bluuebunny/crossref_metadata_2025 huggingface dataset:
Scoring ligand similarity in structure‐based virtual screening
Authors: Zavodszky Maria I. , Rohatgi Anjali , Van Voorst Jeffrey R. , Yan Honggao , Kuhn Leslie A.
Published: February 2009

Scoring to identify high‐affinity compounds remains a challenge in virtual screening. On one hand, protein–ligand scoring focuses on weighting favorable and unfavorable interactions between the two molecules. Ligand‐based scoring, on the other hand, focuses on how well the shape and chemistry of each ligand candidate overlay on a three‐dimensional reference ligand. Our hypothesis is that a hybrid approach, using ligand‐based scoring to rank dockings selected by protein–ligand scoring, can ensure that high‐ranking molecules mimic the shape and chemistry of a known ligand while also complementing the binding site. Results from applying this approach to screen nearly 70 000 National Cancer Institute (NCI) compounds for thrombin inhibitors tend to support the hypothesis. EON ligand‐based ranking of docked molecules yielded the majority (4/5) of newly discovered, low to mid‐micromolar inhibitors from a panel of 27 assayed compounds, whereas ranking docked compounds by protein–ligand scoring alone resulted in one new inhibitor. Since the results depend on the choice of scoring function, an analysis of properties was performed on the top‐scoring docked compounds according to five different protein–ligand scoring functions, plus EON scoring using three different reference compounds. The results indicate that the choice of scoring function, even among scoring functions measuring the same types of interactions, can have an unexpectedly large effect on which compounds are chosen from screening. Furthermore, there was almost no overlap between the top‐scoring compounds from protein–ligand versus ligand‐based scoring, indicating the two approaches provide complementary information. Matchprint analysis, a new addition to the SLIDE (Screening Ligands by Induced‐fit Docking, Efficiently) screening toolset, facilitated comparison of docked molecules' interactions with those of known inhibitors. The majority of interactions conserved among top‐scoring compounds for a given scoring function, and from the different scoring functions, proved to be conserved interactions in known inhibitors. This was particularly true in the S1 pocket, which was occupied by all the docked compounds. Copyright © 2009 John Wiley & Sons, Ltd.
Recent trends of thunderstorm and hailstorm frequency and their relation to atmospheric characteristics in southwest Germany
Authors: Kunz M. , Sander J. , Kottmeier Ch.
Published: February 2009

In the context of climate change, it is of particular interest whether extreme events connected to severe thunderstorms have been increasing in number or intensity over the past few decades. Due to their small horizontal extent, such events are not entirely and uniquely captured by current observation systems. To obtain comprehensive information about the convective activity in the state of Baden‐Württemberg (southwest Germany), we analysed different datasets for the period 1974–2003. They comprise thunderstorm days detected at synoptic stations, hail damage data from a building insurance company, large‐scale circulation and weather patterns, and convective indices derived from radiosonde observations at 12:00 UTC.

While the annual number of thunderstorm days remained almost unchanged in the mean, hail damage and hail days significantly increased in the last three decades. Both damage and additional radar data indicate that the majority of hail days can be attributed to three specific circulation patterns. Two of the three patterns associated with the preferable occurrence of hail show a significant increase.

Most of the commonly used convective indices that depend upon surface temperature and moisture reveal a positive trend regarding both the annual extreme values and the number of days above/below specific thresholds. A relationship was established between the indices and the annual number of hail damage days, yielding correlation coefficients between 0.65 and 0.80. In contrast to this, indices derived from temperature and moisture at higher levels exhibit either a negative or no significant trend. It is shown that the trend directions of the indices may be attributed to differential temperature and moisture stratification in the various atmospheric layers. The significant positive trends of both surface temperature and water vapour can be concisely expressed by an increase in wet‐bulb potential temperature. This indicates the presence of warmer parcels throughout the whole troposphere during convection. Copyright © 2009 Royal Meteorological Society
Growth and vibrational spectroscopic studies of strontium tartrate (C4H4O6Sr): a nonlinear optical single crystal
Authors: Krishnakumar V. , Dheivamalar S.
Published: February 2009

The nonlinear optical crystal strontium tartrate (SrT) was grown by the gel method. The vibrational spectra were recorded to determine the symmetries of molecular vibrations. The microhardness of the crystal was also tested. The observed, infrared (IR) bands were also assigned and discussed. The optical transmission spectral study was also carried out. The nonlinear property is confirmed. Copyright © 2009 John Wiley & Sons, Ltd.
Density functional theory calculations and vibrational spectra of p‐bromonitrobenzene
Authors: Krishnakumar V. , Jayamani N. , Mathammal R.
Published: February 2009

FT‐IR and FT‐Raman spectra of p‐bromonitrobenzene (p‐BNB) have been recorded in the region 4000–400 cm−1 and 4000–50 cm−1, respectively. The molecular structure, geometry optimization, vibrational wavenumbers have been investigated. The spectra were interpreted with the aid of normal coordinate analysis based on the density functional theory (DFT) using the standard B3LYP/6‐31G method and basis set combination and was scaled using multiple scale factors yielding good agreement between observed and calculated wavenumbers. The results of the calculations are applied to simulate infrared and Raman spectra of the title compound which showed reasonable agreement with the observed spectra. Copyright © 2009 John Wiley & Sons, Ltd.
Different contrast information obtained from CARS and nonresonant FWM images
Authors: Akimov Denis , Chatzipapadopoulos Susana , Meyer Tobias , Tarcea Nicolae , Dietzek Benjamin , Schmitt Michael , Popp Jürgen
Published: February 2009

