bluuebunny/crossref_metadata_2025 huggingface dataset:
Teens telling tales: How maternal and peer audiences support narrative identity development
Authors: McLean Kate C. , Jennings Lauren E.
Published: December 2011

Prior research has shown that parents help children to develop the requisite skills to construct an autobiographical self in past event conversations, yet research in adolescence is lacking. Further, friendships increase in importance during adolescence, and these new relationships may play a role in narrative identity development. The current study examined past event conversations between adolescents (n = 22; mean age = 13) and their friends, and adolescents and their mothers. Conversations were reliably coded for degree of personal meaning communicated and listener scaffolding behavior. Results showed that friends showed less frequent explicit scaffolding of narrative identity than mothers, although listener scaffolding behavior was associated with adolescent meaning‐making for both friends and mothers. Additional qualitative analysis of the conversations suggests that friends may be more engaged in scaffolding the self‐presentational aspects of narrative identity, as well as providing a safe arena for exploration away from mothers.
Puerto Rican adolescents’ disclosure and lying to parents about peer and risky activities: Associations with teens’ perceptions of Latino values
Authors: Villalobos Myriam , Smetana Judith G.
Published: December 2011

Disclosure and lying to mothers and fathers about different activities, as defined within social domain theory, were examined as a function of Latino family values in 109 Puerto Rican lower socioeconomic status middle adolescents (M = 15.58 years, SD = 1.18) living in the United States. Questionnaires revealed that teens sometimes disclosed to parents about their risky prudential (unhealthy or unsafe) and peer activities. Lying was infrequent, although greater for risky than for peer issues. In general, path analyses demonstrated that teens’ greater adherence to Latino family values and trust in parents were associated with more disclosure and less lying to mothers. However, these findings were moderated by the type of issue considered and perceptions of parents’ Latino family values.
Functional characterisation of human SGLT‐5 as a novel kidney‐specific sodium‐dependent sugar transporter
Authors: Grempler Rolf , Augustin Robert , Froehner Stefanie , Hildebrandt Tobias , Simon Eric , Mark Michael , Eickelmann Peter
Published: December 2011

Sodium glucose cotransporters (SGLT) actively catalyse carbohydrate transport across cellular membranes. Six of the 12 known SGLT family members have the capacity to bind and/or transport monosaccharides (SGLT‐1 to 6); of these, all but SGLT‐5 have been characterised. Here we demonstrate that human SGLT‐5 is exclusively expressed in the kidney. Four splice variants were detected and the most abundant SGLT‐5‐mRNA was functionally characterised. SGLT‐5 mediates sodium‐dependent [14C]‐α‐methyl‐d‐glucose (AMG) transport that can be inhibited by mannose, fructose, glucose, and galactose. Uptake studies using demonstrated high capacity transport for mannose and fructose and, to a lesser extent, glucose, AMG, and galactose. SGLT‐5 mediated mannose, fructose and AMG transport was weakly (μM potency) inhibited by SGLT‐2 inhibitors. In summary, we have characterised SGLT‐5 as a kidney mannose transporter. Further studies are warranted to explore the physiological role of SGLT‐5.
FLU, a negative feedback regulator of tetrapyrrole biosynthesis, is physically linked to the final steps of the Mg++‐branch of this pathway
Authors: Kauss Dominika , Bischof Sylvain , Steiner Sandro , Apel Klaus , Meskauskiene Rasa
Published: December 2011

FLU
physically interacts with
CHL27
,
PORB
,
PORC
and
CHLP
by anti tag co‐immunoprecipitation (View interaction)
Mycobacterium massilienseoutbreak after intramuscular injection, South Korea
Authors: KIM H. J. , CHO Y. , LEE S. , KOOK Y. , LEE D. , LEE J. , PARK B. J.
Published: January 2012

We conducted an epidemic investigation to discover the route of transmission and the host factors of an outbreak of post-injection abscesses. Of the 2984 patients who visited a single clinic, 77 cases were identified and 208 age- and sex-matched controls were selected for analysis. Injected medicationsper sewere not found to be responsible, and a deviation from safe injection practice suggested the likelihood of diluent contamination. Therefore the injected medications were classified according to whether there was a need for a diluent, and two medications showed a statistically significant association, i.e. injection with pheniramine [adjusted odds ratios (aOR) 5·93, 95% confidence interval (CI) 2·97–11·87] and ribostamycin (aOR 47·95, 95% CI 11·08–207·53). However, when considered concurrently, pheniramine lost statistical significance (aOR 8·71, 95% CI 0·44–171·61) suggesting that normal saline was the causative agent of this outbreak. Epidemiological evidence strongly suggested that this post-injection outbreak was caused by saline contaminated withMycobacterium massiliensewithout direct microbiological evidence.
Organizations, Politics, and Public Purposes: Analyzing Public Organizations and Public Management
Authors: Rainey Hal G.
Published: January 2012

