bluuebunny/crossref_metadata_2025 huggingface dataset:
ChemInform Abstract: Ab initio Molecular Orbital Studies of Singlet Oxygen Reactions of Olefins, Enol Ethers, and Enamines.
Authors: YOSHIOKA Y. , YAMADA S. , KAWAKAMI T. , NISHINO M. , YAMAGUCHI K. , SAITO I.
Published: August 2010

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: Resolution of cis‐4‐O‐TBS‐2‐Cyclopenten‐1,4‐diol.
Authors: CURRAN T. T. , HAY D. A.
Published: August 2010

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: An Asymmetric Synthesis of L‐694,458, a Human Leukocyte Elastase Inhibitor, via Novel Enzyme Resolution of β‐Lactam Esters.
Authors: CVETOVICH R. J. , CHARTRAIN M. , HARTNER F. W. JUN. , ROBERGE C. , AMATO J. S. , GRABOWSKI E. J. J.
Published: August 2010

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: Novel 5‐(2‐(N,N‐Di‐n‐propylamino)ethyl)benzimidazole‐Derived High Affinity Dopaminergic Ligands
Authors: DRAGOVIC D. , KOSTIC‐RAJACIC S. , SOSKIC V. , JOKSIMOVIC J.
Published: August 2010

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: Research on Antifungal and Antimycobacterial Agents. Synthesis and Activity of 4‐Alkylthiopyridine‐2‐carbothioamides.
Authors: KLIMESOVA V. , SVOBODA M. , WAISSER K. , MACHACEK M. , BUCHTA V. , ODLEROVA Z.
Published: August 2010

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: Enantioselective Synthesis of Cuparane Sesquiterpenes. Synthesis of (‐) ‐Cuparene and (‐)‐δ‐Cuparenol.
Authors: ABAD A. , AGULLO C. , ARNO M. , CUNAT A. C. , GARCIA M. T. , ZARAGOZA R. J.
Published: August 2010

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: A Novel and Facile Synthesis of Barbatusol Methyl Ether.
Authors: WANG X. , CUI Y. , PAN X. , CHEN Y.
Published: August 2010

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: A Radical Prototype to Steroids: Synthesis of d,l‐5α‐D‐ Homoandrostane‐4α‐methyl‐3,17a‐dione.
Authors: ZORETIC P. A. , CHEN Z. , ZHANG Y. , RIBEIRO A. A.
Published: August 2010

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: Synthesis and Antibacterial Activity of 1‐β‐Methylcarbapenems ( VIII) Having a 1,3‐Diazabicyclo(3.3.0)octan‐4‐one Moiety
Authors: NAM K. H. , OH C.‐H. , CHO J. K. , KIM H. J. , LEE K.‐S. , CHO J.‐H.
Published: August 2010

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: Catalytic Dimerization of Alkyl Acrylates
Authors: TEMBE G. L. , BANDYOPADHYAY A. R. , GANESHPURE P. A. , SATISH S.
Published: August 2010

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: The Chemistry of C‐Sulfonyldithioformates
Authors: YASSIN S. M.
Published: August 2010

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: Overview of Modern Magnetism
Authors: COEY J. M. D.
Published: August 2010

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A pediatric phase I trial and pharmacokinetic study of ispinesib: A Children's Oncology Group phase I consortium study
Authors: Souid Abdul‐Kader , Dubowy Ronald L. , Ingle Ashish M. , Conlan Maureen G. , Sun Junfeng , Blaney Susan M. , Adamson Peter C.
Published: August 2010

Purpose

To determine the maximum‐tolerated dose, dose‐limiting toxicities, and pharmacokinetics of the kinesin spindle protein inhibitor ispinesib in pediatric patients with recurrent or refractory solid tumors.

Subjects and Methods

Ispinesib was administered as 1‐hr intravenous infusion weekly × 3, every 28 days. Cohorts of 3–6 patients were enrolled at 5, 7, 9, and 12 mg/m2/dose. Serial plasma samples for pharmacokinetic analyses were obtained after the first dose.

Results

Twenty‐four (13 females) patients with a median (range) age of 10 years (1–19) were enrolled in the study. At the 12 mg/m2 dose level dose‐limiting neutropenia occurred in 2/6 patients and hyperbilirubinemia in 1/6 patients, while at the 9 mg/m2 dose level 1/6 patients had dose‐limiting neutropenia. There were no objective responses, but three patients (diagnoses of anaplastic astrocytoma, alveolar soft part sarcoma, and ependymoblastoma) had stable disease for 4–7 courses. There was substantial interpatient variation in drug disposition. The median (range) terminal elimination half‐life was 16 (8–44) hr and the plasma drug clearance was 5 (1–14) L/hr/m2.

