of programs, called (loosely)guarded programs. Whereas reasoning with general programs in OASP is undecidable, the FPL translation of (loosely) guarded programs falls in the decidable (loosely) guarded fixed-point logic (μ(L)GF). Moreover, we reduce normal closed ASP to loosely guarded OASP, enabling, for the first time, a characterization of an answer set semantics by μLGF formulas.

We further extend the open answer set semantics for programs with generalized literals. Suchgeneralized programs (gPs)have interesting properties, for example, the ability to express infinity axioms. We restrict the syntax of gPs such that both rules and generalized literals areguarded. Via a translation to guarded fixed-point logic, we deduce 2-EXPTIME-completeness of satisfiability checking in suchguarded gPs(GgPs).Bound GgPsare restricted GgPs with EXPTIME-complete satisfiability checking, but still sufficiently expressive to optimally simulatecomputation tree logic(CTL). We translate Datalog lite programs to GgPs, establishing equivalence of GgPs under an open answer set semantics, alternation-free μGF, and Datalog LITE.
Verifiable agent interaction in abductive logic programming
Authors: Alberti Marco , Chesani Federico , Gavanelli Marco , Lamma Evelina , Mello Paola , Torroni Paolo
Published: September 2008

SCIFF is a framework thought to specify and verify interaction in open agent societies. The SCIFF language is equipped with a semantics based on abductive logic programming; SCIFF's operational component is a new abductive logic programming proof procedure, also named SCIFF, for reasoning with expectations in dynamic environments. In this article we present the declarative and operational semantics of the SCIFF language, and the termination, soundness, and completeness results of the SCIFF proof procedure, and we demonstrate SCIFF's possible application in the multiagent domain.
Correlated pattern mining in quantitative databases
Authors: Ke Yiping , Cheng James , Ng Wilfred
Published: September 2008

We study mining correlations from quantitative databases and show that this is a more effective approach than mining associations to discover useful patterns. We propose the novel notion of
quantitative correlated pattern
(QCP), which is founded on two formal concepts, mutual information and all-confidence. We first devise a normalization on mutual information and apply it to the problem of QCP mining to capture the dependency between the attributes. We further adopt all-confidence as a quality measure to ensure, at a finer granularity, the dependency between the attributes with specific quantitative intervals. We also propose an effective supervised method that combines the consecutive intervals of the quantitative attributes based on mutual information, such that the interval-combining is guided by the dependency between the attributes. We develop an algorithm,
QCoMine
, to mine QCPs efficiently by utilizing normalized mutual information and all-confidence to perform bilevel pruning. We also identify the redundancy existing in the set of QCPs and propose effective techniques to eliminate the redundancy. Our extensive experiments on both real and synthetic datasets verify the efficiency of
QCoMine
and the quality of the QCPs. The experimental results also justify the effectiveness of our proposed techniques for redundancy elimination. To further demonstrate the usefulness and the quality of QCPs, we study an application of QCPs to classification. We demonstrate that the classifier built on the QCPs achieves higher classification accuracy than the state-of-the-art classifiers built on association rules.
Workload-aware anonymization techniques for large-scale datasets
Authors: LeFevre Kristen , DeWitt David J. , Ramakrishnan Raghu
Published: September 2008

Protecting individual privacy is an important problem in microdata distribution and publishing. Anonymization algorithms typically aim to satisfy certain privacy definitions with minimal impact on the quality of the resulting data. While much of the previous literature has measured quality through simple one-size-fits-all measures, we argue that quality is best judged with respect to the workload for which the data will ultimately be used.

This article provides a suite of anonymization algorithms that incorporate a target class of workloads, consisting of one or more data mining tasks as well as selection predicates. An extensive empirical evaluation indicates that this approach is often more effective than previous techniques. In addition, we consider the problem of scalability. The article describes two extensions that allow us to scale the anonymization algorithms to datasets much larger than main memory. The first extension is based on ideas from scalable decision trees, and the second is based on sampling. A thorough performance evaluation indicates that these techniques are viable in practice.
Efficient online index construction for text databases
Authors: Lester Nicholas , Moffat Alistair , Zobel Justin
Published: September 2008

Inverted index structures are a core element of current text retrieval systems. They can be constructed quickly using offline approaches, in which one or more passes are made over a static set of input data, and, at the completion of the process, an index is available for querying. However, there are search environments in which even a small delay in timeliness cannot be tolerated, and the index must always be queryable and up to date. Here we describe and analyze a
geometric partitioning
mechanism for online index construction that provides a range of tradeoffs between costs, and can be adapted to different balances of insertion and querying operations. Detailed experimental results are provided that show the extent of these tradeoffs, and that these new methods can yield substantial savings in online indexing costs.
A distributed and self-organizing scheduling algorithm for energy-efficient data aggregation in wireless sensor networks
Authors: Chatterjea Supriyo , Nieberg Tim , Meratnia Nirvana , Havinga Paul
Published: September 2008