We demonstrate that coherent anti‐Stokes Raman scattering (CARS) microscopy can be used not to obtain vibrational contrast related to a particular chemical species only, but furthermore, it directly yields topological contrast. Topological contrast is due to the spatially dependent refractive index of the sample and a number of linear effects as interference, refraction and absorption contribute to the topological contrast inherent to CARS images. In order to distinguish between different contrast mechanisms we propose an image correction method based on the analysis of the nonresonant four‐wave mixing (FWM) signal distribution. Copyright © 2009 John Wiley & Sons, Ltd.
Analysis of marine biogenic sulfur compounds using Raman spectroscopy: dimethyl sulfide and methane sulfonic acid
Authors: Barletta Robert E. , Gros Brittney N. , Herring Michael P.
Published: February 2009

Biogenic sulfur compounds, such as dimethyl sulfide (DMS), dimethyl sulfoniopropionate (DMSP), dimethyl sulfoxide (DMSO), and methane sulfonic acid (MSA), are important components of the global sulfur cycle and, as contributors to the formation of non‐anthropogenic aerosols, impact global climate. In general, these chemicals are found in the marine environment in extremely low concentrations (nM), but under certain circumstances, e.g. intracellular accumulations and inclusions in glacial ice, they can be found with concentration orders of higher magnitude (µM or greater). Current analytical methods, which are designed to measure concentrations in the nM range, do so by sacrificing detailed knowledge of the chemical environment and spatial distribution of these compounds. An alternative approach to the quantitative measurement of biogenic sulfur compounds directly (i.e. without pre‐processing) has been investigated in de‐ionized water and artificial seawater. The detection limits for the measurement of DMSO and MSA using Raman spectroscopy with both visible and UV excitation have been measured. For DMSO, a sensitivity of < 10 mM has been determined. For MSA, concentrations as low as 3 mM can be detected. It has been determined that, for aqueous solutions, the use of water as an internal standard for quantitative measurement appears to be adequate for measurement with high linearity over several decades of concentration. For DMSO and MSA, the measured sensitivities for quantitative Raman detection are adequate to address important issues in the biogeochemistry of these compounds. Moreover, for MSA it was determined that, based on measured band positions, previous studies of MSA in glacial ice have incorrectly attributed the species to solid salt rather than the, more likely, free ion in concentrated aqueous solution. In addition to sensitivity measurements, resonance/pre‐resonance enhancement of the Raman spectrum of DMSO and MSA, respectively, has been found with 248 nm excitation. Finally, the previously unreported Raman spectrum of Mg(MSA)2 has been measured. Copyright © 2009 John Wiley & Sons, Ltd.
Excited‐state structural dynamics and vibronic coupling of 1,3‐dithiole‐2‐thione—resonance Raman spectroscopy and density functional theory calculation study
Authors: Wang Huigang , Liu Bo , Wan Junmin , Xu Jun , Zheng Xuming
Published: February 2009

1,3‐Dithiole‐2‐thione (DTT) was synthesized and characterized using NMR, FT‐Raman, FT‐IR, UV spectroscopies. Resonance Raman spectra (RRs) were obtained with 341.5, 354.7 and 368.9 nm excitation wavelengths and density functional calculations were done to elucidate the electronic transitions and the RRs of DTT in cyclohexane solution. The RRs indicate that the Franck‐Condon region photodynamics is predominantly along the CS stretch+ H‐CC‐H scissor υ4, accompanied by the H‐CC‐H scissor υ3, S‐C‐S symmetric stretch υ6, CC stretch υ2, and overtone of the non‐totally symmetric SC‐S2 out‐of‐plane deformation 2υ11. The excited‐state dynamics and the force constant of CS stretch calculated by the RRs were discussed. Copyright © 2009 John Wiley & Sons, Ltd.
Synthesis and vibrational analysis of N‐(2′‐Furyl)‐Imidazole
Authors: Ledesma A. E. , Zinczuk J. , Ben Altabef A. , López González J. J. , Brandán S. A.
Published: February 2009

The N‐(2′‐furyl)‐imidazole (1) has been prepared and characterized using infrared, Raman and multidimensional nuclear magnetic resonance spectroscopies. Theoretical calculations have been carried out by employing the Density Functional Theory (DFT) method, in order to optimize the geometry of their two conformers in the gas phase and to support the assignments of the vibrational bands of1to their normal modes. For a complete assignment of the compound, DFT calculations were combined with Scaled Quamtum Mecanic Force Field (SQMFF) methodology in order to fit the theoretical wavenumber values to the experimental one. Furthermore, Natural Bond Orbital (NBO) and topological properties by Atoms In Molecules (AIM) calculations were performed to analyze the nature and magnitude of the intramolecular interactions. The result reveals that two conformers are expected in liquid phase. Copyright © 2009 John Wiley & Sons, Ltd.
Theoretical and vibrational spectral investigation of sodium salt of acenocoumarol
Authors: Joe I. Hubert , Kostova Irena , Ravikumar C. , Amalanathan M. , Cîntǎ Pînzaru Simona
Published: February 2009

