bluuebunny/crossref_metadata_2025 huggingface dataset:
Including shared peptides for estimating protein abundances: A significant improvement for quantitative proteomics
Authors: Blein‐Nicolas Mélisande , Xu Hao , de Vienne Dominique , Giraud Christophe , Huet Sylvie , Zivy Michel
Published: July 2012

Inferring protein abundances from peptide intensities is the key step in quantitative proteomics. The inference is necessarily more accurate when many peptides are taken into account for a given protein. Yet, the information brought by the peptides shared by different proteins is commonly discarded. We propose a statistical framework based on a hierarchical modeling to include that information. Our methodology, based on a simultaneous analysis of all the quantified peptides, handles the biological and technical errors as well as the peptide effect. In addition, we propose a practical implementation suitable for analyzing large data sets. Compared to a method based on the analysis of one protein at a time (that does not include shared peptides), our methodology proved to be far more reliable for estimating protein abundances and testing abundance changes. The source codes are available at http://pappso.inra.fr/bioinfo/all_p/.
A Bovine PeptideAtlas of milk and mammary gland proteomes
Authors: Bislev Stine L. , Deutsch Eric W. , Sun Zhi , Farrah Terry , Aebersold Ruedi , Moritz Robert L. , Bendixen Emøke , Codrea Marius C.
Published: July 2012

Proteome information resources of farm animals are lagging behind those of the classical model organisms despite their important biological and economic relevance. Here, we present a Bovine PeptideAtlas, representing a first collection of Bos taurus proteome data sets within the PeptideAtlas framework. This database was built primarily as a source of information for designing selected reaction monitoring assays for studying milk production and mammary gland health, but it has an intrinsic general value for the farm animal research community. The Bovine PeptideAtlas comprises 1921 proteins at 1.2% false discovery rate (FDR) and 8559 distinct peptides at 0.29% FDR identified in 107 samples from six tissues. The PeptideAtlas web interface has a rich set of visualization and data exploration tools, enabling users to interactively mine information about individual proteins and peptides, their prototypic features, genome mappings, and supporting spectral evidence.
Profiling of the human monocytic cell secretome by quantitative label‐free mass spectrometry identifies stimulus‐specific cytokines and proinflammatory proteins
Authors: Groessl M. , Luksch H. , Rösen‐Wolff A. , Shevchenko A. , Gentzel M.
Published: July 2012

The immune response to pathogens or injury relies on the concerted release of cytokines and proteins with biological activity important for host protection, host defense, and wound healing. Consequently, the secretome of immune cells provides a promising resource for discovery of specific molecular markers and targets for pharmacological intervention. Here, we employ label‐free MS for unbiased, quantitative profiling of the human monocytic cell secretome under different proinflammatory stimuli. The quantitative secretome profiles reveal the highly stimulus‐dependent cellular response and differential, specific secretion of more than 200 proteins, including important proinflammatory proteins and cytokines.
MS Data Miner: A web‐based software tool to analyze, compare, and share mass spectrometry protein identifications
Authors: Dyrlund Thomas F. , Poulsen Ebbe T. , Scavenius Carsten , Sanggaard Kristian W. , Enghild Jan J.
Published: July 2012

Data processing and analysis of proteomics data are challenging and time consuming. In this paper, we present MS Data Miner (MDM) (http://sourceforge.net/p/msdataminer), a freely available web‐based software solution aimed at minimizing the time required for the analysis, validation, data comparison, and presentation of data files generated in MS software, including Mascot (Matrix Science), Mascot Distiller (Matrix Science), and ProteinPilot (AB Sciex). The program was developed to significantly decrease the time required to process large proteomic data sets for publication. This open sourced system includes a spectra validation system and an automatic screenshot generation tool for Mascot‐assigned spectra. In addition, a Gene Ontology term analysis function and a tool for generating comparative Excel data reports are included. We illustrate the benefits of MDM during a proteomics study comprised of more than 200 LC‐MS/MS analyses recorded on an AB Sciex TripleTOF 5600, identifying more than 3000 unique proteins and 3.5 million peptides.
Preparation of sandwich‐structured graphene/mesoporous silica composites with C8‐modified pore wall for highly efficient selective enrichment of endogenous peptides for mass spectrometry analysis
Authors: Yin Peng , Wang Yuhua , Li Yan , Deng Chunhui , Zhang Xiangmin , Yang Pengyuan
Published: July 2012