The title of this lecture refers to organizations, politics, and public purposes to emphasize developments in the analysis of public organizations and their management and the need for that analysis to include politics as an influence on those organizations. The Gaus Award recognizes contributions in the joint tradition of public administration and political science. Organizations serve as essential components of the administrative branch of government and of virtually all other aspects of human life and many other forms of life. Social scientists that I call “organization theorists” have developed theory and research about organizations and the people in them. This body of work provides concepts and insights useful for the analysis of the organizations in government, which I call “public organizations.” Organizations play crucial roles in the pursuit of values and goals shared by large aggregates of people. “Organizations, Politics, and Public Purposes: Analyzing Public Organizations and Public Management” refers to these shared values and goals as public purposes. Organizations are essential to public administration and we cannot effectively analyze organizations in public administration without concepts developed by political scientists; we need to draw on political science.
Taking the Temperature: Implications for Adoption of Election Day Registration, State-Level Voter Turnout, and Life Expectancy
Authors: Wuffle A , Brians Craig Leonard , Coulter Kristine
Published: January 2012

We consider the neglected importance of temperature as an explanatory variable. We show that: (1) colder states have turnout that is high relative to the national average; (2) the coldest states in the United States were more likely to adopt Election Day Registration (EDR) than other states, and very hot states never did so; and (3) those who live in colder states live longer.
Thermostatic Voting: Presidential Elections in Light of New Policy Data
Authors: Bølstad Jørgen
Published: January 2012

Existing studies imply a model of “thermostatic voting”—a phenomenon characterized by negative feedback from government policy to election outcomes, suggesting that a party's success in setting policy diminishes its electoral prospects. This phenomenon could give politicians an incentive to constrain the fulfillment of public demands, which would conflict with the notion of electoral accountability, which also forms part of the theoretical framework in question. This article addresses this paradox and provides new data that expand an existing time series of American policy liberalism. Employing the new data, the article identifies thermostatic voting in American presidential elections, but in light of the analysis, certain empirical features are also identified that reduce the possible incentive to withhold promised policy changes.
Addressing “Representation and Renewal” at the 2012 Annual Meeting
Authors: Pewett Melissa L.
Published: January 2012

How can political scientists reconsider the ideals attached to representation? What impedes the realization of those ideals in practice? How can we address these questions with a focus on renewal? Exploring these questions and many others related to the theme “Representation and Renewal” will be the focus of the 2012 Annual Meeting. Developed by program chairs Lynn Vavreck, University of California, Los Angeles, and John Carey, Dartmouth College, the 2012 theme statement calls for research that addresses questions about representation, asks what representative relationships can and cannot achieve, and explores how these relationships might be renewed, reformed, or retooled.
Gazing at Fiction in Brussels: Europe as Forgery in David Černý's Entropa
Authors: Zigelyte Lina
Published: January 2012

This article explores issues of visual representations and the interaction between fiction and reality in the making of the ‘idea of Europe’. It specifically focuses on David Černý's installation Entropa, exhibited at the headquarters of the Council of the European Union in 2009. The article argues that, despite the use of national stereotypes as the most characteristic representational element of the installation, Entropa does not limit itself to a sardonic critique of a political institution and a ridicule of national identities. Rather, it unveils the uneasiness of facing European identity as fiction. Entropa challenges the boundary between theatricality and reality, because it is exhibited in a political institution. The installation is addressed as a narrative of confusion, where fiction and fact interact in the construction of ideas on Europe, its history, politics, and culture. Therefore, the article concludes, such interaction potentially accommodates a critical standpoint towards the idea of Europe itself.
Can experience with co-speech gesture influence the prosody of a sign language? Sign language prosodic cues in bimodal bilinguals
Authors: BRENTARI DIANE , NADOLSKE MARIE A. , WOLFORD GEORGE
Published: January 2012

In this paper the prosodic structure of American Sign Language (ASL) narratives is analyzed in deaf native signers (L1-D), hearing native signers (L1-H), and highly proficient hearing second language signers (L2-H). The results of this study show that the prosodic patterns used by these groups are associated both with their ASL language experience (L1 or L2) and with their hearing status (deaf or hearing), suggesting that experience using co-speech gesture (i.e. gesturing while speaking) may have some effect on the prosodic cues used by hearing signers, similar to the effects of the prosodic structure of an L1 on an L2.
Improving AFM Images with Harmonic Interference by Spectral Analysis
Authors: Kiwilszo Marek , Zieliński Artur , Smulko Janusz , Darowicki Kazimierz
Published: January 2012

Atomic force microscopy (AFM) is one of the most sensitive tools for nanoscale imaging. As such, it is very sensitive to external noise sources that can affect the quality of collected data. The intensity of the disturbance depends on the noise source and the mode of operation. In some cases, the internal noise from commercial AFM controllers can be significant and difficult to remove. Thus, a new method based on spectrum analysis of the scanned images is proposed to reduce harmonic disturbances. The proposal is a post-processing method and can be applied at any time after measurements. This article includes a few methods of harmonic cancellation (e.g., median filtering, wavelet denoising, Savitzky-Golay smoothing) and compares their effectiveness. The proposed method, based on Fourier transform of the scanned images, was more productive than the other methods mentioned before. The presented data were achieved for images of conductive layers taken in a contact AFM mode.
Exploration of parametric uncertainty in a surface mass balance model applied to the Greenland ice sheet
Authors: Fitzgerald P. W. , Bamber J. L. , Ridley J. K. , Rougier J. C.
Published: January 2012