The FT‐IR and FT‐Raman spectra of sodium salt of 4‐hydroxy‐3[1‐(4‐nitrophenyl)‐3‐oxobutyl]‐2H‐1‐benzopyran‐2‐one (acenocoumarol sodium salt) in solid phase have been recorded and analyzed. The optimization geometry, intramolecular hydrogen bonding, and harmonic vibrational wavenumbers of acenocoumarol sodium salt have been investigated with the help of B3LYP density functional theory (DFT) methods. The infrared and Raman spectra were predicted theoretically from the calculated intensities. Natural bond orbital (NBO) analysis indicates the presence of CH···O hydrogen bonding in the molecule. The first static hyperpolarizability of the molecule has been computed. Copyright © 2009 John Wiley & Sons, Ltd.
Lymph node assessment in cervical cancer: Prognostic and therapeutic implications
Authors: Gien L.T. , Covens A.
Published: February 2009

Lymph node status is not part of the staging system for cervical cancer, but provides important information for prognosis and treatment. This article reviews the incidence and patterns of lymph node metastasis, and the issues surrounding surgical assessment of lymph nodes. The preoperative assessment of lymph nodes by imaging, as well as the intraoperative assessment by sentinel nodes will be discussed. Finally, the prognostic and therapeutic implications of lymphadenectomy in cervical cancer will be reviewed. J. Surg. Oncol. 2009;99:242–247. © 2008 Wiley‐Liss, Inc.
Lymph node assessment and lymphadenectomy in bladder cancer
Authors: Sharir Sharon , Fleshner Neil E.
Published: February 2009

Lymph node status is a key prognostic indicator in patients with bladder cancer, so lymphadenectomy is important for accurate staging. Moreover, lymphadenectomy is curative for some patients with nodal metastases. Although there is evidence that the quality of regional node dissection is associated with oncologic outcome, controversy exists because other factors may also explain this observation. Consequently, there is no consensus regarding the optimal extent of lymphadenectomy and number of nodes that should be assessed. J. Surg. Oncol. 2009;99:225–231. © 2009 Wiley‐Liss, Inc.
Surgery after neoadjuvant chemotherapy for colorectal liver metastases is safe and feasible in elderly patients
Authors: Tamandl Dietmar , Gruenberger Birgit , Herberger Beata , Kaczirek Klaus , Gruenberger Thomas
Published: February 2009

Background

Surgery for colorectal liver metastases is part of the endeavor to cure metastatic colorectal cancer (mCRC). Neoadjuvant chemotherapy increases progression free survival in resectable patients. The safety and feasibility of this concept has not been investigated in elderly patients.

Methods

We performed a comparative analysis of data from 244 patients who were resected for colorectal liver metastases between 1999 and 2004 at our institution. Seventy patients were aged 70 or older; they form the basis of this analysis.

Results

Twenty‐nine patients received neoadjuvant chemotherapy (oxaliplatin‐based chemotherapy (XELOX), 19; 5‐fluorouracil (5‐FU), 10) prior to surgery. XELOX was associated with higher response rates to chemotherapy (CR + PR: XELOX 68% vs. 5‐FU 0%, P = 0.001), and responding patients had a better overall (OS, P < 0.001) and recurrence free survival (RFS, P < 0.001) compared to others. Response to neoadjuvant chemotherapy was the only factor on multivariate analysis predicting longer OS and RFS (P = 0.01 and P = 0.001).

Conclusion

Neoadjuvant chemotherapy can be administered safely in patients older than 70 years and appears to be effective in prolonging long‐term outcome. Patients responding to neoadjuvant treatment have a significantly better prognosis after liver resection. J. Surg. Oncol. 2009;100:364–371. © 2009 Wiley‐Liss, Inc.
Losing a loved one to homicide: Prevalence and mental health correlates in a national sample of young adults
Authors: Zinzow Heidi M. , Rheingold Alyssa A. , Hawkins Alesia O. , Saunders Benjamin E. , Kilpatrick Dean G.
Published: February 2009

The present study examined the prevalence, demographic distribution, and mental health correlates of losing a loved one to homicide. A national sample of 1,753 young adults completed structured telephone interviews measuring violence exposure, mental health diagnoses, and loss of a family member or close friend to a drunk driving accident (vehicular homicide) or murder (criminal homicide). The prevalence of homicide survivorship was 15%. African Americans were more highly represented among criminal homicide survivors. Logistic regression analyses found that homicide survivors were at risk for past year posttraumatic stress disorder (OR = 1.88), major depressive episode (OR = 1.64), and drug abuse/dependence (OR = 1.77). These findings highlight the significant mental health needs of homicide survivors.
Evidence for a curvilinear relationship between posttraumatic growth and posttrauma depression and PTSD in assault survivors
Authors: Kleim Birgit , Ehlers Anke
Published: February 2009

Two studies of assault survivors (Ns = 180, 70) examined associations between posttraumatic growth (PTG) and posttrauma psychopathology. Both studies found significant curvilinear associations between PTG and posttraumatic stress disorder, whereas only Study 1 found a curvilinear association between PTG and depression symptom severity. Survivors with no or high growth levels reported fewer symptoms than those who reported moderate growth. Study 1 also investigated potential PTG predictors. Non‐Caucasian ethnicity, religiousness, peritraumatic fear, shame, and ruminative thinking style, assessed at 2 weeks, predicted growth at 6 months. Posttraumatic growth may thus be most relevant in trauma survivors who attach enduring significance to the trauma for their lives and show initial distress. Moderate levels of PTG do not seem to ameliorate posttrauma psychopathology.
Test of the role of nicotine dependence in the relation between posttraumatic stress disorder and panic spectrum problems
Authors: Feldner Matthew T. , Smith Rose C. , Babson Kimberly A. , Sachs‐Ericsson Natalie , Schmidt Norman B. , Zvolensky Michael J.
Published: February 2009

