bluuebunny/crossref_metadata_2025 huggingface dataset:
Timing and climatic impact of Greenland interstadials recorded in stalagmites from northern Turkey
Authors: Fleitmann D. , Cheng H. , Badertscher S. , Edwards R. L. , Mudelsee M. , Göktürk O. M. , Fankhauser A. , Pickering R. , Raible C. C. , Matter A. , Kramers J. , Tüysüz O.
Published: October 2009

A 50 kyr‐long exceptionally well‐dated and highly resolved stalagmite oxygen (δ18O) and carbon (δ13C) isotope record from Sofular Cave in northwestern Turkey helps to further improve the dating of Greenland Interstadials (GI) 1, and 3–12. Timing of most GI in the Sofular record is consistent within ±10 to 300 years with the “iconic” Hulu Cave record. Larger divergences (>500 years) between Sofular and Hulu are only observed for GI 4 and 7. The Sofular record differs from the most recent NGRIP chronology by up to several centuries, whereas age offsets do not increase systematically with depth. The Sofular record also reveals a rapid and sensitive climate and ecosystem response in the eastern Mediterranean to GI, whereas a phase lag of ∼100 years between climate and full ecosystem response is evident. Finally, results of spectral analyses of the Sofular isotope records do not support a 1,470‐year pacing of GI.
Using atmospheric model output to simulate the meteorological tsunami response to Tropical Storm Helene (2000)
Authors: Mecking J. V. , Fogarty C. T. , Greatbatch R. J. , Sheng J. , Mercer D.
Published: October 2009

In the fall of both 1999 and 2000, unexpected “rapid tides” occurred along the coast of the Avalon Peninsula of Newfoundland. These rapid tides have been linked to the passing of Tropical Storm Jose (1999) and Tropical Storm Helene (2000) over the Grand Banks. Here we examine the dynamic ocean response to Tropical Storm Helene (2000) using a barotropic shallow water ocean model forced by atmospheric pressure and surface winds derived from a simulation of Helene using a dynamical model of the atmosphere. The ocean model is able to capture the main features of the observed response at the coast of Newfoundland as seen in the available tide gauge data. Results show that the simulated sea level response at the coast is driven by a combination of wind stress and atmospheric pressure forcing, the former generally dominating. An exception is Conception Bay, Newfoundland, where the response is captured mainly by atmospheric pressure forcing. Offshore near the edge of the Grand Banks, atmospheric pressure and wind stress forcing are equally important. The wind‐forced response depends on the divergence of the surface wind stress and hence on the structure of the storm in the atmospheric model simulation. Sensitivity studies show the importance of having a small time interval (on the order of minutes) at which the atmospheric forcing is supplied to the ocean model and show the importance of the location of the storm track.
Characteristics of the Tropical Easterly Jet: Long‐term trends and their features during active and break monsoon phases
Authors: Roja Raman M. , Jagannadha Rao V. V. M. , Venkat Ratnam M. , Rajeevan M. , Rao S. V. B. , Narayana Rao D. , Prabhakara Rao N.
Published: October 2009

Using high–vertical resolution Indian mesosphere‐stratosphere‐troposphere (MST) radar and GPS sonde observations from Gadanki (13.5°N, 79.2°E), an attempt has been made for the first time to delineate the characteristics of Indian summer monsoon winds with special emphasis on the Tropical Easterly Jet stream (TEJ), its day‐to‐day, monthly, and interannual variability using observations available for more than a decade (1996–2008). For comparison, data available during 1996–2008 from routine radiosonde observations from nearby India Meteorological Department (IMD) observatory located at Chennai (13.0°N, 80.1°E) and National Centers for Environmental Prediction–National Center for Atmospheric Research (NCEP‐NCAR) reanalysis data sets have been considered. Relatively poor vertical resolution data from IMD lead to underestimation of the jet characteristics like jet width, vertical shear above and below the jet, and the wind reversal height. Although reanalysis data sets represented well the spatial variability, they underestimate the peak zonal winds by about 5 m/s when compared to Indian MST radar and GPS sonde observations. Large day‐to‐day variability of TEJ characteristics (peak jet speed, jet height, jet width, zonal wind reversal height, and vertical shear of zonal wind) over Gadanki is noticed. No significant trend is observed in peak jet speed using reanalysis data sets either over Gadanki grid or over jet core region in Indian summer monsoon months. However, MST radar and GPS sonde observations show increasing trend (∼1 m/s/yr) in peak jet speed particularly from the year 2000. Characteristics of the TEJ during active and break phases showed quite different features. Thus, statistics generated using the long‐term database from Indian MST radar and GPS sonde provide valuable information for studying the TEJ characteristics and will be useful to incorporate in the future reanalysis data sets.
Early Intervention Services With American Indian Tribes in New Mexico
Authors: Pedersen Mette J. , Vining Christine B.
Published: October 2009