Computational modeling of Earth system processes often requires simplifying assumptions of the real system. These necessary assumptions result in the definition of internal model parameters that can take a number of different values but must be explicitly defined for any one model simulation. The main issue with such an uncertain multidimensional input space is that many simulations are needed to adequately explore it. This study presents a generalized parameter screening experiment for use in future earth system modeling. This approach identifies model parameters that dominate uncertainty, therefore reducing to a manageable number the simulations required to explore the input space. The approach we adopt is relatively inexpensive to implement and can be applied at both the aggregate and disaggregate (e.g., regional) level. To demonstrate the potential of such a method, it is applied to a surface mass balance model of intermediate complexity over the Greenland ice sheet. All identified parameters were related to the surface melt parameterization, with albedo parameters being identified as the most important. Spatial distributions of the parameter sensitivities show that, in recent years, most parameter sensitivities are concentrated around the southwest and northern ice sheet margins. Simulations for the 21st century indicate an increase in sensitivity in these high melt areas especially in the northeast. Melt contributions from temperature and radiative effects are shown to be important on the order of parameters identified, and as a consequence, sensitivities are dependent on the present climate used for modeling surface mass balance.
Specificity of Training in the Lingual Musculature
Authors: Clark Heather M.
Published: January 2012

Purpose

Training specificity for a number of exercise parameters has been demonstrated for the limb musculature. The current study is a Phase I exploration of training specificity in the lingual musculature.

Method

Twenty-five healthy participants were assigned to 1 of 5 training conditions. Four groups completed 4 weeks of lingual exercise targeting strength, endurance, power, or speed; a control group did not exercise. Performance measures of strength, endurance, power, and speed were obtained before and after training.

Results

Although statistically significant group effects were not detected, specificity was observed with respect to effect size for the performance variables of strength, endurance, and power. Further evidence of specificity was provided by the finding that training isotonic endurance did not increase performance on an isometric endurance task. Speed training did not improve performance on any of the outcome measures, nor did speed increase following training with any of the exercises.

Conclusions

The findings provide initial evidence that training specificity may be observed in the lingual musculature. The reported effect sizes can inform future studies examining the benefit of training muscle functions underlying speech and swallowing.
IUPAC-NIST Solubility Data Series. 92. Metal Carbonates. Part 1. Solubility and Related Thermodynamic Quantities of Cadmium(II) Carbonate in Aqueous Systems
Authors: Churagulov B. R. , Schmidt P. , Zeng D.
Published: December 2011

This paper, devoted to cadmium(II) carbonate, is the first in a series dedicated to the solubility of compounds relevant to mobility of metals in the environment. Here, we present compilations and critical evaluation of the experimental solubility data for cadmium(II) carbonate, otavite, in aqueous ternary and higher-order systems. The solubility of cadmium(II) carbonate depends on temperature, carbon dioxide partial pressure, pH, the presence of complexing ions, and ionic strength of the solution. Papers referring to solubility of cadmium(II) carbonate have been published since 1901; the thorough search of the literature in this field covered the period from 1901 through 2009. The compilation of the available experimental data is introduced with a critical evaluation. The evaluation of the experimental data considers the possible correlation between the data obtained under similar experimental conditions of temperature, carbon dioxide partial pressure, electrolyte, and ionic strength. Those experiments where the solid phase was well identified and the interactions between the electrolyte and the dissolved cadmium(II) ion were considered practically negligible were used to determine the thermodynamic properties of the solid cadmium(II) carbonate. Recommended values for the thermodynamic quantities are lg*Kps0∘ = 6.11 ± 0.10, ΔfG°(CdCO3, cr, 298.15 K) = −(674.3 ± 0.6) kJ mol−1, ΔfH°(CdCO3, cr, 298.15 K) = −(752.2 ± 0.8) kJ mol−1, S°(CdCO3, cr, 298.15 K) = (103.9 ± 0.2) J K−1 mol−1.
Retention Indices for Frequently Reported Compounds of Plant Essential Oils
Authors: Babushok V. I. , Linstrom P. J. , Zenkevich I. G.
Published: December 2011

Gas chromatographic retention indices were evaluated for 505 frequently reported plant essential oil components using a large retention index database. Retention data are presented for three types of commonly used stationary phases: dimethyl silicone (nonpolar), dimethyl silicone with 5% phenyl groups (slightly polar), and polyethylene glycol (polar) stationary phases. The evaluations are based on the treatment of multiple measurements with the number of data records ranging from about 5 to 800 per compound. Data analysis was limited to temperature programmed conditions. The data reported include the average and median values of retention index with standard deviations and confidence intervals.
New Equations for the Sublimation Pressure and Melting Pressure of H2O Ice Ih
Authors: Wagner Wolfgang , Riethmann Thomas , Feistel Rainer , Harvey Allan H.
Published: December 2011