Posttraumatic stress disorder (PTSD) frequently co‐occurs with panic spectrum problems. Relatively little empirical work has tested possible mechanisms accounting for this association. Nicotine dependence often ensues subsequent to PTSD onset and research suggests smoking high numbers of cigarettes daily may lead to panic problems. The current study tested the hypotheses that nicotine dependence partially mediates the relations between PTSD and both panic attacks and panic disorder within a nationally representative sample of 5,692 (3,020 women; MAge = 45, SD = 18) adults from the National Comorbidity Survey–Replication. Results were consistent with hypotheses. These findings support the theory suggesting smoking among people with PTSD may be involved in the development of panic problems.
Sexual harassment in the Marines, posttraumatic stress symptoms, and perceived health: Evidence for sex differences
Authors: Shipherd Jillian C. , Pineles Suzanne L. , Gradus Jaimie L. , Resick Patricia A.
Published: February 2009

Sex differences and pretrauma functioning have been understudied in examinations of posttraumatic stress symptoms (PSS) and health. This study examined relationships between sexual harassment and assault in the military (MST), PSS, and perceived physical health when accounting for pre‐MST PSS, pre‐MST health, and current depression. Relationships were examined separately in 226 female and 91 male Marines endorsing recent MST (past 6 months). MST predicted increased PSS for women and especially men. For men, higher levels of MST were associated with worse perceived physical health, whereas for women, lower levels of MST were associated with worse perceived health. For men with MST, there was some evidence for the association being partially mediated by PSS, but no mediation was found in women.
Meta‐abilities and outsourcing: an individual based conceptual framework
Authors: Choudrie Jyoti , Grey Susan , Selamat Mohamad Hisyam
Published: February 2009

Outsourcing is a strategy being considered appropriate to cope with the current turbulent times. In the information systems (IS) area, outsourcing has fastly become an essential part of an organization's IS strategy. By signing outsourcing agreements, firms expect to reduce their overall information technology (IT) costs, focus on their core competencies, and gain superior technical resources. This paper offers a conceptual model for the area of outsourcing, which is based primarily on the concept of meta‐abilities. The principal argument offered by this paper is that organizations need to develop meta‐abilities in order to facilitate the process of outsourcing. Copyright © 2009 John Wiley & Sons, Ltd.
Project‐based company's vital condition: structural coupling. An autopoietic view
Authors: Koskinen Kaj U.
Published: February 2009

This conceptual paper describes, with the help of autopoietic epistemology, the phenomenon of structural coupling in project‐based companies. First the concept of project‐based company is described. Then the discussion deals with the epistemological assumptions with the goal of getting a better understanding of the nature of knowledge and how it develops. This is followed by a brief illustrations of autopoietic and allopoietic systems. After that the concepts of structural determinism and coupling are highlighted. Then follow descriptions of the knowledge creation at both the individual and organizational levels. Also three factors (i.e. absorptive capacity, creative tension and resistance to change) that either foster or weaken possibilities to achieve structural coupling are illustrated. The paper's end concludes with a discussion concerning why structural coupling is necessary for project‐based companies, since because without it the company—in other words, an autopoietic system—disintegrates and the company's activities come to an end. Copyright © 2009 John Wiley & Sons, Ltd.
Applying wikis to managing knowledge—A socio‐technical approach
Authors: Kosonen Miia , Kianto Aino
Published: February 2009

As organizations are increasingly moving towards geographically dispersed and virtual forms of collaboration, knowledge sharing through social software such as wikis is widely acknowledged as an important area of research and practice. However, social software remains an under‐investigated issue in the literature on knowledge management (KM), and there is a lack of studies demonstrating how organizations can successfully incorporate these technologies into their everyday operations. To bridge this gap, our paper examines a case of successful wiki implementation. We claim that understanding the implementation of wikis requires a socio‐technical perspective focusing on the organizational context and activity system in which they are implemented rather than on their technological proficiency. Furthermore, we claim that their implementation brings about change in existing social systems, and results in new kinds of social constellations, interactions, and identities, which are manageable and controllable only to a limited extent. Copyright © 2009 John Wiley & Sons, Ltd.
Microphase‐Separated Poly(vinylpyridine) Block Copolymer Prepared with a Novel Bifunctional Initiator
Authors: Shoji Masami , Eguchi Masao , Layman John M. , Cashion Matthew P. , Long Timothy E. , Nishide Hiroyuki
Published: February 2009

A vinylpyridine block copolymer was prepared by stepwise controlled/living radical polymerization with a novel bifunctional initiator, 4‐(2‐bromopropanoyloxy)‐N‐(p‐methylbenzyloxy)‐2,2,6,6‐tetramethylpiperidine. The initiator was synthesized in a facile manner using commercially available p‐xylene and 4‐hydroxy‐2,2,6,6‐tetramethylpiperidine‐1‐oxyl (4‐hydroxy TEMPO). Through stepwise atom transfer radical polymerization (ATRP) of methyl methacrylate (MMA) and nitroxide‐mediated radical polymerization (NMRP) of 4‐vinylpyridine (4VP), the PMMA‐b‐P4VP copolymer was prepared with a wide range of the copolymer compositions. Microphase‐separation was demonstrated in cross sectional TEM images of self‐standing block copolymer membranes.