Wireless sensor networks (WSNs) are increasingly being used to monitor various parameters in a wide range of environmental monitoring applications. In many instances, environmental scientists are interested in collecting raw data using long-running queries injected into a WSN for analyzing at a later stage, rather than injecting snap-shot queries containing data-reducing operators (e.g., MIN, MAX, AVG) that aggregate data. Collection of raw data poses a challenge to WSNs as very large amounts of data need to be transported through the network. This not only leads to high levels of energy consumption and thus diminished network lifetime but also results in poor data quality as much of the data may be lost due to the limited bandwidth of present-day sensor nodes. We alleviate this problem by allowing certain nodes in the network to aggregate data by taking advantage of spatial and temporal correlations of various physical parameters and thus eliminating the transmission of redundant data. In this article we present a distributed scheduling algorithm that decides when a particular node should perform this novel type of aggregation. The scheduling algorithm autonomously reassigns schedules when changes in network topology, due to failing or newly added nodes, are detected. Such changes in topology are detected using cross-layer information from the underlying MAC layer. We first present the theoretical performance bounds of our algorithm. We then present simulation results, which indicate a reduction in message transmissions of up to 85% and an increase in network lifetime of up to 92% when compared to collecting raw data. Our algorithm is also capable of completely eliminating dropped messages caused by buffer overflow.
Implementing public-key infrastructure for sensor networks
Authors: Malan David J. , Welsh Matt , Smith Michael D.
Published: September 2008

We present a critical evaluation of the first known implementation of elliptic curve cryptography over F

2
p

for sensor networks based on the 8-bit, 7.3828-MHz MICA2 mote. We offer, along the way, a primer for those interested in the field of cryptography for sensor networks. We discuss, in particular, the decisions underlying our design and alternatives thereto. And we elaborate on the methodologies underlying our evaluation.

Through instrumentation of UC Berkeley's TinySec module, we argue that, although symmetric cryptography has been tractable in this domain for some time, there has remained a need, unfulfilled until recently, for an efficient, secure mechanism for distribution of secret keys among nodes. Although public-key infrastructure has been thought impractical, we show, through analysis of our original implementation for TinyOS of point multiplication on elliptic curves, that public-key infrastructure is indeed viable for TinySec keys' distribution, even on the MICA2. We demonstrate that public keys can be generated within 34 seconds and that shared secrets can be distributed among nodes in a sensor network within the same time, using just over 1 kilobyte of SRAM and 34 kilobytes of ROM. We demonstrate that communication costs are minimal, with only 2 packets required for transmission of a public key among nodes. We make available all of our source code for other researchers to download and use. And we discuss recent results based on our work that corroborate and improve upon our conclusions.
Least privilege and privilege deprivation
Authors: Song Hui , Zhu Sencun , Zhang Wensheng , Cao Guohong
Published: September 2008

Mobile sinks are needed in many sensor network applications for efficient data collection, data querying, localized sensor reprogramming, identifying, and revoking compromised sensors, and other network maintenance. Employing mobile sinks however raises a new security challenge: if a mobile sink is given too many privileges, it will become very attractive for attack and compromise. Using a compromised mobile sink, an adversary may easily bring down or even take over the sensor network. Thus, security mechanisms that can tolerate mobile sink compromises are essential. In this article, based on the
principle of least privilege
, we first propose an efficient scheme to restrict the privilege of a mobile sink without impeding its ability to carry out any authorized operations for an assigned task. In addition, we present an extension to allow conditional trajectory change due to unexpected events. To further reduce the possible damage caused by a compromised mobile sink, we propose efficient message forwarding schemes for deleting the privilege assigned to a compromised mobile sink immediately after its compromise has been detected. Through detailed analysis, simulation, and real implementation, we show that our schemes are secure and efficient, and are highly practical for sensor networks consisting of the current generation of sensors.
The impact of spatial correlation on routing with compression in wireless sensor networks
Authors: Pattem Sundeep , Krishnamachari Bhaskar , Govindan Ramesh
Published: September 2008

The efficacy of data aggregation in sensor networks is a function of the degree of spatial correlation in the sensed phenomenon. The recent literature has examined a variety of schemes that achieve greater data aggregation by routing data with regard to the underlying spatial correlation. A well known conclusion from these papers is that the nature of optimal routing with compression depends on the correlation level. In this article we show the existence of a simple, practical, and static correlation-unaware clustering scheme that satisfies a min-max near-optimality condition. The implication for system design is that a static correlation-unaware scheme can perform as well as sophisticated adaptive schemes for joint routing and compression.
Asynchronous in-network prediction
Authors: Edara Pavan , Limaye Ashwin , Ramamritham Krithi
Published: September 2008