New reference equations, adopted by the International Association for the Properties of Water and Steam (IAPWS), are presented for the sublimation pressure and melting pressure of ice Ih as a function of temperature. These equations are based on input values derived from the phase-equilibrium condition between the IAPWS-95 scientific standard for thermodynamic properties of fluid H2O and the equation of state of H2O ice Ih adopted by IAPWS in 2006, making them thermodynamically consistent with the bulk-phase properties. Compared to the previous IAPWS formulations, which were empirical fits to experimental data, the new equations have significantly less uncertainty. The sublimation-pressure equation covers the temperature range from 50 K to the vapor–liquid–solid triple point at 273.16 K. The ice Ih melting-pressure equation describes the entire melting curve from 273.16 K to the ice Ih–ice III–liquid triple point at 251.165 K. For completeness, we also give the IAPWS melting-pressure equation for ice III, which is slightly adjusted to agree with the ice Ih melting-pressure equation at the corresponding triple point, and the unchanged IAPWS melting-pressure equations for ice V, ice VI, and ice VII.
Thermodynamic Properties of Dimethyl Carbonate
Authors: Zhou Yong , Wu Jiangtao , Lemmon Eric W.
Published: December 2011

A thermodynamic property formulation for dimethyl carbonate has been developed with the use of available experimental thermodynamic property data. The equation of state was developed with multiproperty fitting methods involving pressure-density-temperature (pρT), heat capacity, vapor pressure, and saturated-liquid density data. The equation of state conforms to the Maxwell criterion for two-phase liquid-vapor equilibrium states, and is valid for temperatures from the triple-point temperature (277.06 ± 0.63) K to 600 K, for pressures up to 60 MPa, and for densities up to 12.12 mol dm−3. The extrapolation behavior of the equation of state at low and high temperatures and pressures is reasonable. The uncertainties (k = 2, indicating a 95% confidence level) of the equation of state in density are 0.05% for saturated-liquid states below 350 K, rising to 0.1% in the single phase between 278 K and 400 K at pressures up to 60 MPa. Due to the lack of reliable data outside this region, the estimated uncertainties increase to 0.5% to 1% in the vapor and critical regions. The uncertainties in vapor pressure are 0.6% from 310 K to 400 K, and increase to 1% at higher temperatures and to 2% at lower temperatures due to a lack of experimental data. The uncertainty in isobaric heat capacity and speed of sound in the liquid phase at saturation or atmospheric pressure is 0.5% from 280 K to 335 K. The uncertainties are higher for all properties in the critical region. Detailed comparisons between experimental and calculated data, and an analysis of the equation, have been performed.
Equation of State for Solid Phase I of Carbon Dioxide Valid for Temperatures up to 800 K and Pressures up to 12 GPa
Authors: Martin Trusler J. P.
Published: December 2011

The available thermodynamic-property data for solid phase I of carbon dioxide (“dry ice”) are reviewed and used to determine the parameters of a new fundamental equation of state constructed in the form of a Helmholtz energy function with temperature and molar volume as the independent variables. The experimental data considered include the pressure, molar volume, and isobaric heat capacity along the sublimation curve, the melting-pressure curve, and molar volume in the compressed solid at temperatures from 295 to 764 K and pressures up to 12 GPa. The equation of state is based on the quasi-harmonic approximation, incorporating a Debye oscillator distribution for the vibrons, two discrete modes for the librons and a further three distinct modes for the internal vibrations of the CO2 molecule. A small anharmonic correction term is included, which is significant mainly in the region of the triple point. The estimated relative uncertainty of molar volume at specified temperature and pressure calculated from the equation of state is 0.02% on the sublimation curve and 1.5% in the compressed solid; for isobaric heat capacity on the sublimation curve, the uncertainty varies from 5.0% to 0.5% between 2 and 195 K. Auxiliary equations for the pressure and molar volume on the sublimation and melting curves are given. The equation of state is valid at temperatures from 0 to 800 K and at pressures from the solid–fluid phase boundary to 12 GPa.
Electric transport through nanometric CoFe2O4 thin films investigated by conducting atomic force microscopy
Authors: Foerster M. , Gutierrez D. F. , Rebled J. M. , Arbelo E. , Rigato F. , Jourdan M. , Peiró F. , Fontcuberta J.
Published: January 2012

A systematic study of electric transport through thin (2–8 nm) CoFe2O4 films deposited on epitaxial SrRuO3 bottom electrodes was performed by conducting atomic force microscopy (CAFM). Experimental procedures to investigate transport through thin insulating films by CAFM are critically revised, and the potential of CoFe2O4 films for the use as spin-filtering barriers is assessed. It is concluded that, at room-temperature, a non-tunnel channel significantly contributes to the electric transport, thus limiting the spin-filtering efficiency.
Ar plasma induced deep levels in epitaxial n-GaAs
Authors: Venter A. , Nyamhere C. , Botha J. R. , Auret F. D. , Janse van Rensburg P. J. , Meyer W. E. , Coelho S. M. M. , Kolkovsky V. l.
Published: January 2012

Ar plasma etching of n-type (Si doped) GaAs introduces several electron traps (Ec - 0.04 eV, Ec - 0.07 eV, Ec - 0.19 eV, Ec - 0.31 eV, Ec - 0.53 eV, and Ec - 0.61 eV). The trap, Ec - 0.04 eV, labelled E1′ and having a trap signature similar to irradiation induced defect E1, appears to be metastable. Ec - 0.31 eV and Ec - 0.61 eV are metastable too and they are similar to the M3/M4 defect configuration present in hydrogen plasma exposed n-GaAs.
Enhancement of impact-induced mechanoluminescence by swift heavy ion irradiation
Authors: Zhan T. Z. , Xu C. N. , Yamada H. , Terasawa Y. , Zhang L. , Iwase H. , Kawai M.
Published: January 2012