Typical approaches to early intervention services, as carried out in many parts of the United States, may not be practical or successful with traditional American Indian families and communities. New Mexico, home to 22 tribes (19 pueblos, Navajo, and 2 Apache tribes) with eight indigenous languages, has worked through its Part C Family Infant Toddler (FIT) Program to support services for all communities in ways that meet community and cultural norms. This has led to examination of service delivery approaches, community based services guided by local American Indian leadership, and scrutiny of early assessment and evaluation in a culturally appropriate manner, compatible with state and federal regulation. This overview of the early intervention system, its challenges and opportunities, shares features of early intervention programs serving New Mexico tribes, and speech-language services in the context of family-centered philosophy, and culturally competent service delivery.
Intergrain current flow in a randomly oriented polycrystalline SmFeAsO0.85 oxypnictide
Authors: Kametani F. , Li P. , Abraimov D. , Polyanskii A. A. , Yamamoto A. , Jiang J. , Hellstrom E. E. , Gurevich A. , Larbalestier D. C. , Ren Z. A. , Yang J. , Dong X. L. , Lu W. , Zhao Z. X.
Published: October 2009

We report a direct current transport study of the local intergrain connections in a polycrystalline SmFeAsO0.85 (Sm1111) bulk, for which we earlier estimated significant intergranular critical current density Jc. Our combined low temperature laser scanning microscopy and scanning electron microscopy observations revealed only few grain-to-grain transport current paths, most of which switched off when a magnetic field was applied. These regions typically occur where current crosses Fe–As, which is a normal-metal wetting-phase that surrounds Sm1111 grains, producing a dense array of superconducting-normal-superconducting contacts. Our study points out the need to reduce the amount of grain boundary-wetting Fe–As phase, as well as the crack density within pnictide grains, as these defects produce a multiply connected current-blocking network.
Integrated nanostructures for direct detection of DNA at attomolar concentrations
Authors: Soleymani Leyla , Fang Zhichao , Kelley Shana O. , Sargent Edward H.
Published: October 2009

We report an integrated chip that senses nucleic acid biomarkers at exceptionally low concentrations. To achieve such sensitivities we exploit four concepts. (1) Nanostructured electrodes allow efficient display of probe sequences. (2) The use of uncharged probe sequences lowers the background signal in our read-out system. (3) Electrocatalysis provides built-in amplification of the electrical signal that reports hybridization events. (4) An optimal self-assembled monolayer of thiol-functionalized probe molecules is best achieved with the aid of a short spacer molecule to confer enhanced accessibility. We show herein that via joint optimization along these four axes we achieve attomolar sensitivity.
Lower limit to the lattice thermal conductivity of nanostructured Bi2Te3-based materials
Authors: Chiritescu Catalin , Mortensen Clay , Cahill David G. , Johnson David , Zschack Paul
Published: October 2009

We investigate the lower limit to the lattice thermal conductivity of Bi2Te3 and related materials using thin films synthesized by the method of elemental reactants. The thermal conductivities of single layer films of (Bi0.5Sb0.5)2Te3 and multilayer films of (Bi2Te3)m(TiTe2)n and [(BixSb1−x)2Te3]m(TiTe2)n are measured by time-domain thermoreflectance; the thermal conductivity data are compared to our prior work on nanocrystalline Bi2Te3 and a Debye–Callaway model of heat transport by acoustic phonons. The homogeneous nanocrystalline films have average grain sizes 30<d<100 nm as measured by the width of the (003) x-ray diffraction peak. Multilayer films incorporating turbostratic TiTe2 enable studies of the effective thermal conductivity of Bi2Te3 layers as thin as 2 nm. In the limit of small grain size or layer thickness, the thermal conductivity of Bi2Te3 approaches the predicted minimum thermal conductivity of 0.31 W/m K. The dependence of the thermal conductivity on grain size is in good agreement with our Debye–Callaway model. The use of alloy (Bi,Sb)2Te3 layers further reduces the thermal conductivity of the nanoscale layers to as low as 0.20 W/m K.
Toward a gauge theory for evolution equations on vector-valued spaces
Authors: Cardanobile Stefano , Mugnolo Delio
Published: October 2009

We investigate symmetry properties of vector-valued diffusion and Schrödinger equations. For a separable Hilbert space H we characterize the subspaces of L2(R3;H) that are local (i.e., defined pointwise) and discuss the issue of their invariance under the time evolution of the differential equation. In this context, the possibility of a connection between our results and the theory of gauge symmetries in mathematical physics is explored.
The origins of electromechanical indentation size effect in ferroelectrics
Authors: Gharbi M. , Sun Z. H. , Sharma P. , White K.
Published: October 2009

Metals exhibit a size-dependent hardening when subject to indentation. Mechanisms for this phenomenon have been intensely researched in recent times. Does such a size effect also exist in the electromechanical behavior of ferroelectrics?—if yes, what are the operative mechanisms? Our experiments on BaTiO3 indeed suggest an elastic electromechanical size effect. We argue, through theoretical calculations and differential experiments on another nonferroelectric piezoelectric (quartz), that the phenomenon of flexoelectricity (as opposed to dislocation activity) is most likely responsible for our observations. Flexoelectricity is the coupling of strain gradients to polarization and exists in both ordinary and piezoelectric dielectrics. In particular, ferroelectrics exhibit an unusually large flexoelectric response.
Design and characterization of supersonic nozzles for wide focus laser-plasma interactions
Authors: Lemos N. , Lopes N. , Dias J. M. , Viola F.
Published: October 2009