Conclusions

The maximum tolerated and recommended phase II dose for ispinesib administered weekly × 3 every 28 days for children with solid tumors is 9 mg/m2/dose. Plans for a phase II trial in select pediatric solid tumors are in development. Pediatr Blood Cancer. 2010;55:1323–1328. © 2010 Wiley‐Liss, Inc.
Race‐specific transition patterns among alcohol use classes in adolescent girls
Authors: Dauber Sarah E. , Paulson James F. , Leiferman Jenn A.
Published: August 2010

We used data from the National Longitudinal Study of Adolescent Health to examine transitions among alcohol use classes in 2225 White and African American adolescent girls, and race differences in predictors of transition into and out of problematic drinking classes. Latent class analysis confirmed four classes for White girls and three for AA girls, defined in a previous study. Latent transition analysis revealed more stable abstainers and decreasing alcohol use among AA girls, and more increasing alcohol use among White girls, though stable abstainers were the largest group in both races. Increasing use was predicted by delinquency, academic misbehavior, substance use, and peer support for White girls, and by older age and delinquency for AA girls. Decreasing use was predicted by older age and depressive symptoms for White girls, and by family relationship quality and substance use for AA girls. Study limitations and implications of findings are discussed.
The JNK inhibitor SP600125 enhances dihydroartemisinin‐induced apoptosis by accelerating Bax translocation into mitochondria in human lung adenocarcinoma cells
Authors: Lu Ying-Ying , Chen Tong-Sheng , Wang Xiao-Ping , Qu Jun-Le , Chen Min
Published: August 2010

The C‐Jun N‐terminal Kinase (JNK) inhibitor SP600125 is widely used to inhibit the JNK‐mediated Bax activation and cell apoptosis. However, this report demonstrates that SP600125 synergistically enhances the dihydroartemisinin (DHA)‐induced human lung adenocarcinoma cell apoptosis by accelerating Bax translocation and subsequent intrinsic apoptotic pathway involving mitochondrial membrane depolarization, cytochrome c release, caspase‐9 and caspase‐3 activation. The dynamical analysis of GFP‐Bax mobility inside single living cells using fluorescence recovery after photobleaching revealed that SP600125 aggravated the DHA‐induced decrease of Bax mobility and Bax translocation. These results for the first time present a novel pro‐apoptotic action of SP600125 in DHA‐induced apoptosis.
Madonna or Don McLean? The effect of order of exposure on relative liking
Authors: Pandelaere Mario , Millet Kobe , Van den Bergh Bram
Published: August 2010

While many studies have shown that exposure frequency affects consumer attitudes and preferences, the current paper provides evidence that exposure order also does so. Three studies show that people like stimuli to which they are first exposed better than later encountered, similar stimuli. Controlling for exposure frequency and duration, individuals prefer the version of a song they heard first to a version they heard later and images they saw first to mirror images they saw later. In addition, our results suggest that perceived originality contributes to the preference for a first encountered stimulus. Our results are discussed in relation to research on order effects in sequential rating formats.
Nutritional Factors That Influence Change in Bone Density and Stress Fracture Risk Among Young Female Cross‐Country Runners
Authors: Nieves Jeri W. , Melsop Kathryn , Curtis Meredith , Kelsey Jennifer L. , Bachrach Laura K. , Greendale Gail , Sowers Mary Fran , Sainani Kristin L.
Published: August 2010

Objective

To identify nutrients, foods, and dietary patterns associated with stress fracture risk and changes in bone density among young female distance runners.

Design and Setting

Two‐year, prospective cohort study. Observational data were collected in the course of a multicenter randomized trial of the effect of oral contraceptives on bone health.

Participants

One hundred and twenty‐five female competitive distance runners ages 18‐26 years.

Assessment of Risk Factors

Dietary variables were assessed with a food frequency questionnaire.

Main Outcome Measurements

Bone mineral density and content (BMD/BMC) of the spine, hip, and total body were measured annually by dual x‐ray absorptiometry (DEXA). Stress fractures were recorded on monthly calendars, and had to be confirmed by radiograph, bone scan, or magnetic resonance imaging.

Results

Seventeen participants had at least one stress fracture during follow‐up. Higher intakes of calcium, skim milk, and dairy products were associated with lower rates of stress fracture. Each additional cup of skim milk consumed per day was associated with a 62% reduction in stress fracture incidence (P < .05); and a dietary pattern of high dairy and low fat intake was associated with a 68% reduction (P < .05). Higher intakes of skim milk, dairy foods, calcium, animal protein, and potassium were associated with significant (P < .05) gains in whole‐body BMD and BMC. Higher intakes of calcium, vitamin D, skim milk, dairy foods, potassium, and a dietary pattern of high dairy and low fat were associated with significant gains in hip BMD.