In this Letter, we report a strategy using swift heavy ion (SHI) irradiation to enhance the impact-induced mechanoluminescence (ML) in ML materials. The impact-induced ML intensity of CaSrAl2Si2O8:Eu2+ was enhanced by about one order of magnitude by using SHI irradiation. Furthermore, the enhancement was found to depend on electronic stopping power and irradiation fluence. The density of traps of a type suitable for impact-induced ML is considered to be increased by the SHI irradiation, resulting in the impact-induced ML enhancement.
Changing inter-molecular spin-orbital coupling for generating magnetic field effects in phosphorescent organic semiconductors
Authors: Yan Liang , Shao Ming , Graeff Carlos F. O. , Hummelgen Ivo , Ma Dongge , Hu Bin
Published: January 2012

Phosphorescent organic semiconductors normally show negligible magnetic field effects in electronic and optic responses. These phenomena have been generally attributed to strong spin-orbital coupling which can dominate internal spin-dephasing process as compared with applied magnetic field. This paper reports both positive and negative magnetocurrents from phosphorescent organic semiconductors through dissociation and charge-reaction channels when the intermolecular spin-orbital coupling is changed based on materials mixing. Our experimental results indicate that inter-molecular spin-orbital coupling is essentially responsible for the generation of magnetic field effects in phosphorescent organic semiconductors.
Dynamic (hyper)polarizabilities of the sulphur dioxide molecule: Coupled cluster calculations including vibrational corrections
Authors: Naves Emílio S. , Castro Marcos A. , Fonseca Tertius L.
Published: January 2012

In this work we report results for dynamical (hyper)polarizabilities of the sulphur dioxide molecule with inclusion of vibrational corrections. The electronic contributions were computed analytically at the single and double coupled cluster level through response theories for the frequencies 0, 0.0239, 0.0428, 0.0656, 0.0720, and 0.0886 hartree. Contributions of the connected triple excitations to the dynamic electronic properties were also estimated through the multiplicative correction scheme. Vibrational corrections were calculated by means of the perturbation theoretical method. The results obtained show that the zero point vibrational correction is very small for all properties studied while the pure vibrational correction is relevant for the dc-Pockels effect, intensity dependent refractive index, and dc-Kerr effect. For these nonlinear optical processes, the pure vibrational corrections represent approximately 75%, 13%, and 6% of the corresponding electronic contributions for the higher frequencies quoted. The results presented for the polarizability are in good agreement with experimental values available in the literature. For the hyperpolarizabilities we have not obtained experimental results with precision sufficient for comparison.
Quantum numbers, Chern classes, and a bodhisattva
Authors: Yang Chen Ning
Published: January 2012

A physics Nobel laureate reflects on how he came to understand the significance of a youthful lunchtime encounter with a famous mathematician.
Slow slip: A new kind of earthquake
Authors: Vidale John E. , Houston Heidi
Published: January 2012

Sandwiched between the shallow region of sudden, infrequent earthquakes and the deeper home to continuous viscous motion lies an intermediate realm of intermittent sliding and rumbling. Discovered in recent years, it still harbors many secrets.
Optimal 3D single-molecule localization for superresolution microscopy with aberrations and engineered point spread functions
Authors: Quirin Sean , Pavani Sri Rama Prasanna , Piestun Rafael
Published: December 2011

Photo-activation localization microscopy is a far-field superresolution imaging technique based on the localization of single molecules with subdiffraction limit precision. Known under acronyms such as PALM (photo-activated localization microscopy) or STORM (stochastic optical reconstruction microscopy), these techniques achieve superresolution by allowing only a sparse, random set of molecules to emit light at any given time and subsequently localizing each molecule with great precision. Recently, such techniques have been extended to three dimensions, opening up unprecedented possibilities to explore the structure and function of cells. Interestingly, proper engineering of the three-dimensional (3D) point spread function (PSF) through additional optics has been demonstrated to theoretically improve 3D position estimation and ultimately resolution. In this paper, an optimal 3D single-molecule localization estimator is presented in a general framework for noisy, aberrated and/or engineered PSF imaging. To find the position of each molecule, a phase-retrieval enabled maximum-likelihood estimator is implemented. This estimator is shown to be efficient, meaning it reaches the fundamental Cramer–Rao lower bound of
x
,
y
, and
z
localization precision. Experimental application of the phase-retrieval enabled maximum-likelihood estimator using a particular engineered PSF microscope demonstrates unmatched low-photon-count 3D wide-field single-molecule localization performance.
Paleoenvironmental history of the West Baray, Angkor (Cambodia)
Authors: Day Mary Beth , Hodell David A. , Brenner Mark , Chapman Hazel J. , Curtis Jason H. , Kenney William F. , Kolata Alan L. , Peterson Larry C.
Published: January 2012