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Biocomposites of Cellulose Acetate Butyrate with Modified Hemp Cellulose Fibres
Authors: Ouajai Sirisart , Shanks Robert A.
Published: February 2009

Cellulose acetate butyrate biocomposites, plasticized with tributyl citrate at volume fraction Vf = 0.1–0.3, were prepared with modified hemp. Inclusion of modified hemp fibres at Vf = 0.4 enhanced the modulus and strength of the flexible plasticized cellulose acetate butyrate. Composites containing pectate lyase enzyme treated fibres showed a modulus greater than untreated or alkali treated fibres, when compared at a similar fibre length of 100 µm. Composites containing the shortest alkali treated fibres of 45 µm gave the greatest property improvement, while 500 µm fibres showed worsened properties. Ball‐milled fibres provided reduced values of properties due to cellulose structural disruption, while compression moulding gave better compaction by removing voids.

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ROCK inhibition enhances the recovery and growth of cryopreserved human embryonic stem cells and human induced pluripotent stem cells
Authors: Claassen David A. , Desler Michelle M. , Rizzino Angie
Published: February 2009

Poor recovery of cryopreserved human embryonic stem (hES) cells and induced pluripotent stem (iPS) cells is a significant impediment to progress with pluripotent stem cells. In this study, we demonstrate that Y‐27632, a specific inhibitor of Rho kinase (ROCK) activity, significantly enhances recovery of hES cells from cryopreserved stocks when cultured with or without a growth inactivated feeder layer. Furthermore, treatment with the ROCK inhibitor for several days increased the number of colonies and colony size of hES cells compared to shorter exposures. Remarkably, hES cells that had formed relatively few colonies 5 days after thawing exhibited rapid growth upon addition of Y‐27632. Additionally, we determined that Y‐27632 significantly improves the recovery of cryopreserved human iPS cells and their growth upon subculture. Thus, Y‐27632 provides a means to “kick‐start” slow‐growing human pluripotent stem cells, especially after being thawed from frozen stocks. Together, these results argue that Y‐27632 is a useful tool in overcoming obstacles to studies involving the cultivation of both hES cells and human iPS cells. Mol. Reprod. Dev. 76: 722–732, 2009. © 2009 Wiley‐Liss, Inc.
On the cycle polytope of a directed graph and its relaxations
Authors: Balas Egon , Stephan Rüdiger
Published: February 2009

We continue the investigation of the cycle polytope of a digraph begun by Balas and Oosten (Networks 36 (2000), 34–46) and derive a rich family of facets that cut off the origin and are not related to facets of the traveling salesman polytope. This disproves a claim in (Balas and Oosten 36 (2000), 34–46) that the only such facets are those defined by the linear ordering inequalities. After examining the relationship between the cycle polytope, its dominant, and the upper cycle polyhedron, we turn to the polar relationship between cycles and permutations or transitive tournaments. Our central result is a characterization of the relationship between facets of the dominant of the cycle polytope, facets of the cycle polytope that cut off the origin, and vertices of the linear relaxation of the transitive tournament polytope. © 2009 Wiley Periodicals, Inc. NETWORKS, 2009
Ionic conductivity in poly (L‐leucine)1,3‐diamino propane–lithium iodide solid polymer electrolyte
Authors: Kaus N. H. , Lahazan N. , Ahmad A. H.
Published: February 2009

The pelletized Poly(L‐Leucine)‐1,3‐diamino propane–lithium iodide (LiI) samples have been prepared by using a low temperature sintering method. Results from impedance spectroscopy have proven this mixture to be a superionic material with maximum conductivity obtained in the range of 10−3 S/cm for the samples containing 50 wt% LiI. The high ionic conductivity achieved was due to the increased number of charge carrier from LiI. Improved conductivity could also be due to hopping of lithium ion through the side chain of polymer. Infrared spectroscopy showed that both LiI and poly amino acid may co‐exist together. From the spectra it is revealed that the CO band at 1643 cm−1 shifted to higher wave number indicating that chelation of Li+ may have occurred at oxygen atom. Results from X‐ray diffraction show that the prepared samples were partially crystalline in nature. Some of the peaks have disappeared and this confirmed that some complexation has occurred within the sample. Copyright © 2009 John Wiley & Sons, Ltd.
Avoidance motivation, risk perception and emotional processing
Authors: Leikas Sointu , Lindeman Marjaana , Roininen Katariina , Lähteenmäki Liisa
Published: February 2009

The present studies examined the moderating role of state motivation on the associations between trait avoidance motivation, risk perception and emotional processing. In Studies 1 and 2, avoidance or approach states were evoked in participants who then completed a risk perception task and a trait avoidance motivation measure. Both studies showed that trait avoidance only correlated with risk perceptions among individuals in approach state. In Study 3, emotional interpretation was measured. State and trait avoidance motivation did not interact in predicting emotional interpretation. The results showed that the effect of state motivation can explain the low correlations found between trait avoidance and risk perceptions, and suggested that the avoidance system may operate on an on–off principle rather than synergistically. Copyright © 2009 John Wiley & Sons, Ltd.
Combined analysis of transcriptome and proteome data as a tool for the identification of candidate biomarkers in renal cell carcinoma
Authors: Seliger Barbara , Dressler Sven P. , Wang Ena , Kellner Roland , Recktenwald Christian V. , Lottspeich Friedrich , Marincola Francesco M. , Baumgärtner Maja , Atkins Derek , Lichtenfels Rudolf
Published: February 2009