Conclusions

In young female runners, low‐fat dairy products and the major nutrients in milk (calcium, vitamin D, and protein) were associated with greater bone gains and a lower stress fracture rate. Potassium intake was also associated with greater gains in hip and whole‐body BMD.
On the Decay of Distractor-Response Episodes
Authors: Frings Christian
Published: August 2010

Distractor-to-distractor repetition effects can be explained by retrieval and/or inhibitory processes. Interestingly, the two accounts predict different effects from repeated distractors: Inhibition theories always predict benefits, whereas stimulus-response-retrieval theories predict an interaction of response repetition and distractor repetitions, resulting in benefits with response repetitions and costs with response changes. In the present experiment the time-course and the temporal separability of a stimulus-response episode on distractor-to-distractor repetitions were analyzed. The results showed that the interaction of response repetition and distractor repetitions was affected by a simple decay function. In addition, distractor repetition effects were affected by the temporal separability. In concert, the data yield evidence for retrieval-based explanations of distractor-to-distractor repetitions.
Can Emotion Modulate Attention? Evidence for Reciprocal Links in the Attentional Network Test
Authors: Cohen Noga , Henik Avishai , Mor Nilly
Published: August 2010

Evolution theory suggests that adaptive behavior depends on our ability to give preferential attention to emotional information when it is necessary for our survival, and to down-regulate irrelevant emotional influence. However, empirical work has shown that the interaction between emotion and attention varies, based on the attentional network in question. The aim of the current research was to examine the influence of stimulus emotionality on attention in three attentional networks: alerting, orienting, and executive functions. In two studies, using negative and neutral cues in a modified version of the Attention Network Test, it was found that negative cues impaired task performance in the absence of executive conflict, but not when executive processes were activated. Moreover, it was found that the influence of negative cues on task performance in a given trial was attenuated following activation of executive processes in the previous trial. These results suggest that when executive resources are required, inhibitory mechanisms are recruited to decrease the disruptive effect of emotional stimuli. More importantly, these findings indicate that the effect of emotional stimuli on attention is down-regulated both during cognitive conflict and after the conflict has already ended.
Parallel Constraint Satisfaction in Memory-Based Decisions
Authors: Glöckner Andreas , Hodges Sara D.
Published: August 2010

Three studies sought to investigate decision strategies in memory-based decisions and to test the predictions of the parallel constraint satisfaction (PCS) model for decision making (Glöckner & Betsch, 2008). Time pressure was manipulated and the model was compared against simple heuristics (take the best and equal weight) and a weighted additive strategy. From PCS we predicted that fast intuitive decision making is based on compensatory information integration and that decision time increases and confidence decreases with increasing inconsistency in the decision task. In line with these predictions we observed a predominant usage of compensatory strategies under all time-pressure conditions and even with decision times as short as 1.7 s. For a substantial number of participants, choices and decision times were best explained by PCS, but there was also evidence for use of simple heuristics. The time-pressure manipulation did not significantly affect decision strategies. Overall, the results highlight intuitive, automatic processes in decision making and support the idea that human information-processing capabilities are less severely bounded than often assumed.
The effects of nanopillar surface texturing on the photoluminescence of polymer films
Authors: Kim Taehyung , Kurunthu Dharmalingam , Burdett Jonathan J. , Bardeen Christopher J.
Published: August 2010

We report on the enhancement of photoluminescence (PL) from polymer thin films by nanotexturing their surfaces using nanoporous anodic alumina oxide templates. Chromophore-embedded polystyrene films with nanostructured surfaces are prepared by imprinting 200 nm diameter nanopillars with various heights, and their PL output and angular emission are observed. The PL output increases and the angular distributions broaden as the height of the nanopillars increases. For 5 μm tall nanopillars, the PL output is enhanced by a factor of 2.5 relative to the smooth surface. An effective refractive index model provides a qualitative description of the angular emission and PL output of nanotextured surface but underestimates the degree of PL enhancement. Comparison of the nanopillared films with surfaces randomly roughened using sandpaper shows that the details of the texturing have a significant impact on the PL output characteristics. These results show that imprinted nanopillars provide a simple and controlled way to increase the PL output of luminescent polymer films.
Meltblowing: II-linear and nonlinear waves on viscoelastic polymer jets
Authors: Yarin A. L. , Sinha-Ray S. , Pourdeyhimi B.
Published: August 2010

The work is devoted to the theory of meltblown polymer jets. Polymer jets are experiencing strong stretching and flapping being subjected to the pulling action of a high speed surrounding axisymmetric gas jet. The bending perturbations of polymer melt jets are triggered by the surrounding turbulent eddies and enhanced by the distributed lift force acting on the jets. We study first growth of small perturbations in the framework of the linear stability theory. Then, the fully nonlinear case of large-amplitude planar bending perturbations of polymer jet is solved numerically. Both isothermal and nonisothermal cases are considered. The cooling of the surrounding gas jet results in cooling of the polymer jet inside, and to the arrest of the bending perturbation growth due to melt solidification.
Dielectric response of polycrystalline Sr1−1.5xBixTiO3 thin films under direct current bias
Authors: Okhay Olena , Wu Aiying , Vilarinho Paula M. , Tkach Alexander
Published: August 2010