Angkor (Cambodia) was the seat of the Khmer Empire from the 9th to 15th century AD. The site is noted for its monumental architecture and complex hydro-engineering systems, comprised of canals, moats, embankments, and large reservoirs, known as barays. We infer a 1,000-y,
14
C-dated paleoenvironmental record from study of an approximately 2-m sediment core taken in the largest Khmer reservoir, the West Baray. The baray was utilized and managed from the time of construction in the early 11th century, through the 13th century. During that time, the West Baray received relatively high rates of detrital input. In the 14th century, linear sedimentation rates diminished by an order of magnitude, yielding a condensed section that correlates temporally with episodes of regional monsoon failure during the late 14th and early 15th century, recorded in tree ring records from Vietnam. Our results demonstrate that changes in the water management system were associated with the decline of the Angkorian kingdom during that period. By the 17th century, the West Baray again functioned as a limnetic system. Ecologic and sedimentologic changes over the last millennium, detected in the baray deposits, are attributed to shifts in regional-scale Khmer water management, evolving land use practices in the catchment, and regional climate change.
Affinity of talin-1 for the β3-integrin cytosolic domain is modulated by its phospholipid bilayer environment
Authors: Moore David T. , Nygren Patrik , Jo Hyunil , Boesze-Battaglia Kathleen , Bennett Joel S. , DeGrado William F.
Published: December 2011

Binding of the talin-1 FERM (4.1/ezrin/radixin/moesin) domain to the β3 cytosolic tail causes activation of the integrin αIIbβ3. The FERM domain also binds to acidic phospholipids. Although much is known about the interaction of talin-1 with integrins and lipids, the relative contribution of each interaction to integrin regulation and possible synergy between them remain to be clarified. Here, we examined the thermodynamic interplay between FERM domain binding to phospholipid bilayers and to its binding sites in the β3 tail. We found that although both the F0F1 and F2F3 subdomains of the talin-1 FERM domain bind acidic bilayers, the full-length FERM domain binds with an affinity similar to F2F3, indicating that F0F1 contributes little to the overall interaction. When free in solution, the β3 tail has weak affinity for the FERM domain. However, appending the tail to acidic phospholipids increased its affinity for the FERM domain by three orders of magnitude. Nonetheless, the affinity of the FERM for the appended tail was similar to its affinity for binding to bilayers alone. Thus, talin-1 binding to the β3 tail is a ternary interaction dominated by a favorable surface interaction with phospholipid bilayers and set by lipid composition. Nonetheless, interactions between the FERM domain, the β3 tail, and lipid bilayers are not optimized for a high-affinity synergistic interaction, even at the membrane surface. Instead, the interactions appear to be tuned in such a way that the equilibrium between inactive and active integrin conformations can be readily regulated.
Micro-chemical synthesis of molecular probes on an electronic microfluidic device
Authors: Keng Pei Yuin , Chen Supin , Ding Huijiang , Sadeghi Saman , Shah Gaurav J. , Dooraghi Alex , Phelps Michael E. , Satyamurthy Nagichettiar , Chatziioannou Arion F. , Kim Chang-Jin “CJ” , van Dam R. Michael
Published: December 2011

We have developed an all-electronic digital microfluidic device for microscale chemical synthesis in organic solvents, operated by electrowetting-on-dielectric (EWOD). As an example of the principles, we demonstrate the multistep synthesis of [
18
F]FDG, the most common radiotracer for positron emission tomography (PET), with high and reliable radio-fluorination efficiency of [
18
F]FTAG (88 ± 7%,
n
 = 11) and quantitative hydrolysis to [
18
F]FDG (> 95%,
n
 = 11). We furthermore show that batches of purified [
18
F]FDG can successfully be used for PET imaging in mice and that they pass typical quality control requirements for human use (including radiochemical purity, residual solvents, Kryptofix, chemical purity, and pH). We report statistical repeatability of the radiosynthesis rather than best-case results, demonstrating the robustness of the EWOD microfluidic platform. Exhibiting high compatibility with organic solvents and the ability to carry out sophisticated actuation and sensing of reaction droplets, EWOD is a unique platform for performing diverse microscale chemical syntheses in small volumes, including multistep processes with intermediate solvent-exchange steps.
Large-scale, spatially-explicit test of the refuge strategy for delaying insecticide resistance
Authors: Carrière Yves , Ellers-Kirk Christa , Hartfield Kyle , Larocque Guillaume , Degain Ben , Dutilleul Pierre , Dennehy Timothy J. , Marsh Stuart E. , Crowder David W. , Li Xianchun , Ellsworth Peter C. , Naranjo Steven E. , Palumbo John C. , Fournier Al , Antilla Larry , Tabashnik Bruce E.
Published: January 2012

The refuge strategy is used worldwide to delay the evolution of pest resistance to insecticides that are either sprayed or produced by transgenic
Bacillus thuringiensis
(Bt) crops. This strategy is based on the idea that refuges of host plants where pests are not exposed to an insecticide promote survival of susceptible pests. Despite widespread adoption of this approach, large-scale tests of the refuge strategy have been problematic. Here we tested the refuge strategy with 8 y of data on refuges and resistance to the insecticide pyriproxyfen in 84 populations of the sweetpotato whitefly (
Bemisia tabaci
) from cotton fields in central Arizona. We found that spatial variation in resistance to pyriproxyfen within each year was not affected by refuges of melons or alfalfa near cotton fields. However, resistance was negatively associated with the area of cotton refuges and positively associated with the area of cotton treated with pyriproxyfen. A statistical model based on the first 4 y of data, incorporating the spatial distribution of cotton treated and not treated with pyriproxyfen, adequately predicted the spatial variation in resistance observed in the last 4 y of the study, confirming that cotton refuges delayed resistance and treated cotton fields accelerated resistance. By providing a systematic assessment of the effectiveness of refuges and the scale of their effects, the spatially explicit approach applied here could be useful for testing and improving the refuge strategy in other crop–pest systems.
Localization of the proteasomal ubiquitin receptors Rpn10 and Rpn13 by electron cryomicroscopy
Authors: Sakata Eri , Bohn Stefan , Mihalache Oana , Kiss Petra , Beck Florian , Nagy Istvan , Nickell Stephan , Tanaka Keiji , Saeki Yasushi , Förster Friedrich , Baumeister Wolfgang
Published: January 2012