Results obtained from expression profilings of renal cell carcinoma using different “ome”‐based approaches and comprehensive data analysis demonstrated that proteome‐based technologies and cDNA microarray analyses complement each other during the discovery phase for disease‐related candidate biomarkers. The integration of the respective data revealed the uniqueness and complementarities of the different technologies. While comparative cDNA microarray analyses though restricted to up‐regulated targets largely revealed genes involved in controlling gene/protein expression (19%) and signal transduction processes (13%), proteomics/PROTEOMEX‐defined candidate biomarkers include enzymes of the cellular metabolism (36%), transport proteins (12%), and cell motility/structural molecules (10%). Candidate biomarkers defined by proteomics and PROTEOMEX are frequently shared, whereas the sharing rate between cDNA microarray and proteome‐based profilings is limited. Putative candidate biomarkers provide insights into their cellular (dys)function and their diagnostic/prognostic value but still warrant further validation in larger patient numbers. Based on the fact that merely three candidate biomarkers were shared by all applied technologies, namely annexin A4, tubulin α‐1A chain, and ubiquitin carboxyl‐terminal hydrolase L1, the analysis at a single hierarchical level of biological regulation seems to provide only limited results thus emphasizing the importance and benefit of performing rather combinatorial screenings which can complement the standard clinical predictors.
Serum protein profiling by solid phase extraction and mass spectrometry: A future diagnostics tool?
Authors: Callesen Anne K. , Madsen Jonna S. , Vach Werner , Kruse Torben A. , Mogensen Ole , Jensen Ole N.
Published: February 2009

Serum protein profiling by MS is a promising method for early detection of disease. Important characteristics for serum protein profiling are preanalytical factors, analytical reproducibility and high throughput. Problems related to preanalytical factors can be overcome by using standardized and rigorous sample collection and sample handling protocols. The sensitivity of the MS analysis relies on the quality of the sample; consequently, the blood sample preparation step is crucial to obtain pure and concentrated samples and enrichment of the proteins and peptides of interest. This review focuses on the serum sample preparation step prior to protein profiling by MALDI MS analysis, with particular focus on various SPE methods. The application of SPE techniques with different chromatographic properties such as RP, ion exchange, or affinity binding to isolate specific subsets of molecules (subproteomes) is advantageous for increasing resolution and sensitivity in the subsequent MS analysis. In addition, several of the SPE sample preparation methods are simple and scalable and have proven easy to automate for higher reproducibility and throughput, which is important in a clinical proteomics setting.
The art of observing rare protein species in proteomes with peptide ligand libraries
Authors: Boschetti Egisto , Righetti Pier Giorgio
Published: February 2009

The present review deals with the use of combinatorial ligand libraries, composed by hexapeptides, in the capture and concentration of the low‐abundance proteome. This method, first reported in 2005, is compared with other current methodologies aimed at exploring the “deep proteome”, such as: depletion of high‐abundance proteins (especially in sera and cerebrospinal fluid) by individual or combined antibodies (up to 20 against the most abundant species); narrow (1‐pH‐unit) IPGs (zoom gels) and prefractionation with multicompartment electrolyzers or with Off‐Gel electrophoresis. The physico‐chemical properties of the hexapeptide library are also explored, namely in assessing the proper length of the baits and the behavior of shorter oligopeptides, down to capture elicited by single amino acids. A number of examples on the use of this library is given, such as the analysis of biological fluids (human sera, urine, bile, cerebrospinal fluid) and of cell lysates (platelets, red blood cells). In all cases, it was possible to detected from three to five times as many proteins as compared to control, untreated samples. Perhaps the most spectacular results were obtained with the erythrocyte proteome, where 1570 proteins could be identified in the “minority” proteome, representing only 2% of the total cell lysate. Another interesting area of application regards the concentration and detection of trace impurities contaminanting r‐DNA proteins meant for human consumption: several host proteins, never reported before, could be revealed for the first time. Other nonhuman samples are currently under investigation, such as egg‐white (where no less than 148 unique gene products could be identified), egg yolk (with 255 unique species) and latex from Hevea brasiliensis. It is anticipated that the ligand library could be a most useful tool for detecting biomarkers for different pathologies and for drug treatment. As a future outlook, one could envision the synthesis of specialized libraries able to capture given classes of proteins (e.g., phospho‐ and glyco‐proteins). Additionally, the library could be used in association with other techniques currently in vogue, such as zoom gels, Off‐Gels, and the like.
Immuno‐MALDI‐TOF MS: New perspectives for clinical applications of mass spectrometry
Authors: Sparbier Katrin , Wenzel Thomas , Dihazi Hassan , Blaschke Sabine , Müller Gerhard‐Anton , Deelder André , Flad Thomas , Kostrzewa Markus
Published: February 2009