In this work we optimize the contour of supersonic nozzles to produce long and stable gas jets suitable to be used in loose focus laser-plasma applications. The nozzle design method takes into account the inclusion of a boundary layer that increases the length of the usable gas jet. Two 8 mm supersonic nozzles were characterized, one with a Mach number of 3 and another with a Mach number of 6, using a Mach–Zehnder interferometer performed with a He:Ne 4 cm expanded laser beam. The experimental results confirm that the inclusion of the boundary layer produces an 8 mm constant longitudinal density profile for the nozzle with a Mach number of 6 (NM6) and a 4.5 mm constant longitudinal density profile for the nozzle with a Mach number of 3 (NM3).
A megahertz bandwidth dual amplifier for driving piezoelectric actuators and other highly capacitive loads
Authors: Fleming Andrew J.
Published: October 2009

Due to their high stiffness, small dimensions, and low mass, piezoelectric stack actuators are capable of developing large displacements over bandwidths of greater than 100 kHz. However, due to their large electrical capacitance, the associated driving amplifier is usually limited in bandwidth to a few kilohertz or less. In this paper the limiting characteristics of piezoelectric drives are identified as the small-signal bandwidth, output impedance, cable inductance, and power dissipation. A new dual amplifier is introduced that exhibits a small-signal bandwidth of 2 MHz with a 100 nF capacitive load. The dual amplifier is comprised of a standard high-voltage amplifier combined with a fast low-voltage amplifier to improve performance at higher frequencies. Experiments demonstrate a 300 kHz sine wave of 20 Vp-p amplitude being applied to a 100 nF load with negligible phase delay and a peak-to-peak current of 3.8 A. With a voltage range of 200 V and peak current of 1.9 A a standard amplifier would require a worst-case power dissipation of 380 W. However, the dual-amplifier arrangement has a worst-case power dissipation of only 30 W. The penalty is reduced range at high frequencies and slower operation from the high-voltage stage.
Thermal evolution and electrical correlation of defect states in Hf-based high-κ dielectrics on n-type Ge (100): Local atomic bonding symmetry
Authors: Chung K. B. , Long J. P. , Seo H. , Lucovsky G. , Nordlund D.
Published: October 2009

The crystal field splittings and Jahn–Teller (J-T) distortions in Hf-based high-κ dielectric oxides on n-type Ge (100) substrates were investigated through the examination of O K1 edge spectra, obtained via x-ray absorption spectroscopy. Second derivative analysis of these O K1 edge spectra provided unambiguous evidence of J-T d-state degeneracy removal, resulting from the symmetry of the local atomic bonding environment. Additionally, two distinct defect states were found below the conduction band edge. The conduction band’s molecular orbital energy structure, including defect states, was determined based on the results of these investigations. Moreover, the thermal evolution of the defect states was found to be dependent on both postdeposition annealing temperature and Hf-based high-κ dielectric oxides. These subband-edge defect states were determined to be electrically active, and their density and the local atomic bonding symmetry were found to be correlated with the effective electron charge trapping measured in related device structures.
Using the ONIOM hybrid method to apply equation of motion CCSD to larger systems: Benchmarking and comparison with time-dependent density functional theory, configuration interaction singles, and time-dependent Hartree–Fock
Authors: Caricato Marco , Vreven Thom , Trucks Gary W. , Frisch Michael J. , Wiberg Kenneth B.
Published: October 2009

Equation of motion coupled-cluster singles and doubles (EOM-CCSD) is one of the most accurate computational methods for the description of one-electron vertical transitions. However, its O(N6) scaling, where N is the number of basis functions, often makes the study of molecules larger than 10–15 heavy atoms prohibitive. In this work we investigate how accurately less expensive methods can approximate the EOM-CCSD results. We focus on our own N-layer integrated molecular orbital molecular mechanics (ONIOM) hybrid scheme, where the system is partitioned into regions which are treated with different levels of theory. For our set of benchmark calculations, the comparison of conventional configuration interaction singles (CIS), time-dependent Hartree–Fock (TDHF), and time-dependent density functional theory (TDDFT) methods and ONIOM (with different low level methods) showed that the best accuracy-computational time combination is obtained with ONIOM(EOM:TDDFT), which has a rms of the error with respect to the conventional EOM-CCSD of 0.06 eV, compared with 0.47 eV of the conventional TDDFT.
Strain tuned magnetoelectric coupling in orthorhombic YMnO3 thin films
Authors: Marti X. , Fina I. , Skumryev V. , Ferrater C. , Varela M. , Fábrega L. , Sánchez F. , Fontcuberta J.
Published: October 2009

Orthorhombic YMnO3 epitaxial thin films were grown on Nb(0.5%)-doped SrTiO3(001) substrates. Film’s thickness was varied to tune the epitaxial strain. Structural and magnetic properties are well correlated, presenting a more pronounced ferromagnetic behavior as the unit cell becomes more distorted. Dielectric properties were investigated as a function of the temperature and magnetic field. The dielectric peak occurring at temperatures below the antiferromagnetic ordering is proved to be magnetoelectric and its amplitude is dependent on the unit cell distortion. These findings allow tailoring ferromagnetic and magnetoelectric properties via epitaxial strain.
Phase separation in GaN/AlGaN quantum dots
Authors: Benaissa M. , Gu L. , Korytov M. , Huault T. , van Aken P. A. , Brault J. , Vennéguès P.
Published: October 2009