In this study, sandwich‐structured graphene/mesoporous silica composites (C8‐modified graphene@mSiO2) were synthesized by coating mesoporous silica onto hydrophilic graphene nanosheets through a surfactant‐mediated cocondensation sol‐gel process. The newly prepared C8‐modified graphene@mSiO2 nanocomposites possess unique properties of extended plate‐like morphology, good water dispersibility, highly open pore structure, uniform pore size (2.8 nm), high surface area (632 m2/g), and C8‐modified‐interior pore walls. The unique structure of the C8‐modified graphene@mSiO2 composite nanosheets not only provide extended planes with hydrophilic surface that prevents aggregation in solution, but also offer a huge number of C8‐modified mesopores with high surface area that can ensure an efficient adsorption of peptides through hydrophobic–hydrophobic interaction between C8‐moified pore walls and target molecules. The obtained C8‐modified graphene@mSiO2 materials were utilized for size selectively and specifically enriching peptides in standard peptide mixtures and endogenous peptides in real biological samples (mouse brain tissue).
The preparation of a complex of insulin–phospholipids and their interaction mechanism
Authors: Zhou Cuiping , Xia Xuejun , Liu Yuling , Li Lin
Published: July 2012

Subcutaneous injections of insulin remain the standard treatment for insulin‐dependent diabetic patients, and noninvasive routes are studied but with little success. One of the reasons is that insulin is a hydrophilic compounds and is difficult to cross the mucosa barrier. In this paper, we developed a novel technique to fabricate the insulin–phospholipids complex by a solvent evaporation method with the aim of improving the lipophilicity of insulin. A systematic study on the preparation conditions of the insulin–phospholipids complex is reported in the present work. The formation mechanism and the physicochemical properties of the complex are studied. The associated efficiency of the phospholipids and insulin can be up to 100% when their mass ratio is 7.5 : 1 or more, and the solubility of the complex is improved more than 40 000 times compared with that of insulin alone in the n‐octyl alcohol. The results of the insulin content in the complex and hypoglycemic effects in diabetic mice indicated that insulin was able to withstand the preparation procedure. The stability results showed that the complex was stable for 1 year at −20 °C. The interaction mechanism of this formation is that the peptide bonds of insulin interact with the water‐soluble head of phospholipids, forming a reverse micelle‐like structure. This novel complex will be of great importance in the drug delivery system for insulin via noninvasive routes. This method is cost effective, scalable, and can be used in many other peptide drugs. Copyright © 2012 European Peptide Society and John Wiley & Sons, Ltd.
A slow gradient approach for the purification of synthetic polypeptides by reversed phase high performance liquid chromatography
Authors: Harris Paul W.R. , Lee Dong Jun , Brimble Margaret A.
Published: July 2012

Unquestionably, the purification of polypeptides by chromatographic methods is a considerable bottleneck in their preparation. Peptides synthesised by solid phase synthesis typically contain chromatographically similar impurities that complicate purification by reversed phase high performance liquid chromatography (HPLC) techniques. We report on the application of a slow gradient HPLC protocol that allows, in a single chromatographic step, the purification of hundreds of milligrammes of material. This technique was applied to an extensive collection of synthetic polypeptides some incorporating non‐proteinogenic functionality. In all cases examined, the peptides were not only obtained in high purity peptides but were also recovered in multi‐milligramme amounts. Copyright © 2012 European Peptide Society and John Wiley & Sons, Ltd.
A general framework of marker design with optimal allocation to assess clinical utility
Authors: Tang Liansheng , Zhou Xiao‐Hua
Published: July 2012

This paper proposes a general framework of marker validation designs, which includes most of existing validation designs. The sample size calculation formulas for the proposed general design are derived on the basis of the optimal allocation that minimizes the expected number of treatment failures. The optimal allocation is especially important in the targeted design which is often motivated by preliminary evidence that marker‐positive patients respond to one treatment better than the other. Our sample size calculation also takes into account the classification error of a marker. The numerical studies are conducted to investigate the expected reduction on the treatment failures and the relative efficiency between the targeted design and the traditional design based on the optimal ratios. We illustrate the calculation of the optimal allocation and sample sizes through a hypothetical stage II colon cancer trial. Copyright © 2012 John Wiley & Sons, Ltd.
Metabolomic profiling reveals that Drosophila melanogaster larvae with the y mutation have altered lysine metabolism
Authors: Bratty Mohammed Al , Chintapalli Venkateswara R. , Dow Julian A.T. , Zhang Tong , Watson David G.
Published: July 2012