The discovery of novel biomarkers by means of advanced detection tools based on proteomic analysis technologies necessitates the development of improved diagnostic methods for application in clinical routine. On the basis of three different application examples, this review presents the limitations of conventional routine diagnostic assays and illustrates the advantages of immunoaffinity enrichment combined with MALDI‐TOF MS. Applying this approach increases the specificity of the analysis supporting a better diagnostic recognition, sensitivity, and differentiation of certain diseases. The use of MALDI‐TOF MS as detection method facilitates the identification of modified peptides and proteins providing additional information. Further, employing respective internal standard peptides allows for relative and absolute quantitation which is mandatory in the clinical context. Although MALDI‐TOF MS is not yet established for clinical routine diagnostics this technology has a high potential for improvement of clinical diagnostics and monitoring therapeutic efficacy.
Strategy for surveying the proteome using affinity proteomics and mass spectrometry
Authors: Wingren Christer , James Peter , Borrebaeck Carl A. K.
Published: February 2009

Antibody‐based microarrays is a rapidly evolving technology that has gone from the first proof‐of‐concept studies to more demanding proteome profiling applications, during the last years. Miniaturized microarrays can be printed with large number of antibodies harbouring predetermined specificities, capable of targeting high‐ as well as low‐abundant analytes in complex, nonfractionated proteomes. Consequently, the resolution of such proteome profiling efforts correlate directly to the number of antibodies included, which today is a key limiting factor. To overcome this bottleneck and to be able to perform in‐depth global proteome surveys, we propose to interface affinity proteomics with MS‐based read‐out, as outlined in this technical perspective. Briefly, we have defined a range of peptide motifs, each motif being present in 5–100 different proteins. In this manner, 100 antibodies, binding 100 different motifs commonly distributed among different proteins, would potentially target a protein cluster of 104 individual molecules, i.e. around 50% of the nonredundant human proteome. Notably, these motif‐specific antibodies would be directly applicable to any proteome in a specie independent manner and not biased towards abundant proteins or certain protein classes. The biological sample is digested, exposed to these immobilized antibodies, whereby motif‐containing peptides are specifically captured, enriched and subsequently detected and identified using MS.
Randomized controlled trial of mindfulness‐based stress reduction (MBSR) for survivors of breast cancer
Authors: Lengacher Cecile A. , Johnson‐Mallard Versie , Post‐White Janice , Moscoso Manolete S. , Jacobsen Paul B. , Klein Thomas W. , Widen Raymond H. , Fitzgerald Shirley G. , Shelton Melissa M. , Barta Michelle , Goodman Matthew , Cox Charles E. , Kip Kevin E.
Published: February 2009

Objectives: Considerable morbidity persists among survivors of breast cancer (BC) including high levels of psychological stress, anxiety, depression, fear of recurrence, and physical symptoms including pain, fatigue, and sleep disturbances, and impaired quality of life. Effective interventions are needed during this difficult transitional period.

Methods: We conducted a randomized controlled trial of 84 female BC survivors (Stages 0–III) recruited from the H. Lee Moffitt Cancer and Research Institute. All subjects were within 18 months of treatment completion with surgery and adjuvant radiation and/or chemotherapy. Subjects were randomly assigned to a 6‐week Mindfulness‐Based Stress Reduction (MBSR) program designed to self‐regulate arousal to stressful circumstances or symptoms (n=41) or to usual care (n=43). Outcome measures compared at 6 weeks by random assignment included validated measures of psychological status (depression, anxiety, perceived stress, fear of recurrence, optimism, social support) and psychological and physical subscales of quality of life (SF‐36).

Results: Compared with usual care, subjects assigned to MBSR(BC) had significantly lower (two‐sided p<0.05) adjusted mean levels of depression (6.3 vs 9.6), anxiety (28.3 vs 33.0), and fear of recurrence (9.3 vs 11.6) at 6 weeks, along with higher energy (53.5 vs 49.2), physical functioning (50.1 vs 47.0), and physical role functioning (49.1 vs 42.8). In stratified analyses, subjects more compliant with MBSR tended to experience greater improvements in measures of energy and physical functioning.

Conclusions: Among BC survivors within 18 months of treatment completion, a 6‐week MBSR(BC) program resulted in significant improvements in psychological status and quality of life compared with usual care. Copyright © 2009 John Wiley & Sons, Ltd
Rapid degradation of ground ice in a ventilated talus slope: Flüela Pass, Swiss Alps
Authors: Phillips Marcia , Mutter Evelyn Zenklusen , Kern‐Luetschg Martina , Lehning Michael
Published: February 2009

The degradation of ground ice in talus deposits, which are important forms of debris storage in mountain environments, can cause mass movements, subsidence or instability of mountain infrastructure. Two 20 m deep boreholes instrumented with thermistors and located in a talus slope at 2400 m asl above a lake at Flüela Pass in the eastern Swiss Alps allow the analysis of the evolution of ground temperature and permafrost thickness between 2003 and 2008. The occurrence of intra‐talus ventilation can be discerned due to thermal anomalies within a layer of coarse blocks with large voids at around 15 m depth near the base of the slope and at 10 m depth mid‐slope. Intra‐talus ventilation is particularly effective in winter when subzero air temperatures coincide with snow depths less than 50 cm and reverses to a gravity discharge of intra‐talus air when air temperatures become positive. Despite the lack of annual variability in active layer depth, rapid permafrost degradation and thinning of ground ice (from 7 m thickness to 3.5 m in 4 years) is currently occurring. It is attributed to latent heat transfer from the moving air stream, caused by the flux of vapour from the relatively warm lake water table at 20 m depth and its condensation at the base of the permafrost body. Copyright © 2009 John Wiley & Sons, Ltd.
Parasitic angiosperms, semagenesis and general strategies for plant–plant signaling in the rhizosphere
Authors: Palmer Andrew G , Chen Michael C , Kinger Nikhar P , Lynn David G
Published: February 2009

BACKGROUND: In addition to their roles in eukaryotic defense and development, reactive oxygen species (ROS) have recently been identified as critical for host attachment by the parasitic angiosperms. In a process known as semagenesis, ROS generated at the root tip of Striga asiatica (L.) Kuntze (Scrophulariaceae) function together with host peroxidases to oxidize monolignols at the host root surface. As a result, para‐benzoquinone products accumulate as both necessary and sufficient components for inducing development of the host attachment organ, the haustorium. This event constitutes the critical vegetative/pathogenic transition in the parasite.