Local investigations using high-angle annular-dark-field imaging combined with electron low-energy-loss spectroscopy were performed to closely characterize the GaN/Al0.5Ga0.5N quantum dots heterostructure. It is found that the Al0.5Ga0.5N barrier tends to exhibit phase separation. Gallium-rich arms arise from the top rims of the truncated quantum dots while the space between these arms is filled with aluminum-rich AlGaN. This phase separation, due to morphological and strain nonuniformities of the GaN front surface, provokes an optical-property modulation in the neighborhood of the quantum dots which, from a practical point of view, could affect the electronic barrier homogeneity.
Energetic disorder limits energy transfer in semiconductor nanocrystal–DNA–dye conjugates
Authors: Becker Klaus , Rogach Andrey L. , Feldmann Jochen , Talapin Dmitri V. , Lupton John M.
Published: October 2009

We demonstrate the influence of spectral linewidths of individual donor-acceptor couples on energy transfer efficiency in semiconductor nanocrystal–DNA–organic dye conjugates. Temperature-dependent single molecule and ensemble spectroscopy data are analyzed using the Förster theory within the macroscopic and microscopic approaches. The results obtained evidence on the importance of the spectral overlap between emission of a single donor and absorption of a single acceptor in its close vicinity, which determines the microscopic resonance and transfer efficiency between individual neighbors. This realization poses important implications on the applicability of ensemble spectral overlap for the analysis of distance dependencies of nanoscopic objects.
Empirical electron cross-field mobility in a Hall effect thruster
Authors: Garrigues L. , Pérez-Luna J. , Lo J. , Hagelaar G. J. M. , Boeuf J. P. , Mazouffre S.
Published: October 2009

Electron transport across the magnetic field in Hall effect thrusters is still an open question. Models have so far assumed 1∕B2 or 1∕B scaling laws for the “anomalous” electron mobility, adjusted to reproduce the integrated performance parameters of the thruster. We show that models based on such mobility laws predict very different ion velocity distribution functions (IVDF) than measured by laser induced fluorescence (LIF). A fixed spatial mobility profile, obtained by analysis of improved LIF measurements, leads to much better model predictions of thruster performance and IVDF than 1∕B2 or 1∕B mobility laws for discharge voltages in the 500–700V range.
Time-dependent electroforming in NiO resistive switching devices
Authors: Buh Gyoung-Ho , Hwang Inrok , Park Bae Ho
Published: October 2009

Time-dependent electroforming phenomena in NiO capacitors are investigated. Different current-voltage characteristics between dc sweep mode and pulse mode indicate that electroforming is time-dependent process. Statistical time-dependent dielectric breakdown (TDDB) measurements show the exponential dependence of electroforming time on applied voltage, confirming that forming process is not a spontaneous process at some critical voltage, but an upsurge process resulting from stress-induced defects. The statistical TDDB analysis explains not only the nature of electroforming process but also the anomalous forming and large variations in forming parameters.
A new scheme for perturbation contribution in density functional theory and application to solvation force and critical fluctuations
Authors: Zhou Shiqi
Published: October 2009

To surpass a traditional mean field density functional approximation for a perturbation term of interparticle potential function in liquid state, a correlation term is introduced by using weighted density approximation to deal with the perturbation free energy beyond the mean field one. Consequently, a free energy density functional approximation is advanced by combining the mean field term and correlation term with a hard sphere term treated with a Lagrangian theorem-based density functional approximation in the present work. The present free energy density functional approximation is applied in the framework of classical density functional theory (DFT) to a hard core attractive Yukawa (HCAY) fluid subject to external fields; comparison of the resulted predictions for density profiles with available simulation data is favorable for the present DFT approach as a highly accurate predictive approach. Then, the DFT approach is employed to investigate influencing factors for solvation forces between two infinite planar surfaces immersed in an intervening solvent with the HCAY potential function. It is found that (i) critical fluctuations induce negative adsorptions and long-ranged solvation forces; (ii) for narrow slit, the effect of external potential range is kept down; instead strength of the external field contact potential plays dominating role; (iii) state point in the bulk phase diagram, where the most remarkable critical effects are displayed, is the one with a bulk density a little higher than the critical density; remnants of critical fluctuations remain close to the bulk gas-liquid coexistence curve.
Influence of temperature on coherent dynamics of a two-level system immersed in a dissipative spin bath
Authors: Lü Zhiguo , Zheng Hang
Published: October 2009

The quantum dynamics of a two-level system coupled to an Ohmic spin bath is studied by means of the perturbation approach based on a unitary transformation. A scattering function ξk is introduced in the transformation to take into account quantum fluctuations. By the master equation within the Born approximation, nonequilibrium dynamics quantities are calculated. The method works well for the coupling constant 0<α<αc and a finite bare tunneling Δ. It is found that (i) only at zero temperature with small coupling or moderate one does the spin-spin-bath model display identical behavior as the well-known spin-boson-bath model; (ii) in comparison with the known results of spin-boson-bath model, the coherence-incoherence transition point, which occurs at αc=12[1+ηΔ/ωc], is temperature independent; and (iii) the nonequilibrium correlation function P(t)=⟨τz(t)⟩, evolves without temperature dependence, while ⟨τx(t)⟩ depends on temperature. Both P(t) and ⟨τx(t)⟩ not only satisfy their initial conditions, respectively, and also have correct long time limits. Besides, the Shiba relation and sum rule are exactly satisfied in the coherent regime for this method. Our results show that increasing temperature does not help the system suppress decoherence in the coherent regime, i.e., finite temperature does not favor the coherent dynamics in this regime. Thus, the finite-temperature dynamics induced by two kinds of baths (spin-bath and boson-bath) exhibit distinctly different physics.
Large energy soliton erbium-doped fiber laser with a graphene-polymer composite mode locker
Authors: Zhang Han , Bao Qiaoliang , Tang Dingyuan , Zhao Luming , Loh Kianping
Published: October 2009