Yellow (y) encodes a protein which is closely similar to major royal jelly proteins produced by bees. However, the function of y remains largely unknown. Metabolomic profiling was carried out on third instar Oregon R (OR) and yellow (y) Drosophila melanogaster larvae. Phenylalanine, tyrosine and DOPA were all elevated in y as might be expected since the mutation blocks melanin biosynthesis. The most consistent effects were related to lysine metabolism, with the lysine metabolite saccharopine being much higher in y. In addition, lysine acetate was elevated, and the levels of methyl lysines were lower, in y than in OR.
NSort/DB: An Intranuclear Compartment Protein Database
Authors: Willadsen Kai , Mohamad Nurul , Bodén Mikael
Published: July 2012

Distinct substructures within the nucleus are associated with a wide variety of important nuclear processes. Structures such as chromatin and nuclear pores have specific roles, while others such as Cajal bodies are more functionally varied. Understanding the roles of these membraneless intra-nuclear compartments requires extensive data sets covering nuclear and compartment-associated proteins. NSort/DB is a database providing access to intra- or sub-nuclear compartment associations for the mouse nuclear proteome. Based on resources ranging from large-scale curated data sets to detailed experiments, this data set provides a high-quality set of annotations of non-exclusive association of nuclear proteins with structures such as promyelocytic leukaemia bodies and chromatin. The database is searchable by protein identifier or compartment, and has a documented web service API. The search interface, web service and data download are all freely available online at http://www.nsort.org/db/. Availability of this data set will enable systematic analyses of the protein complements of nuclear compartments, improving our understanding of the diverse functional repertoire of these structures.
Hidden realities: What women do when they want to terminate an unwanted pregnancy in Bolivia
Authors: Bury Louise , Aliaga Bruch Sandra , Machicao Barbery Ximena , Garcia Pimentel Franklin
Published: July 2012

Objective

To explore women's experience of unwanted pregnancy and induced abortion in Bolivia, where nearly all induced abortions are carried out in clandestine, unregulated, and unsafe conditions.

Methods

Qualitative and quantitative research methods, including focus group discussions, in‐depth interviews and a structured survey of women of reproductive age, were used to explore the experience of unwanted pregnancy and induced abortion in poor urban areas of 5 Bolivian cities.

Results

Of the 1175 sexually experienced women surveyed, 13% reported having had an induced abortion. The methods they tried included surgical abortion, taking misoprostol, drinking herbal and chemical preparations, and inflicting physical trauma on themselves. Many women made multiple attempts before successfully terminating a pregnancy. Lack of knowledge and confusion about how to use misoprostol may have contributed to the complications that resulted in seeking postabortion care.

Conclusion

Increased access to accurate information and counseling about abortion options are paramount if women are to make informed decisions and minimize health risks.
Women's experiences of and perspectives on abortion at public facilities in Mexico City three years following decriminalization
Authors: Olavarrieta Claudia Díaz , Garcia Sandra G. , Arangure Angélica , Cravioto Vanessa , Villalobos Aremis , AbiSamra Roula , Rochat Roger , Becker Davida
Published: July 2012

Objective

To understand the experiences of women undergoing legal first‐trimester abortion through Mexico City's Ministry of Health (MOH) services. Aims included comparing satisfaction with medical and surgical abortion services; drawing evidence‐based recommendations for program improvement; and measuring contraceptive uptake following abortion.

Methods

A total of 350 women completed a 65‐item survey questionnaire at 2 main MOH abortion facilities. Moreover, a subset of 20 participated in an in‐depth interview. Multivariate analysis was performed to investigate satisfaction with abortion care and in‐depth interview (IDI) data were analyzed.

Results

The participants overwhelmingly reported satisfaction with the care they received, with no significant differences between the medical and surgical abortion groups. However, qualitative data revealed a need for a more sympathetic staff, reduced waiting times, more comprehensive information on surgical abortion, and counseling that includes psychosocial issues. Postabortion contraception uptake was high, with most women opting for the intrauterine device.