Given a sensor network and aggregate queries over the values sensed by subsets of nodes in the network, how do we ensure that high quality results are served for the maximum possible time? The issues underlying this question relate to the fidelity of query results and lifetime of the network. To maximize both, we propose a novel technique called
asynchronous in-network prediction
incorporating two computationally efficient methods for in-network prediction of partial aggregate values. These values are propagated via a tree whose construction is cognizant of (a) the coherency requirements associated with the queries, (b) the remaining energy at the sensors, and (c) the communication and message processing delays. Finally, we exploit
in-network filtering
and
in-network aggregation
to reduce the energy consumption of the nodes in the network. Experimental results over real world data support our claim that, for aggregate queries with associated coherency requirements, a prediction-based, asynchronous scheme provides higher quality results for a longer amount of time than a synchronous scheme. Also, whereas aggregate dissemination techniques proposed so far for sensor networks appear to have to trade-off quality of data for energy efficiency, we demonstrate that this is not always necessary.
A semantics-based approach to malware detection
Authors: Preda Mila Dalla , Christodorescu Mihai , Jha Somesh , Debray Saumya
Published: September 2008

Malware detection is a crucial aspect of software security. Current malware detectors work by checking for
signatures
, which attempt to capture the syntactic characteristics of the machine-level byte sequence of the malware. This reliance on a syntactic approach makes current detectors vulnerable to code obfuscations, increasingly used by malware writers, that alter the syntactic properties of the malware byte sequence without significantly affecting their execution behavior.

This paper takes the position that the key to malware identification lies in their semantics. It proposes a semantics-based framework for reasoning about malware detectors and proving properties such as soundness and completeness of these detectors. Our approach uses a trace semantics to characterize the behavior of malware as well as that of the program being checked for infection, and uses abstract interpretation to “hide” irrelevant aspects of these behaviors. As a concrete application of our approach, we show that (1) standard signature matching detection schemes are generally sound but not complete, (2) the semantics-aware malware detector proposed by Christodorescu et al. is complete with respect to a number of common obfuscations used by malware writers and (3) the malware detection scheme proposed by Kinder et al. and based on standard model-checking techniques is sound in general and complete on some, but not all, obfuscations handled by the semantics-aware malware detector.
Nominal logic programming
Authors: Cheney James , Urban Christian
Published: September 2008

Nominal logic is an extension of first-order logic which provides a simple foundation for formalizing and reasoning about abstract syntax modulo consistent renaming of bound names (that is, α-equivalence). This article investigates logic programming based on nominal logic. We describe some typical nominal logic programs, and develop the model-theoretic, proof-theoretic, and operational semantics of such programs. Besides being of interest for ensuring the correct behavior of implementations, these results provide a rigorous foundation for techniques for analysis and reasoning about nominal logic programs, as we illustrate via examples.
Two-dimensional bidirectional object layout
Authors: Gil Joseph (Yossi) , Pugh William , Weddell Grant E. , Zibin Yoav
Published: September 2008

Object layout schemes used in C++ and other languages rely on (sometimes numerous) compiler generated fields. We describe a language-independent object layout scheme, which is space optimal, that is, objects are contiguous, and contain
no compiler generated fields
other than a single type identifier. As in C++ and other multiple inheritance languages such as CECIL and DYLAN, the new scheme sometimes requires extra levels of indirection to access some of the fields. Using a data set of 28 hierarchies, totaling almost 50,000 types, we show that this scheme improves field access efficiency over standard implementations, and competes favorably with (the non-space-optimal) highly optimized C++ specific implementations. The benchmark includes an analytical model for computing the frequency of indirections in a sequence of field access operations. Our layout scheme relies on whole-program analysis, which requires about 10 microseconds per type on a contemporary architecture (Pentium III, 900Mhz, 256MB machine), even in very large hierarchies. We also present a layout scheme for separate compilation using the user-annotation of
virtual inheritance edge
that is used in C++.
A type system equivalent to a model checker
Authors: Naik Mayur , Palsberg Jens
Published: September 2008

Type systems and model checking are two prevalent approaches to program verification. A prominent difference between them is that type systems are typically defined in a syntactic and modular style whereas model checking is usually performed in a semantic and whole-program style. This difference between the two approaches makes them complementary to each other: type systems are good at explaining why a program was accepted while model checkers are good at explaining why a program was rejected.

We present a type system that is equivalent to a model checker for verifying temporal safety properties of imperative programs. The model checker is natural and may be instantiated with any finite-state abstraction scheme such as predicate abstraction. The type system, which is also parametric, type checks exactly those programs that are accepted by the model checker. It uses a variant of function types to capture flow sensitivity and intersection and union types to capture context sensitivity. Our result sheds light on the relationship between type systems and model checking, provides a methodology for studying their relative expressiveness, is a step towards sharing results between the two approaches, and motivates synergistic program analyses involving interplay between them.