The effect of dc electric field Edc on the dielectric behavior of sol-gel derived Sr1−1.5xBixTiO3 films on Si/SiO2/TiO2/Pt substrates is systematically studied between 10 and 300 K. The rounded peak in the temperature dependence of the dielectric constant ε′(T) of all Sr1−1.5xBixTiO3 films is strongly suppressed under dc bias. The observed dielectric behavior is attributed to the formation of polar dipoles by the introduction of Bi into Sr site. A high tunability (∼40%) and communication quality factor (∼10 000) under 100 kV/cm make moderately Bi-doped SrTiO3 films a promising material for tunable devices.
The multiscale coarse-graining method: Assessing its accuracy and introducing density dependent coarse-grain potentials
Authors: Izvekov Sergei , Chung Peter W. , Rice Betsy M.
Published: August 2010

The ability of particle-based coarse-grain potentials, derived using the recently proposed multiscale coarse-graining (MS-CG) methodology [S. Izvekov and G. A. Voth, J. Phys. Chem. B 109, 2469 (2005); J. Chem. Phys. 123, 134105 (2005)] to reconstruct atomistic free-energy surfaces in coarse-grain coordinates is discussed. The MS-CG method is based on force-matching generalized forces associated with the coarse-grain coordinates. In this work, we show that the MS-CG method recovers only part of the atomistic free-energy landscape in the coarse-grain coordinates (termed the potential of mean force contribution). The portion of the atomistic free-energy landscape that is left out in the MS-CG procedure contributes to a pressure difference between atomistic and coarse-grain ensembles. Employing one- and two-site coarse-graining of nitromethane as worked examples, we discuss the virial and compressibility constraints to incorporate a pressure correction interaction into the MS-CG potentials and improve performance at different densities. The nature of the pressure correction interaction is elucidated and compared with those used in structure-based coarse-graining. As pairwise approximations to the atomistic free-energy, the MS-CG potentials naturally depend on the variables describing a thermodynamic state, such as temperature and density. Such dependencies limit state-point transferability. For nitromethane, the one- and two-site MS-CG potentials appear to be transferable across a broad range of temperatures. In particular, the two-site models, which are matched to low and ambient temperature liquid states, perform well in simulations of the ambient crystal structure. In contrast, the transferability of the MS-CG models of nitromethane across different densities is found to be problematic. To achieve better state-point transferability, density dependent MS-CG potentials are introduced and their performance is examined in simulations of nitromethane under various thermodynamic conditions, including shocked states.
Concerted electron and proton transfer in ionic crystals mapped by femtosecond x-ray powder diffraction
Authors: Woerner Michael , Zamponi Flavio , Ansari Zunaira , Dreyer Jens , Freyer Benjamin , Prémont-Schwarz Mirabelle , Elsaesser Thomas
Published: August 2010

X-ray powder diffraction, a fundamental technique of structure research in physics, chemistry, and biology, is extended into the femtosecond time domain of atomic motions. This allows for mapping (macro)molecular structure generated by basic chemical and biological processes and for deriving transient electronic charge density maps. In the experiments, the transient intensity and angular positions of up to 20 Debye Scherrer reflections from a polycrystalline powder are measured and atomic positions and charge density maps are determined with a combined spatial and temporal resolutions of 30 pm and 100 fs. We present evidence for the so far unknown concerted transfer of electrons and protons in a prototype material, the hydrogen-bonded ionic ammonium sulfate [(NH4)2SO4]. Photoexcitation of ammonium sulfate induces a sub-100 fs electron transfer from the sulfate groups into a highly confined electron channel along the c-axis of the unit cell. The latter geometry is stabilized by transferring protons from the adjacent ammonium groups into the channel. Time-dependent charge density maps derived from the diffraction data display a periodic modulation of the channel’s charge density by low-frequency lattice motions with a concerted electron and proton motion between the channel and the initial proton binding site. Our results set the stage for femtosecond structure studies in a wide class of (bio)molecular materials.
Fast high fidelity hole spin initialization in a single InGaAs quantum dot
Authors: Godden T. M. , Boyle S. J. , Ramsay A. J. , Fox A. M. , Skolnick M. S.
Published: August 2010

We demonstrate fast initialization of a single hole spin trapped in an InGaAs quantum dot with a fidelity F>99% and a 1/e time of ∼30 ps, by applying a magnetic field parallel to the growth direction. We show that the fidelity of the hole spin, prepared by ionization of a photo-generated electron-hole pair, is limited by the precession of the exciton spin due to the anisotropic exchange interaction.
Insertion of an organic interlayer for hole current enhancement in inverted organic light emitting devices
Authors: Park Soon Mi , Kim Yoon Hak , Yi Yeonjin , Oh Hyoung-Yun , Won Kim Jeong
Published: August 2010