Conclusion

The quantitative analysis suggests that although most women were satisfied with the services, some areas were identified as requiring improvement. The IDI data suggest that women wanted counseling to better address psychosocial needs and allow for discussion on a wider range of contraceptive methods.
Loading effects of anterior cervical spine fusion on adjacent segments
Authors: Wang Chien‐Shiung , Chang Jia‐Hao , Chang Ti‐Sheng , Chen Hung‐Yi , Cheng Ching‐Wei
Published: July 2012

Adjacent segment degeneration typically follows anterior cervical spine fusion. However, the primary cause of adjacent segment degeneration remains unknown. Therefore, in order to identify the loading effects that cause adjacent segment degeneration, this study examined the loading effects to superior segments adjacent to fused bone following anterior cervical spine fusion. The C3–C6 cervical spine segments of 12 sheep were examined. Specimens were divided into the following groups: intact spine (group 1); and C5–C6 segments that were fused via cage‐instrumented plate fixation (group 2). Specimens were cycled between 20° flexion and 15° extension with a displacement control of 1°/second. The tested parameters included the range of motion (ROM) of each segment, torque and strain on both the body and inferior articular process at the superior segments (C3–C4) adjacent to the fused bone, and the position of the neutral axis of stress at under 20° flexion and 15° extension. Under flexion and Group 2, torque, ROM, and strain on both the bodies and facets of superior segments adjacent to the fused bone were higher than those of Group 1. Under extension and Group 2, ROM for the fused segment was less than that of Group 1; torque, ROM, and stress on both the bodies and facets of superior segments adjacent to the fused bone were higher than those of Group 1. These analytical results indicate that the muscles and ligaments require greater force to achieve cervical motion than the intact spine following anterior cervical spine fusion. In addition, ROM and stress on the bodies and facets of the joint segments adjacent to the fused bone were significantly increased. Under flexion, the neutral axis of the stress on the adjacent segment moved backward, and the stress on the bodies of the segments adjacent to the fused bone increased. These comparative results indicate that increased stress on the adjacent segments is caused by stress‐shielding effects. Furthermore, increased stress and ROM of the adjacent segments after long‐term bone fusion may accelerate degeneration in adjacent segment.
Investment Treaty Arbitration
Authors: Rigo Sureda Andrés
Published: July 2012

Investment claims have exposed the vague nature of the standards by which arbitral tribunals are expected to adjudicate them and the policy reasons which explicitly or implicitly have an influence. The ad hoc nature of the tribunals and the decisions reached on various controversial issues have brought to the fore the issue of consistency. Andrés Rigo Sureda's Hersch Lauterpacht Memorial Lecture examines how arbitral discretion is exercised in the face of uncertainty of the law. It explores the choices made by arbitral tribunals as they approach treaty interpretation, as they search for limits in determining jurisdiction and the content of the standards of protection and as they search for consistency in the exercise of arbitral discretion.
Socratic Method and Political Science
Authors: MECKSTROTH CHRISTOPHER
Published: July 2012

This article advances a novel theoretical account of what a “method” is and what makes one “rigorous,” and shows how it could advance contemporary debates in political theory and empirical methodology. Plato's Socrates invented the notion of method, and his characteristic practice of immanent refutation through questioning escapes key problems in more familiar views. Socratic method is (1) antifoundational, (2) non-algorithmic, and (3) indirect and relative to competing hypotheses, and it (4) develops its own standards of objectivity from the logic of asking questions. The article reconstructs Socrates’ method from the Platonic texts and shows how it provides reasonable criteria for judgment while remaining critical, sensitive to difference, and open to innovation. Socratic method avoids a forced choice between universalism and particularism in political theory, and it provides a common language for evaluating both quantitative and qualitative methods by drawing out a critical logic of empirical inquiry shared by both.
EDITORIAL FOREWORD
Authors: Baron Beth , Pursley Sara
Published: July 2012

This issue starts with a section on modern Morocco, in anticipation of the upcoming IJMES special issue on Maghribi histories in the modern era. Our call for papers for the special issue was released in December 2010, just before the events of the “Arab Spring” accelerated what was likely the already growing importance of Maghrib scholarship within the broader field of Middle East studies.
Parasites pitched against nature: Pitch Lake water protects guppies (Poecilia reticulata) from microbial and gyrodactylid infections
Authors: SCHELKLE BETTINA , MOHAMMED RYAN S. , COOGAN MICHAEL P. , McMULLAN MARK , GILLINGHAM EMMA L. , VAN OOSTERHOUT COCK , CABLE JOANNE
Published: July 2012