Due to its unique electronic property and the Pauli blocking principle, atomic layer graphene possesses wavelength-independent ultrafast saturable absorption, which can be exploited for the ultrafast photonics application. Through chemical functionalization, a graphene-polymer nanocomposite membrane was fabricated and first used to mode lock a fiber laser. Stable mode locked solitons with 3 nJ pulse energy, 700 fs pulse width at the 1590 nm wavelength have been directly generated from the laser. We show that graphene-polymer nanocomposites could be an attractive saturable absorber for high power fiber laser mode locking.
Irina Conboy: Making the old feel young again
Authors: Powell Kendall
Published: October 2009

Conboy has found her niche in chasing down what ails aged, decrepit muscle stem cells.
Intraflagellar transport particle size scales inversely with flagellar length: revisiting the balance-point length control model
Authors: Engel Benjamin D. , Ludington William B. , Marshall Wallace F.
Published: October 2009

The assembly and maintenance of eukaryotic flagella are regulated by intraflagellar transport (IFT), the bidirectional traffic of IFT particles (recently renamed IFT trains) within the flagellum. We previously proposed the balance-point length control model, which predicted that the frequency of train transport should decrease as a function of flagellar length, thus modulating the length-dependent flagellar assembly rate. However, this model was challenged by the differential interference contrast microscopy observation that IFT frequency is length independent. Using total internal reflection fluorescence microscopy to quantify protein traffic during the regeneration of Chlamydomonas reinhardtii flagella, we determined that anterograde IFT trains in short flagella are composed of more kinesin-associated protein and IFT27 proteins than trains in long flagella. This length-dependent remodeling of train size is consistent with the kinetics of flagellar regeneration and supports a revised balance-point model of flagellar length control in which the size of anterograde IFT trains tunes the rate of flagellar assembly.
Molecular mechanisms that enhance synapse stability despite persistent disruption of the spectrin/ankyrin/microtubule cytoskeleton
Authors: Massaro Catherine M. , Pielage Jan , Davis Graeme W.
Published: October 2009

Loss of spectrin or ankyrin in the presynaptic motoneuron disrupts the synaptic microtubule cytoskeleton and leads to disassembly of the neuromuscular junction (NMJ). Here, we demonstrate that NMJ disassembly after loss of α-spectrin can be suppressed by expression of a WldS transgene, providing evidence for a Wallerian-type degenerative mechanism. We then identify a second signaling system. Enhanced MAPK-JNK-Fos signaling suppresses NMJ disassembly despite loss of presynaptic α-spectrin or ankyrin2-L. This signaling system is activated after an acute cytoskeletal disruption, suggesting an endogenous role during neurological stress. This signaling system also includes delayed, negative feedback via the JNK phosphatase puckered, which inhibits JNK-Fos to allow NMJ disassembly in the presence of persistent cytoskeletal stress. Finally, the MAPK-JNK pathway is not required for baseline NMJ stabilization during normal NMJ growth. We present a model in which signaling via JNK-Fos functions as a stress response system that is transiently activated after cytoskeletal disruption to enhance NMJ stability, and is then shut off allowing NMJ disassembly during persistent cytoskeletal disruption.
Tim–Tipin dysfunction creates an indispensible reliance on the ATR–Chk1 pathway for continued DNA synthesis
Authors: Smith Kevin D. , Fu Michael A. , Brown Eric J.
Published: October 2009

The Tim (Timeless)–Tipin complex has been proposed to maintain genome stability by facilitating ATR-mediated Chk1 activation. However, as a replisome component, Tim–Tipin has also been suggested to couple DNA unwinding to synthesis, an activity expected to suppress single-stranded DNA (ssDNA) accumulation and limit ATR–Chk1 pathway engagement. We now demonstrate that Tim–Tipin depletion is sufficient to increase ssDNA accumulation at replication forks and stimulate ATR activity during otherwise unperturbed DNA replication. Notably, suppression of the ATR–Chk1 pathway in Tim–Tipin-deficient cells completely abrogates nucleotide incorporation in S phase, indicating that the ATR-dependent response to Tim–Tipin depletion is indispensible for continued DNA synthesis. Replication failure in ATR/Tim-deficient cells is strongly associated with synergistic increases in H2AX phosphorylation and DNA double-strand breaks, suggesting that ATR pathway activation preserves fork stability in instances of Tim–Tipin dysfunction. Together, these experiments indicate that the Tim–Tipin complex stabilizes replication forks both by preventing the accumulation of ssDNA upstream of ATR–Chk1 function and by facilitating phosphorylation of Chk1 by ATR.
Cdc42 antagonizes Rho1 activity at adherens junctions to limit epithelial cell apical tension
Authors: Warner Stephen J. , Longmore Gregory D.
Published: October 2009