We report the enhancement of hole current density in the hole transport part of an inverted top-emission organic light emitted diode by applying an organic insertion layer of 1,4,5,8,9,11-hexaazatriphenylene-hexacarbonitrile (HAT-CN). Poor hole transporting performance of Al/4,4′-bis(N-phenyl-1-naphthylamino)biphenyl (NPB)/indium tin oxide is greatly improved by the HAT-CN insertion between Al and NPB layer. The highest occupied molecular orbital level onset of the NPB bends toward Fermi level at the HAT-CN/NPB interface. This extra charge generation layer made of pure organic molecules substantially enhances hole injection from Al anode as revealed by the results of ultraviolet photoelectron spectroscopy and J-V measurement data.
Band gap control of small bundles of carbon nanotubes using applied electric fields: A density functional theory study
Authors: Kim Gunn , Bernholc J. , Kwon Young-Kyun
Published: August 2010

Electrostatic screening between carbon nanotubes (CNTs) in a small CNT bundle leads to a switching behavior induced by electric field perpendicular to the bundle axis. Using a first-principles method, we investigate the electronic structures of bundles consisting of two or three CNTs and the effects of the electric field applied perpendicular to the bundle axis. The applied field causes band gap closure in semiconducting bundles, while a gap opening occurs in metallic ones, which enables considerable modulation of bundle conductivity. The modulation effect originates from symmetry breaking due to electrostatic screening between the adjacent tube walls.
Understanding contact behavior in organic thin film transistors
Authors: Wang S. D. , Yan Y. , Tsukagoshi K.
Published: August 2010

We report the crowding current modeling of contact resistance in organic thin film transistors, and interpret the contact behavior based on the model. For the top-contact configuration, the contact resistance is determined by the transport property of both organic bulk and charge accumulation layer close to the organic/dielectric interface. For the bottom-contact configuration, the contact resistance is mainly determined by the transport property of organic bulk. In the both cases, reducing the charge traps in the organic active layer is considered as the essential approach to good contacts for organic thin film transistors.
Incorporating polaritonic effects in semiconductor nanowire waveguide dispersion
Authors: van Vugt Lambert K. , Piccione Brian , Agarwal Ritesh
Published: August 2010

We present the calculated and measured energy-propagation constant (E-β) dispersion of CdS nanowire waveguides at room temperature, where we include dispersive effects via the exciton-polariton model using physical parameters instead of a phenomenological equation. The experimental data match well with our model while the phenomenological equation fails to capture effects originating due to light-matter interaction in nanoscale cavities. Due to the excitonic-polaritonic effects, the group index of the guided light peaks close to the band edge, which can have important implications for optical switching and sensor applications.
Generation of multiple stress waves in silica glass in high fluence femtosecond laser ablation
Authors: Hu Haofeng , Wang Xiaolei , Zhai Hongchen , Zhang Nan , Wang Pan
Published: August 2010

Shadowgraphs of dynamic processes outside and inside transparent target during the intense femtosecond laser ablation of silica glass are recorded. Two material ejections outside the target and two corresponding stress waves inside the target are observed at different energy fluences. In particular, a third stress wave can be observed at energy fluence as high as 40 J/cm2. The first wave is a thermoelastic wave, while the second and the third may be generated subsequently by the mechanical expansions. In addition, the magnitudes of the three stress waves decrease sequentially based on our analysis.
Patterning by heritage in mouse molar row development
Authors: Prochazka Jan , Pantalacci Sophie , Churava Svatava , Rothova Michaela , Lambert Anne , Lesot Hervé , Klein Ophir , Peterka Miroslav , Laudet Vincent , Peterkova Renata
Published: August 2010

It is known from paleontology studies that two premolars have been lost during mouse evolution. During mouse mandible development, two bud-like structures transiently form that may represent rudimentary precursors of the lost premolars. However, the interpretation of these structures and their significance for mouse molar development are highly controversial because of a lack of molecular data. Here, we searched for typical tooth signaling centers in these two bud-like structures, and followed their fate using molecular markers, 3D reconstructions, and lineage tracing in vitro. Transient signaling centers were indeed found to be located at the tips of both the anterior and posterior rudimentary buds. These centers expressed a similar set of molecular markers as the “primary enamel knot” (pEK), the signaling center of the first molar (M1). These two transient signaling centers were sequentially patterned before and anterior to the M1 pEK. We also determined the dynamics of the M1 pEK, which, slightly later during development, spread up to the field formerly occupied by the posterior transient signaling center. It can be concluded that two rudimentary tooth buds initiate the sequential development of the mouse molars and these have previously been mistaken for early stages of M1 development. Although neither rudiment progresses to form an adult tooth, the posterior one merges with the adjacent M1, which may explain the anterior enlargement of the M1 during mouse family evolution. This study highlights how rudiments of lost structures can stay integrated and participate in morphogenesis of functional organs and help in understanding their evolution, as Darwin suspected long ago.
Nck adaptors are positive regulators of the size and sensitivity of the T-cell repertoire
Authors: Roy Edwige , Togbe Dieudonnée , Holdorf Amy D. , Trubetskoy Dmitry , Nabti Sabrina , Küblbeck Günter , Klevenz Alexandra , Kopp-Schneider Annette , Leithäuser Frank , Möller Peter , Bladt Friedhelm , Hämmerling Günter , Arnold Bernd , Pawson Tony , Tafuri Anna
Published: August 2010