RESULTS: New evidence is presented that semagenesis occurs broadly in plant–plant signaling. Eudicotyledenous seedlings are more sensitive to the xenognostic benzoquinones than monocots, but general root development, including root elongation, root hair initiation and root hair growth, is impacted in both clades. Specific inhibitors of haustorial development in S. asiatica also inhibit benzoquinone‐mediated root development in the non‐parasites. These results suggest a common mechanism for benzoquinone perception.

CONCLUSION: Semagenesis enriches our understanding of the mechanisms available for small‐molecule underground information exchange among plants. Critical differences in this process, as used by parasitic plants, are beginning to emerge and point towards new strategies for managing parasitic angiosperms in agricultural settings. Copyright © 2009 Society of Chemical Industry
Microstructure of CuFeS2–δ–CuInS2 alloys
Authors: Korzun B. V. , Fadzeyeva A. A. , Kloess G. , Bente K.
Published: February 2009

Two series of alloys of the (CuFeS2–δ)1–x(CuInS2)x system with molar part of CuInS2 x = 0.01, 0.03, 0.125, 0.25, 0.375, 0.50, 0.625, 0.75, 0.95, 0.97 and 0.99 and δ being 0 and 0.10 were prepared from the CuFeS2–δ and CuInS2 starting ternary compounds. The samples were investigated by micro structural optics using freshly‐polished samples and XRPD. The studies confirmed two phase coexistences with microstructures dependent on the chemical composition. The geometric‐oriented arrangement of the α‐phase with the structure of CuInS2 is found in the (CuFeS2–δ)1–x(CuInS2)x system up to x equalling 0.50. It was established that the solvus of CuFeS2–δ exceeds 0.05 molar parts of CuInS2, while the solvus of CuInS2 does not exceed 0.03 molar parts of CuFeS2–δ. Additionally, stoichiometric composition of CuFeS2 exhibits a mixture of 3 coexisting phases of CuFeS2–δ, with δ from 0.14 to 0.28, bornite Cu5FeS4 and pyrrhotite Fe1–xS. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electrical and optical properties of Hg3In2Te6 single crystals
Authors: Maslyanchuk O. L. , Kosyachenko L. A. , German I. I. , Rarenko I. M. , Gnatyuk V. A. , Aoki T.
Published: February 2009

The basic properties of n‐Hg3In2Te6 single crystals with resistivity of 1‐2 Ω·cm are studied in their application for 1.55 μm wavelength photodiodes as optimal detectors for quartz fiber communications. The band gap of Hg3In2Te6 in the temperature range of 248‐353 K has been determined on the base of the optical transmission spectra. The absorption curves in the range of 0.4‐1.7 μm (at 300 K) have been obtained from the reflection spectra of polarized light. It is also shown that the electrical conductivity of the semiconductor is controlled by two types of donors with ionization energies of 0.063 and 0.18 eV, respectively, while the charge carrier mobility is predominantly affected by scattering at charged centers. The temperature dependence of the electron concentration in the temperature range from 100 to 370 K is quantitatively described on the base of the electroneutrality equation. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Luminescence properties of ZnGa2O4 and ZnAl2O4 spinels doped with Eu3+ and Tb3+ ions
Authors: Rusu E. , Ursaki V. , Novitschi G. , Vasile M. , Petrenco P. , Kulyuk L.
Published: February 2009

Spinel‐type ZnGa2O4 and ZnAl2O4 powders doped with Eu3+ and Tb3+ ions, including dual doping, have been prepared by solid phase reactions and by deposition from chemical solutions. XRD analysis demonstrates the high quality of spinel grains constituting the powder. The luminescence shows that the rare earth ions are incorporated in the defect regions at the grain boundaries. The emission spectra of the samples with europium are characterized by an intense emission in red region due to the 5D0 → 7F1,2 transitions of Eu3+ ions, whereas in the case of terbium the highest intensity corresponds to the green emission due to the 5D4 → 7F5 transitions of Tb3+ ions. The possibility to change the color of the emission from green to red by the variation of Tb and Eu doping concentration is demonstrated. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
CuIn2n+1Se3n+2 single dot structures: creation and photosensitivity
Authors: Rud Yu. V. , Rud V. Yu. , Bodnar I. V.
Published: February 2009

Photosensitive single dot structures based on CuIn2n+1Se3n+2 (n = 0, 1, 2) bulk single crystals have been creation for the first time by means of electric‐discharge welding (EDW). The stationary current‐voltage characteristics and the photovoltaic properties of the structures based on CuInSe2, CuIn3Se5 and CuIn5Se8 ternary semiconductors have been studied, which show evidence for the rectification effect and photoconversion. The character of interband transitions is established and the energy bandgap variation in this type of ternary compounds is traced. It is concluded that EDW can be successfully used for the creation of photoconverters based on multi‐component semiconductors. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)