In epithelia, cells are arranged in an orderly pattern with a defined orientation and shape. Cadherin containing apical adherens junctions (AJs) and the associated actomyosin cytoskeleton likely contribute to epithelial cell shape by providing apical tension. The Rho guanosine triphosphatases are well known regulators of cell junction formation, maintenance, and function. Specifically, Rho promotes actomyosin activity and cell contractility; however, what controls and localizes this Rho activity as epithelia remodel is unresolved. Using mosaic clonal analysis in the Drosophila melanogaster pupal eye, we find that Cdc42 is critical for limiting apical cell tension by antagonizing Rho activity at AJs. Cdc42 localizes Par6–atypical protein kinase C (aPKC) to AJs, where this complex limits Rho1 activity and thus actomyosin contractility, independent of its effects on Wiskott-Aldrich syndrome protein and p21-activated kinase. Thus, in addition to its role in the establishment and maintenance of apical–basal polarity in forming epithelia, the Cdc42–Par6–aPKC polarity complex is required to limit Rho activity at AJs and thus modulate apical tension so as to shape the final epithelium.
Ethanol Lock Technique: Review of the Literature
Authors: Maiefski Melissa , Rupp Mark E. , Hermsen Elizabeth D.
Published: October 2009

Central venous catheters (CVCs) are commonly used among adult and pediatric patients for administration of fluids, medications, and nutrition. Central line–associated (CLA) bloodstream infection (BSI) is a serious complication following CVC insertion. The aim of this review is to summarize available data regarding the ethanol lock technique, which is a proposed method for sterilizing the lumen of the catheter by instilling an ethanol solution and allowing it to dwell in the catheter for a certain amount of time. Studies on ethanol lock technique differ in ethanol concentrations, luminal dwell times, catheter types, inclusion of anticoagulants, use of systemic antibiotics, and use of the technique for prevention or for treatment of CLA BSI. In vitro studies demonstrate the efficacy of ethanol in the eradication of various pathogens. Definitive catheter integrity data are limited. Clinical trials report tolerable adverse events with ethanol locks, as well as encouraging results for prevention and treatment of CLA BSI.
Between Community and Hospital: Healthcare-Associated Gram-Negative Bacteremia among Hospitalized Patients
Authors: Marschall Jonas , Fraser Victoria J. , Doherty Joshua , Warren David K.
Published: October 2009

Objective.

Healthcare-associated, community-acquired bacteremia is a subcategory of community-acquired bacteremia distinguished by recent exposure of the patient to the healthcare system before hospital admission. Our objective was to apply this category to a prospective cohort of hospitalized patients with gram-negative bacteremia to determine differences in the epidemiological characteristics, treatment, and outcome of community-acquired bacteremia; healthcare-associated, community-acquired bacteremia; and hospital-acquired bacteremia.

Design.

A 6-month prospective cohort study.

Setting.

A 1,250-bed tertiary care hospital.

Patients.

Adults hospitalized with gram-negative bacteremia.

Results.

Among 250 patients, 160 (64.0%) had bacteremia within 48 hours after admission; 132 (82.5%) of these were considered to have healthcare-associated, community-acquired bacteremia, according to previously published criteria. For patients with healthcare-associated, community-acquired bacteremia, compared with patients with community-acquired bacteremia, malignancies (59 [44.7%] of 132 patients vs 3 [10.7%] of 28 patients; P = .001), open wounds at admission (42 [31.8%] vs 3 [10.7%]; P = .02), and intravascular catheter-related infections (26 [19.7%] vs 0; P = .009) were more frequent and Escherichia coli as a causative agent was less frequent (16 [57.1%] vs 33 [25.0%]; P = .001). There was no difference between these 2 groups in inadequate empirical antibiotic treatment (36 [27.3%] vs 6 [21.4%]; P = .5) and hospital mortality (18 [13.6%] vs 2 [[7.1%]; P = .5). Compared with 90 patients with hospital-acquired bacteremia, patients with healthcare-associated, community-acquired bacteremia had a higher Charlson score (odds ratio [OR], 1.31 [95% confidence interval (CI), 1.14–1.49]) but were less likely to have lymphoma (OR, 0.07 [95% CI, 0.01–0.51]), neutropenia (OR, 0.21 [95% CI, 0.07–0.61]), a removable foreign body (OR, 0.08 [95% CI, 0.03–0.20]), or Klebsiella pneumoniae infection (OR, 0.26 [95% CI, 0.11–0.62]).

Conclusions.

Many cases of gram-negative bacteremia that occurred in hospitalized patients were healthcare associated. The patients differed in some aspects from patients with community-acquired bacteremia and from those with hospital-acquired bacteremia, but not in mortality.
Validation of Statewide Surveillance System Data on Central Line–Associated Bloodstream Infection in Intensive Care Units in Australia
Authors: McBryde Emma S. , Brett Judy , Russo Philip L. , Worth Leon J. , Bull Ann L. , Richards Michael J.
Published: October 2009

Objective.

To measure the interobserver agreement, sensitivity, specificity, positive predictive value, and negative predictive value of data submitted to a statewide surveillance system for identifying central line-associated bloodstream infection (BSI).

Design.

Retrospective review of hospital medical records comparing reported data with gold standard according to definitions of central line–associated BSI.

Setting.