The size and sensitivity of the T-cell repertoire governs the effectiveness of immune responses against invading pathogens. Both are modulated by T-cell receptor (TCR) activity through molecular mechanisms, which remain unclear. Here, we provide genetic evidence that the SH2/SH3 domain containing proteins Nck lower the threshold of T-cell responsiveness. The hallmarks of Nck deletion were T-cell lymphopenia and hyporeactivity to TCR-mediated stimulation. In the absence of the Nck adaptors, peripheral T cells expressing a TCR with low avidity for self-antigens were strongly reduced, whereas an overall impairment of T-cell activation by weak antigenic stimulation was observed. Mechanistically, Nck deletion resulted in a significant decrease in calcium mobilization and ERK phosphorylation upon TCR engagement. Taken together, our findings unveil a crucial role for the Nck adaptors in shaping the T-cell repertoire to ensure maximal antigenic coverage and optimal T cell excitability.
The structure of argumentation in health product messages
Authors: Walton Douglas
Published: August 2010

This paper presents an analysis of argumentation in direct-to-consumer health product ads in Newsweek that brings out special features of the arguments used in the ads, including practical reasoning, chained arguments, enthymemes, and prolepsis. A way to help overcome deficiencies in techniques of tailored health communication in consumer health informatics is shown by using argumentation schemes, argument visualisation tools, and dialogue models to frame these persuasive communication messages. The evidence collected is shown to be useful to allow the health informatics communicator and the person to whom message was directed to interact in a dialogue format where arguments can be put forward by both parties in a way that responds to the previous arguments and questions of the other party.
“Your risk is low, because …”: argument-driven online genetic counselling
Authors: Rubinelli Sara , Schulz Peter J. , Hartung Uwe
Published: August 2010

Advances in genetic research have created the need to inform consumers. Yet, the communication of hereditary risk and of the options for how to deal with it is a difficult task. Due to the abstract nature of genetics, people tend to overestimate or underestimate their risk. This paper addresses the issue of how to communicate risk information on hereditary breast and ovarian cancer through an online application. The core of the paper illustrates the design of OPERA, a risk assessment instrument that applies the UK National Institute of Health and Clinical Excellence's guidelines on the basis of (i) the number of relatives on the same side of the family with the same cancer or cancers that are known to run together; (ii) the ages of these relatives at diagnosis and (iii) the closeness of the family relationship with the person who is doing the assessment. By relying on the argumentation theory, we explain how the communication strategy that OPERA implements is essentially based on Perelman and Olbrechts-Tyteca's deductive argumentation by association. By using as premises “facts” (propositions about reality that can be assumed without further justification) and “truths” (propositions that make connections about facts), OPERA delivers its claims with an ex auctoritate causal link aimed at transferring the audience's acceptance of the cause to the effect. Overall, the design of OPERA rests on its capacity to induce users’ active processing of risk information through an appeal to their reasoning faculty. In the conclusion, we present some results from a pilot evaluation of users’ acceptance of OPERA.
A cell-based simulation software for multi-cellular systems
Authors: Hoehme Stefan , Drasdo Dirk
Published: August 2010

CellSys is a modular software tool for efficient off-lattice simulation of growth and organization processes in multi-cellular systems in 2D and 3D. It implements an agent-based model that approximates cells as isotropic, elastic and adhesive objects. Cell migration is modeled by an equation of motion for each cell. The software includes many modules specifically tailored to support the simulation and analysis of virtual tissues including real-time 3D visualization and VRML 2.0 support. All cell and environment parameters can be independently varied which facilitates species specific simulations and allows for detailed analyses of growth dynamics and links between cellular and multi-cellular phenotypes.

Availability: CellSys is freely available for non-commercial use at http://msysbio.com/software/cellsys. The current version of CellSys permits the simulation of growing monolayer cultures and avascular tumor spheroids in liquid environment. Further functionality will be made available ongoing with published papers.

Contact:  hoehme@izbi.uni-leipzig.de; dirk.drasdo@inria.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Search and clustering orders of magnitude faster than BLAST
Authors: Edgar Robert C.
Published: August 2010

Motivation: Biological sequence data is accumulating rapidly, motivating the development of improved high-throughput methods for sequence classification.

Results: UBLAST and USEARCH are new algorithms enabling sensitive local and global search of large sequence databases at exceptionally high speeds. They are often orders of magnitude faster than BLAST in practical applications, though sensitivity to distant protein relationships is lower. UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters. UCLUST offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets.