Two canonical subunits of the 26S proteasome, Rpn10 and Rpn13, function as ubiquitin (Ub) receptors. The mutual arrangement of these subunits—and all other non-ATPase subunits—in the regulatory particle is unknown. Using electron cryomicroscopy, we calculated difference maps between wild-type 26S proteasome from
Saccharomyces cerevisiae
and deletion mutants (
rpn10Δ
,
rpn13Δ
, and
rpn10Δrpn13Δ
). These maps allowed us to localize the two Ub receptors unambiguously. Rpn10 and Rpn13 mapped to the apical part of the 26S proteasome, above the N-terminal coiled coils of the AAA-ATPase heterodimers Rpt4/Rpt5 and Rpt1/Rpt2, respectively. On the basis of the mutual positions of Rpn10 and Rpn13, we propose a model for polyubiquitin binding to the 26S proteasome.
SNPdbe: constructing an nsSNP functional impacts database
Authors: Schaefer Christian , Meier Alice , Rost Burkhard , Bromberg Yana
Published: January 2012

Summary: Many existing databases annotate experimentally characterized single nucleotide polymorphisms (SNPs). Each non-synonymous SNP (nsSNP) changes one amino acid in the gene product (single amino acid substitution;SAAS). This change can either affect protein function or be neutral in that respect. Most polymorphisms lack experimental annotation of their functional impact. Here, we introduce SNPdbe—SNP database of effects, with predictions of computationally annotated functional impacts of SNPs. Database entries represent nsSNPs in dbSNP and 1000 Genomes collection, as well as variants from UniProt and PMD. SAASs come from >2600 organisms; ‘human’ being the most prevalent. The impact of each SAAS on protein function is predicted using the SNAP and SIFT algorithms and augmented with experimentally derived function/structure information and disease associations from PMD, OMIM and UniProt. SNPdbe is consistently updated and easily augmented with new sources of information. The database is available as an MySQL dump and via a web front end that allows searches with any combination of organism names, sequences and mutation IDs.

Availability:  http://www.rostlab.org/services/snpdbe

Contact:  schaefer@rostlab.org; snpdbe@rostlab.org
VarSifter: Visualizing and analyzing exome-scale sequence variation data on a desktop computer
Authors: Teer Jamie K. , Green Eric D. , Mullikin James C. , Biesecker Leslie G.
Published: January 2012

Summary: VarSifter is a graphical software tool for desktop computers that allows investigators of varying computational skills to easily and quickly sort, filter, and sift through sequence variation data. A variety of filters and a custom query framework allow filtering based on any combination of sample and annotation information. By simplifying visualization and analyses of exome-scale sequence variation data, this program will help bring the power and promise of massively-parallel DNA sequencing to a broader group of researchers.

Availability and Implementation: VarSifter is written in Java, and is freely available in source and binary versions, along with a User Guide, at http://research.nhgri.nih.gov/software/VarSifter/.

Contact:  mullikin@mail.nih.gov

Supplementary Information: Additional figures and methods available online at the journal's website.
Approximating the set of local minima in partial RNA folding landscapes
Authors: Sahoo S. , Albrecht A.A.
Published: January 2012

Motivation: We study a stochastic method for approximating the set of local minima in partial RNA folding landscapes associated with a bounded-distance neighbourhood of folding conformations. The conformations are limited to RNA secondary structures without pseudoknots. The method aims at exploring partial energy landscapes pL induced by folding simulations and their underlying neighbourhood relations. It combines an approximation of the number of local optima devised by Garnier and Kallel (2002) with a run-time estimation for identifying sets of local optima established by Reeves and Eremeev (2004).

Results: The method is tested on nine sequences of length between 50 nt and 400 nt, which allows us to compare the results with data generated by RNAsubopt and subsequent barrier tree calculations. On the nine sequences, the method captures on average 92% of local minima with settings designed for a target of 95%. The run-time of the heuristic can be estimated by O(n2Dνlnν), where n is the sequence length, ν is the number of local minima in the partial landscape pL under consideration and D is the maximum number of steepest descent steps in attraction basins associated with pL.

Contact:  a.albrecht@qub.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
influx_s: increasing numerical stability and precision for metabolic flux analysis in isotope labelling experiments
Authors: Sokol Serguei , Millard Pierre , Portais Jean-Charles
Published: January 2012

Motivation: The problem of stationary metabolic flux analysis based on isotope labelling experiments first appeared in the early 1950s and was basically solved in early 2000s. Several algorithms and software packages are available for this problem. However, the generic stochastic algorithms (simulated annealing or evolution algorithms) currently used in these software require a lot of time to achieve acceptable precision. For deterministic algorithms, a common drawback is the lack of convergence stability for ill-conditioned systems or when started from a random point.