The enemy release hypothesis proposes that in parasite depleted habitats, populations will experience relaxed selection and become more susceptible (or less tolerant) to pathogenic infections. Here, we focus on a population of guppies (Poecilia reticulata) that are found in an extreme environment (the Pitch Lake, Trinidad) and examine whether this habitat represents a refuge from parasites. We investigated the efficacy of pitch in preventing microbial infections in Pitch Lake guppies, by exposing them to dechlorinated water, and reducing gyrodactylid infections on non-Pitch Lake guppies by transferring them to Pitch Lake water. We show that (i) natural prevalence of ectoparasites in the Pitch Lake is low compared to reference populations, (ii) Pitch Lake guppies transferred into aquarium water develop microbial infections, and (iii) experimentally infected guppies are cured of their gyrodactylid infections both by natural Pitch Lake water and by dechlorinated water containing solid pitch. These results indicate a role for Pitch Lake water in the defence of guppies from their parasites and suggest that Pitch Lake guppies might have undergone enemy release in this extreme environment. The Pitch Lake provides an ideal ecosystem for studies on immune gene evolution in the absence of parasites and long-term evolutionary implications of hydrocarbon pollution for vertebrates.
Air traffic flow management with heuristic repair
Authors: Junker Ulrich
Published: July 2012

The European air traffic flow management problem poses particular challenges on optimization technology as it requires detailed modelling and rapid online optimization capabilities. Constraint programming proved successful in addressing these challenges for departure time slot allocation by offering fine-grained modelling of resource constraints and fast allocation through heuristic-repair strategies.
Global properties of tight Reeb flows with applications to Finsler geodesic flows on S2
Authors: HRYNIEWICZ UMBERTO L. , SALOMÃO PEDRO A. S.
Published: July 2012

We show that if a Finsler metric on S2 with reversibility r has flag curvatures K satisfying (r/(r+1))2 < K ≤ 1, then closed geodesics with specific contact-topological properties cannot exist, in particular there are no closed geodesics with precisely one transverse self-intersection point. This is a special case of a more general phenomenon, and other closed geodesics with many self-intersections are also excluded. We provide examples of Randers type, obtained by suitably modifying the metrics constructed by Katok [21], proving that this pinching condition is sharp. Our methods are borrowed from the theory of pseudo-holomorphic curves in symplectizations. Finally, we study global dynamical aspects of 3-dimensional energy levels C2-close to S3
Measles outbreak in an asylum-seekers' shelter in Germany: comparison of the implemented with a hypothetical containment strategy
Authors: TAKLA A. , BARTH A. , SIEDLER A. , STÖCKER P. , WICHMANN O. , DELERÉ Y.
Published: July 2012

In order to contain a measles outbreak in a German asylum-seekers' shelter, serological testing of all residents was performed, followed by selective vaccination of those with negative test results/not tested. In this paper we describe the outbreak epidemiologically and then compare the implemented strategy with a hypothetical mass vaccination of all individuals unvaccinated or with unknown vaccination status born after 1970 as recommended by the German Standing Committee on Vaccination in terms of potentially avoided cases, logistics, and costs. Three hundred (70%) residents participated in the serological testing, of which 39 (13%) were seronegative. In total, 144 individuals were eligible for vaccination, while a mass vaccination would have targeted 359 persons. However, serological testing was time- and personnel consuming and revealed several logistical problems. Its costs amounted to €90 000, double that of mass vaccination that additionally might have avoided three of the eight cases. Mass vaccination seems the preferred measure for measles outbreak control in such settings.
High-Resolution Optical Imaging of Zebrafish Larval Ribbon Synapse Protein RIBEYE, RIM2, and CaV 1.4 by Stimulation Emission Depletion Microscopy
Authors: Lv Caixia , Gould Travis J. , Bewersdorf Joerg , Zenisek David
Published: July 2012

The synaptic ribbon is a unique presynaptic structure with an intricate morphology in photoreceptors. Because of the resolution limit in conventional fluorescence microscopy, investigating ribbon protein locations has been challenging, especially in the early development stages of model animals. Here, we used stimulated emission depletion microscopy, a super-resolution imaging technique, to look at retina sections in 4 days post-fertilization (dpf) zebrafish. We observed that in photoreceptor cells, RIBEYE and RIM2 are expressed along the synaptic ribbon, with RIM2 consistently located inside of the horseshoe-shaped synaptic ribbon structure with RIBEYE located on the outside. The L-type calcium channel subunit, CACNA1F, exhibited small spot-like staining beneath the RIM2 and RIBEYE structures. Using morpholino antisense oligonucleotides to knock down RIBEYE expression, we observed fewer and shorter ribbons in the photoreceptor outer plexiform layers of 4 dpf fish retina as well as a reduction in RIM2 expression. The clustering of CACNA1F in these blind fish was no longer observed, but instead showed a diffuse expression in the photoreceptor terminal.
Metabolic Imaging Using Two-Photon Excited NADH Intensity and Fluorescence Lifetime Imaging
Authors: Vergen Jorge , Hecht Clifford , Zholudeva Lyandysha V. , Marquardt Meg M. , Hallworth Richard , Nichols Michael G.
Published: July 2012