Availability: Binaries are available at no charge for non-commercial use at http://www.drive5.com/usearch

Contact:  robert@drive5.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Text mining meets workflow: linking U-Compare with Taverna
Authors: Kano Yoshinobu , Dobson Paul , Nakanishi Mio , Tsujii Jun'ichi , Ananiadou Sophia
Published: August 2010

Summary: Text mining from the biomedical literature is of increasing importance, yet it is not easy for the bioinformatics community to create and run text mining workflows due to the lack of accessibility and interoperability of the text mining resources. The U-Compare system provides a wide range of bio text mining resources in a highly interoperable workflow environment where workflows can very easily be created, executed, evaluated and visualized without coding. We have linked U-Compare to Taverna, a generic workflow system, to expose text mining functionality to the bioinformatics community.

Availability:  http://u-compare.org/taverna.html, http://u-compare.org

Contact:  kano@is.s.u-tokyo.ac.jp

Supplementary information:  Supplementary data are available at Bioinformatics online.
ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments
Authors: Lachmann Alexander , Xu Huilei , Krishnan Jayanth , Berger Seth I. , Mazloom Amin R. , Ma'ayan Avi
Published: August 2010

Motivation: Experiments such as ChIP-chip, ChIP-seq, ChIP-PET and DamID (the four methods referred herein as ChIP-X) are used to profile the binding of transcription factors to DNA at a genome-wide scale. Such experiments provide hundreds to thousands of potential binding sites for a given transcription factor in proximity to gene coding regions.

Results: In order to integrate data from such studies and utilize it for further biological discovery, we collected interactions from such experiments to construct a mammalian ChIP-X database. The database contains 189 933 interactions, manually extracted from 87 publications, describing the binding of 92 transcription factors to 31 932 target genes. We used the database to analyze mRNA expression data where we perform gene-list enrichment analysis using the ChIP-X database as the prior biological knowledge gene-list library. The system is delivered as a web-based interactive application called ChIP Enrichment Analysis (ChEA). With ChEA, users can input lists of mammalian gene symbols for which the program computes over-representation of transcription factor targets from the ChIP-X database. The ChEA database allowed us to reconstruct an initial network of transcription factors connected based on shared overlapping targets and binding site proximity. To demonstrate the utility of ChEA we present three case studies. We show how by combining the Connectivity Map (CMAP) with ChEA, we can rank pairs of compounds to be used to target specific transcription factor activity in cancer cells.

Availability: The ChEA software and ChIP-X database is freely available online at: http://amp.pharm.mssm.edu/lib/chea.jsp

Contact:  avi.maayan@mssm.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Changes in H2A.Z occupancy and DNA methylation during B-cell lymphomagenesis
Authors: Conerly Melissa L. , Teves Sheila S. , Diolaiti Daniel , Ulrich Michelle , Eisenman Robert N. , Henikoff Steven
Published: August 2010

The histone variant H2A.Z has been implicated in the regulation of gene expression, and in plants antagonizes DNA methylation. Here, we ask whether a similar relationship exists in mammals, using a mouse B-cell lymphoma model, where chromatin states can be monitored during tumorigenesis. Using native chromatin immunoprecipitation with microarray hybridization (ChIP-chip), we found a progressive depletion of H2A.Z around transcriptional start sites (TSSs) during MYC-induced transformation of pre-B cells and, subsequently, during lymphomagenesis. In addition, we found that H2A.Z and DNA methylation are generally anticorrelated around TSSs in both wild-type and MYC-transformed cells, as expected for the opposite effects of these chromatin features on promoter competence. Depletion of H2A.Z over TSSs both in cells that are induced to proliferate and in cells that are developing into a tumor suggests that progressive loss of H2A.Z during tumorigenesis results from the advancing disease state. These changes were accompanied by increases in chromatin salt solubility. Surprisingly, ∼30% of all genes showed a redistribution of H2A.Z from around TSSs to bodies of active genes during the transition from MYC-transformed to tumor cells, with DNA methylation lost from gene bodies where H2A.Z levels increased. No such redistributions were observed during MYC-induced transformation of wild-type pre-B cells. The documented role of H2A.Z in regulating transcription suggests that 30% of genes have the potential to be aberrantly expressed during tumorigenesis. Our results imply that antagonism between H2A.Z deposition and DNA methylation is a conserved feature of eukaryotic genes, and that transcription-coupled H2A.Z changes may play a role in cancer initiation and progression.
Increased Activity of the Vacuolar Monosaccharide Transporter TMT1 Alters Cellular Sugar Partitioning, Sugar Signaling, and Seed Yield in Arabidopsis
Authors: Wingenter Karina , Schulz Alexander , Wormit Alexandra , Wic Stefan , Trentmann Oliver , Hoermiller Imke I. , Heyer Arnd G. , Marten Irene , Hedrich Rainer , Neuhaus H. Ekkehard
Published: August 2010