Results: In this article, we present a new deterministic algorithm with significantly increased numerical stability and accuracy of flux estimation compared with commonly used algorithms. It requires relatively short CPU time (from several seconds to several minutes with a standard PC architecture) to estimate fluxes in the central carbon metabolism network of Escherichia coli.

Availability: The software package influx_s implementing this algorithm is distributed under an OpenSource licence at http://metasys.insa-toulouse.fr/software/influx/

Contact:  jean-charles.portais@insa-toulouse.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Small-molecule inhibitor starting points learned from protein–protein interaction inhibitor structure
Authors: Koes David Ryan , Camacho Carlos J.
Published: January 2012

Motivation: Protein–protein interactions (PPIs) are a promising, but challenging target for pharmaceutical intervention. One approach for addressing these difficult targets is the rational design of small-molecule inhibitors that mimic the chemical and physical properties of small clusters of key residues at the protein–protein interface. The identification of appropriate clusters of interface residues provides starting points for inhibitor design and supports an overall assessment of the susceptibility of PPIs to small-molecule inhibition.

Results: We extract Small-Molecule Inhibitor Starting Points (SMISPs) from protein-ligand and protein–protein complexes in the Protein Data Bank (PDB). These SMISPs are used to train two distinct classifiers, a support vector machine and an easy to interpret exhaustive rule classifier. Both classifiers achieve better than 70% leave-one-complex-out cross-validation accuracy and correctly predict SMISPs of known PPI inhibitors not in the training set. A PDB-wide analysis suggests that nearly half of all PPIs may be susceptible to small-molecule inhibition.

Availability:  http://pocketquery.csb.pitt.edu.

Contact:  dkoes@pitt.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Modeling community-wide molecular networks of multicellular systems
Authors: Komurov Kakajan
Published: January 2012

Motivation: Multicellular systems, such as tissues, are composed of different cell types that form a heterogeneous community. Behavior of these systems is determined by complex regulatory networks within (intracellular networks) and between (intercellular networks) cells. Increasingly more studies are applying genome-wide experimental approaches to delineate the contributions of individual cell types (e.g. stromal, epithelial, vascular cells) to collective behavior of heterogeneous cell communities (e.g. tumors). Although many computational methods have been developed for analyses of intracellular networks based on genome-scale data, these efforts have not been extended toward analyzing genomic data from heterogeneous cell communities.

Results: Here, we propose a network-based approach for analyses of genome-scale data from multiple cell types to extract community-wide molecular networks comprised of intra- and intercellular interactions. Intercellular interactions in this model can be physical interactions between proteins or indirect interactions mediated by secreted metabolites of neighboring cells. Applying this method on data from a recent study on xenograft mouse models of human lung adenocarcinoma, we uncover an extensive network of intra- and intercellular interactions involved in the acquired resistance to angiogenesis inhibitors.

Contact:  kakajan.komurov@cchmc.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
CytoSEED: a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created by the Model SEED
Authors: DeJongh Matthew , Bockstege Benjamin , Frybarger Paul , Hazekamp Nicholas , Kammeraad Joshua , McGeehan Travis
Published: January 2012

Summary: CytoSEED is a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created using the Model SEED. The CytoSEED plugin enables users of the Model SEED to create informative visualizations of the reaction networks generated for their organisms of interest. These visualizations are useful for understanding organism-specific biochemistry and for highlighting the results of flux variability analysis experiments.

Availability and Implementation: Freely available for download on the web at http://sourceforge.net/projects/cytoseed/. Implemented in Java SE 6 and supported on all platforms that support Cytoscape.

Contact:  dejongh@hope.edu

Supplementary information: Installation instructions, a tutorial, and full-size figures are available at http://www.cs.hope.edu/cytoseed/.
The evaluation and provision of effective medicines
Authors: Rawlins Michael D.
Published: January 2012

As more new medicines become available, often at a premium price, it has become imperative for individual practitioners, institutions and health care systems to assess whether they represent good value for money. Are they an improvement on existing treatments, either in terms of improved efficacy or safety? And, if so, do they represent a cost effective use of health care resources?...
The cell
Authors: Banting George
Published: January 2012

This section emphasizes the cell as a dynamic entity. Cells are not simply building blocks that are linked together to create an organism: each cell comprises a dynamic network of interacting macromolecules. Just how dynamic has been brought home by recent advances in cell imaging technologies. A host of multisubunit molecular structures must assemble and disassemble in a highly coordinated, exquisitely regulated, and beautifully choreographed manner in order to ensure the integrity of the cell and to provide its ability to function correctly as a single unit within a large multicellular organism....
Ion channels and disease
Authors: Ashcroft Frances M.
Published: January 2012

Ion channels are membrane proteins that act as gated pathways for the movement of ions across cell membranes. They are found in both surface and intracellular membranes, and play essential roles in the physiology of all cell types. An ever-increasing number of human diseases are found to be caused by defects in ion channel function. Ion channel diseases may arise in a number of different ways:...