Six Victorian public hospitals with more than 100 beds.

Methods.

Reporting of surveillance outcomes was undertaken by infection control practitioners at the hospital sites. Retrospective evaluation of the surveillance process was carried out by independent infection control practitioners from the Victorian Hospital Acquired Infection Surveillance System (VICNISS). A sample of records of patients reported to have a central line-associated BSI were assessed to determine whether they met the definition of central line–associated BSI. A sample of records of patients with bacteremia in the intensive care unit during the assessment period who were not reported as having central line–associated BSI were also assessed to see whether they met the definition of central line-associated BSI.

Results.

Records of 108 patients were reviewed; the agreement between surveillance reports and the VICNISS assessment was 67.6% (κ = 0.31). Of the 46 reported central line–associated BSIs, 27 were confirmed to be central line–associated BSIs, for a positive predictive value of 59% (95% confidence interval [CI], 43%–73%). Of the 62 cases of bacteremia reviewed that were not reported as central line–associated BSIs, 45 were not associated with a central line, for a negative predictive value of 73% (95% CI, 60%–83%). Estimated sensitivity was 35%, and specificity was 87%. The positive likelihood ratio was 3.0, and the negative likelihood ratio was 0.72.

Discussion.

The agreement between the reporting of central line–associated BSI and the gold standard application of definitions was unacceptably low. False-negative results were problematic; more than half of central line–associated BSIs may be missed in Victorian public hospitals.
Use of Longitudinal Surveillance Data to Assess the Effectiveness of Infection Control in Critical Care
Authors: Ahern John W. , Alston W. Kemper
Published: October 2009

A simple method for quantifying nosocomial infection and colonization with multidrug-resistant organisms is described. This method is applied to the intensive care unit of an academic medical center where longitudinal surveillance data have been used to assess the impact of infection control interventions and antibiotic use.
Prospective Comparison of Tuberculin Skin Test and QuantiFERON-TB Gold In-Tube Assay for the Detection of Latent Tuberculosis Infection among Healthcare Workers in a Low-Incidence Setting
Authors: Cummings Kristin J. , Smith Tamara S. , Shogren Elizabeth S. , Khakoo Rashida , Nanda Sharmilarani , Bunner Lana , Smithmyer Ann , Soccorsi Darlene , Kashon Michael L. , Mazurek Gerald H. , Friedman Lloyd N. , Weissman David N.
Published: October 2009

We compared the results of the tuberculin skin test with the results of the QuantiFERON-TB Gold In-Tube (QFT-GIT) assay among 182 low-risk healthcare workers. Overall agreement and specificity were high, but the tests did not agree on positive results. Only 2 of 5 positive QFT-GIT assay results could be confirmed with repeat analyses. Indeterminate results were associated with potential immunosuppression.
Effect of Timing of Preharvest Fungicide Applications on Postharvest Botrytis Fruit Rot of Annual Strawberries in Florida
Authors: Mertely James C. , Seijo Teresa E. , MacKenzie Steven J. , Peres Natalia A.
Published: October 2009

Preharvest fungicide applications for postharvest control of Botrytis fruit rot were evaluated over four seasons on annual strawberry in Florida. In the 2002-2003 season, applications of Switch or Elevate immediately prior to harvest were ineffective for controlling Botrytis fruit rot postharvest. In the 2003-2004 season, applications of Captevate or Switch made immediately prior to harvest reduced postharvest Botrytis fruit rot, but not as much as applications made during the flowering period. Similarly, in the 2004-2005 season, Captevate and Pristine provided some control of postharvest Botrytis fruit rot when applied immediately before harvest. In both the 2003-2004 and 2004-2005 seasons, applications made during the flowering period were more effective for postharvest Botrytis fruit rot control than those made prior to harvest. In the 2006-2007 season, applications of Captevate, Thiram, Scala plus Captan, or Switch alternated with Captan during the flowering period provided good control of postharvest Botrytis fruit rot. Although not as effective as bloom applications, fungicides applied immediately before harvest may have some benefit for controlling Botrytis fruit rot if the sprays during the bloom period were not made.

Accepted for publication 21 July 2009. Published 21 September 2009.
Identifying graph clusters using variational inference and links to covariance parametrization
Authors: Barber David
Published: October 2009

Finding clusters of well-connected nodes in a graph is a problem common to many domains, including social networks, the Internet and bioinformatics. From a computational viewpoint, finding these clusters or graph communities is a difficult problem. We use a clique matrix decomposition based on a statistical description that encourages clusters to be well connected and few in number. The formal intractability of inferring the clusters is addressed using a variational approximation inspired by mean-field theories in statistical mechanics. Clique matrices also play a natural role in parametrizing positive definite matrices under zero constraints on elements of the matrix. We show that clique matrices can parametrize all positive definite matrices restricted according to a decomposable graph and form a structured factor analysis approximation in the non-decomposable case. Extensions to conjugate Bayesian covariance priors and more general non-Gaussian independence models are briefly discussed.
Selective inference in complex research
Authors: Benjamini Yoav , Heller Ruth , Yekutieli Daniel
Published: October 2009