The extent to which vacuolar sugar transport activity affects molecular, cellular, and developmental processes in Arabidopsis (Arabidopsis thaliana) is unknown. Electrophysiological analysis revealed that overexpression of the tonoplast monosaccharide transporter TMT1 in a tmt1-2::tDNA mutant led to increased proton-coupled monosaccharide import into isolated mesophyll vacuoles in comparison with wild-type vacuoles. TMT1 overexpressor mutants grew faster than wild-type plants on soil and in high-glucose (Glc)-containing liquid medium. These effects were correlated with increased vacuolar monosaccharide compartmentation, as revealed by nonaqueous fractionation and by chlorophyllab-binding protein1 and nitrate reductase1 gene expression studies. Soil-grown TMT1 overexpressor plants respired less Glc than wild-type plants and only about half the amount of Glc respired by tmt1-2::tDNA mutants. In sum, these data show that TMT activity in wild-type plants limits vacuolar monosaccharide loading. Remarkably, TMT1 overexpressor mutants produced larger seeds and greater total seed yield, which was associated with increased lipid and protein content. These changes in seed properties were correlated with slightly decreased nocturnal CO2 release and increased sugar export rates from detached source leaves. The SUC2 gene, which codes for a sucrose transporter that may be critical for phloem loading in leaves, has been identified as Glc repressed. Thus, the observation that SUC2 mRNA increased slightly in TMT1 overexpressor leaves, characterized by lowered cytosolic Glc levels than wild-type leaves, provided further evidence of a stimulated source capacity. In summary, increased TMT activity in Arabidopsis induced modified subcellular sugar compartmentation, altered cellular sugar sensing, affected assimilate allocation, increased the biomass of Arabidopsis seeds, and accelerated early plant development.
Rapid Assessment of Gene Function in the Circadian Clock Using Artificial MicroRNA in Arabidopsis Mesophyll Protoplasts
Authors: Kim Jeongsik , Somers David E.
Published: August 2010

Rapid assessment of the effect of reduced levels of gene products is often a bottleneck in determining how to proceed with an interesting gene candidate. Additionally, gene families with closely related members can confound determination of the role of even a single one of the group. We describe here an in vivo method to rapidly determine gene function using transient expression of artificial microRNAs (amiRNAs) in Arabidopsis (Arabidopsis thaliana) mesophyll protoplasts. We use a luciferase-based reporter of circadian clock activity to optimize and validate this system. Protoplasts transiently cotransfected with promoter-luciferase and gene-specific amiRNA plasmids sustain free-running rhythms of bioluminescence for more than 6 d. Using both amiRNA plasmids available through the Arabidopsis Biological Resource Center, as well as custom design of constructs using the Weigel amiRNA design algorithm, we show that transient knockdown of known clock genes recapitulates the same circadian phenotypes reported in the literature for loss-of-function mutant plants. We additionally show that amiRNA designed to knock down expression of the casein kinase II β-subunit gene family lengthens period, consistent with previous reports of a short period in casein kinase II β-subunit overexpressors. Our results demonstrate that this system can facilitate a much more rapid analysis of gene function by obviating the need to initially establish stably transformed transgenics to assess the phenotype of gene knockdowns. This approach will be useful in a wide range of plant disciplines when an endogenous cell-based phenotype is observable or can be devised, as done here using a luciferase reporter.
The Type IIArabidopsisFormin14 Interacts with Microtubules and Microfilaments to Regulate Cell Division
Authors: Li Yanhua , Shen Yuan , Cai Chao , Zhong Chenchun , Zhu Lei , Yuan Ming , Ren Haiyun
Published: August 2010

Formins have long been known to regulate microfilaments but have also recently been shown to associate with microtubules. In this study, Arabidopsis thaliana FORMIN14 (AFH14), a type II formin, was found to regulate both microtubule and microfilament arrays. AFH14 expressed in BY-2 cells was shown to decorate preprophase bands, spindles, and phragmoplasts and to induce coalignment of microtubules with microfilaments. These effects perturbed the process of cell division. Localization of AFH14 to microtubule-based structures was confirmed in Arabidopsis suspension cells. Knockdown of AFH14 in mitotic cells altered interactions between microtubules and microfilaments, resulting in the formation of an abnormal mitotic apparatus. In Arabidopsis afh14 T-DNA insertion mutants, microtubule arrays displayed abnormalities during the meiosis-associated process of microspore formation, which corresponded to altered phenotypes during tetrad formation. In vitro biochemical experiments showed that AFH14 bound directly to either microtubules or microfilaments and that the FH2 domain was essential for cytoskeleton binding and bundling. However, in the presence of both microtubules and microfilaments, AFH14 promoted interactions between microtubules and microfilaments. These results demonstrate that AFH14 is a unique plant formin that functions as a linking protein between microtubules and microfilaments and thus plays important roles in the process of plant cell division.