We explain the problem of selective inference in complex research using a recently published study: a replicability study of the associations in order to reveal and establish risk loci for type 2 diabetes. The false discovery rate approach to such problems will be reviewed, and we further address two problems: (i) setting confidence intervals on the size of the risk at the selected locations and (ii) selecting the replicable results.
Observed universality of phase transitions in high-dimensional geometry, with implications for modern data analysis and signal processing
Authors: Donoho David , Tanner Jared
Published: October 2009

We review connections between phase transitions in high-dimensional combinatorial geometry and phase transitions occurring in modern high-dimensional data analysis and signal processing. In data analysis, such transitions arise as abrupt breakdown of linear model selection, robust data fitting or compressed sensing reconstructions, when the complexity of the model or the number of outliers increases beyond a threshold. In combinatorial geometry, these transitions appear as abrupt changes in the properties of face counts of convex polytopes when the dimensions are varied. The thresholds in these very different problems appear in the same critical locations after appropriate calibration of variables. These thresholds are important in each subject area: for linear modelling, they place hard limits on the degree to which the now ubiquitous high-throughput data analysis can be successful; for robustness, they place hard limits on the degree to which standard robust fitting methods can tolerate outliers before breaking down; for compressed sensing, they define the sharp boundary of the undersampling/sparsity trade-off curve in undersampling theorems. Existing derivations of phase transitions in combinatorial geometry assume that the underlying matrices have independent and identically distributed Gaussian elements. In applications, however, it often seems that Gaussianity is not required. We conducted an extensive computational experiment and formal inferential analysis to test the hypothesis that these phase transitions are
universal
across a range of underlying matrix ensembles. We ran millions of linear programs using random matrices spanning several matrix ensembles and problem sizes; visually, the empirical phase transitions do not depend on the ensemble, and they agree extremely well with the asymptotic theory assuming Gaussianity. Careful statistical analysis reveals discrepancies that can be explained as transient terms, decaying with problem size. The experimental results are thus consistent with an asymptotic large-
n
universality across matrix ensembles; finite-sample universality can be rejected.
Classification of sparse high-dimensional vectors
Authors: Ingster Yuri I. , Pouet Christophe , Tsybakov Alexandre B.
Published: October 2009

We study the problem of classification of
d
-dimensional vectors into two classes (one of which is ‘pure noise’) based on a training sample of size
m
. The main specific feature is that the dimension
d
can be very large. We suppose that the difference between the distribution of the population and that of the noise is only in a shift, which is a sparse vector. For Gaussian noise, fixed sample size
m
, and dimension
d
that tends to infinity, we obtain the sharp classification boundary, i.e. the necessary and sufficient conditions for the possibility of successful classification. We propose classifiers attaining this boundary. We also give extensions of the result to the case where the sample size
m
depends on
d
and satisfies the condition

, 0 ≤ γ < 1, and to the case of non-Gaussian noise satisfying the Cramér condition.
Statistical challenges of high-dimensional data
Authors: Johnstone Iain M. , Titterington D. Michael
Published: October 2009

Modern applications of statistical theory and methods can involve extremely large datasets, often with huge numbers of measurements on each of a comparatively small number of experimental units. New methodology and accompanying theory have emerged in response: the goal of this Theme Issue is to illustrate a number of these recent developments. This overview article introduces the difficulties that arise with high-dimensional data in the context of the very familiar linear statistical model: we give a taste of what can nevertheless be achieved when the parameter vector of interest is sparse, that is, contains many zero elements. We describe other ways of identifying low-dimensional subspaces of the data space that contain all useful information. The topic of classification is then reviewed along with the problem of identifying, from within a very large set, the variables that help to classify observations. Brief mention is made of the visualization of high-dimensional data and ways to handle computational problems in Bayesian analysis are described. At appropriate points, reference is made to the other papers in the issue.
Formalizing Darwinism and inclusive fitness theory
Authors: Grafen Alan
Published: October 2009

Inclusive fitness maximization is a basic building block for biological contributions to any theory of the evolution of society. There is a view in mathematical population genetics that nothing is caused to be maximized in the process of natural selection, but this is explained as arising from a misunderstanding about the meaning of fitness maximization. Current theoretical work on inclusive fitness is discussed, with emphasis on the author's ‘formal Darwinism project’. Generally, favourable conclusions are drawn about the validity of assuming fitness maximization, but the need for continuing work is emphasized, along with the possibility that substantive exceptions may be uncovered. The formal Darwinism project aims more ambitiously to represent in a formal mathematical framework the central point of Darwin'sOrigin of Species, that the mechanical processes of inheritance and reproduction can give rise to the appearance of design, and it is a fitting ambition in Darwin's bicentenary year to capture his most profound discovery in the lingua franca of science.
Beyond society: the evolution of organismality
Authors: Queller David C. , Strassmann Joan E.
Published: October 2009

The evolution of organismality is a social process. All organisms originated from groups of simpler units that now show high cooperation among the parts and are nearly free of conflicts. We suggest that this near-unanimous cooperation be taken as the defining trait of organisms. Consistency then requires that we accept some unconventional organisms, including some social insect colonies, some microbial groups and viruses, a few sexual partnerships and a number of mutualistic associations. Whether we call these organisms or not, a major task is to explain such cooperative entities, and our survey suggests that many of the traits commonly used to define organisms are not essential. These non-essential traits include physical contiguity, indivisibility, clonality or high relatedness, development from a single cell, short-term and long-term genetic cotransmission, germ–soma separation and membership in the same species.