Metabolism and mitochondrial dysfunction are known to be involved in many different disease states. We have employed two-photon fluorescence imaging of intrinsic mitochondrial reduced nicotinamide adenine dinucleotide (NADH) to quantify the metabolic state of several cultured cell lines, multicell tumor spheroids, and the intact mouse organ of Corti. Historically, fluorescence intensity has commonly been used as an indicator of the NADH concentration in cells and tissues. More recently, fluorescence lifetime imaging has revealed that changes in metabolism produce not only changes in fluorescence intensity, but also significant changes in the lifetimes and concentrations of free and enzyme-bound pools of NADH. Since NADH binding changes with metabolic state, this approach presents a new opportunity to track the cellular metabolic state.
Swept Field Laser Confocal Microscopy for Enhanced Spatial and Temporal Resolution in Live-Cell Imaging
Authors: Castellano-Muñoz Manuel , Peng Anthony Wei , Salles Felipe T. , Ricci Anthony J.
Published: July 2012

Confocal fluorescence microscopy is a broadly used imaging technique that enhances the signal-to-noise ratio by removing out of focal plane fluorescence. Confocal microscopes come with a variety of modifications depending on the particular experimental goals. Microscopes, illumination pathways, and light collection were originally focused upon obtaining the highest resolution image possible, typically on fixed tissue. More recently, live-cell confocal imaging has gained importance. Since measured signals are often rapid or transient, thus requiring higher sampling rates, specializations are included to enhance spatial and temporal resolution while maintaining tissue viability. Thus, a balance between image quality, temporal resolution, and tissue viability is needed. A subtype of confocal imaging, termed swept field confocal (SFC) microscopy, can image live cells at high rates while maintaining confocality. SFC systems can use a pinhole array to obtain high spatial resolution, similar to spinning disc systems. In addition, SFC imaging can achieve faster rates by using a slit to sweep the light across the entire image plane, thus requiring a single scan to generate an image. Coupled to a high-speed charge-coupled device camera and a laser illumination source, images can be obtained at greater than 1,000 frames per second while maintaining confocality.
Chemical Vapor Deposition of Porous GaN Particles on Silicon
Authors: Carvajal Joan J. , Bilousov Oleksandr V. , Drouin Dominique , Aguiló Magdalena , Díaz Francesc , Rojo J. Carlos
Published: July 2012

We present a technique for the direct deposition of nanoporous GaN particles on Si substrates without requiring any post-growth treatment. The internal morphology of the nanoporous GaN particles deposited on Si substrates by using a simple chemical vapor deposition approach was investigated, and straight nanopores with diameters ranging between 50 and 100 nm were observed. Cathodoluminescence characterization revealed a sharp and well-defined near band-edge emission at ∼365 nm. This approach simplifies other methods used for this purpose, such as etching and corrosion techniques that can damage the semiconductor structure and modify its properties.
Age Differences and Measurement Invariance of Working Memory in 5- to 12-Year-Old Children
Authors: Michalczyk Kurt , Malstädt Nadine , Worgt Maria , Könen Tanja , Hasselhorn Marcus
Published: July 2012

In this study, we investigated working memory structure and measurement invariance of working memory in children between 5 and 12 years. In a sample of 1,669 children, we administered a battery of 12 computer-based working memory subtests. We found the same tripartite structure of working memory with a phonological loop, a visual-spatial sketchpad, and a central executive in the age groups 5–6 years, 7–9 years, and 10–12 years; interrelations of the latent factors were invariant across the age groups. Only the relationships between the phonological loop and the central executive were weaker in the 5- to 6-year-olds than in the older age groups. The results corroborate the tripartite working memory model developed by Baddeley (1986) and show that the functional relationships between working memory components are mostly invariant through childhood. In addition, the findings indicate that future research should focus on extending the model by a fourth factor representing inhibition.
Transfer of Leadership Skills
Authors: Franke Franziska , Felfe Jörg
Published: July 2012

The successful transfer of managerial skills acquired in training is important for organizational performance. As leadership skills are complex, it is highly demanding to learn these skills and to apply them in practice. Therefore, motivation to transfer and organizational support are important determinants of transfer particularly in managerial training. The present study examined the lagged effect of motivation to transfer and organizational support on the leaders’ behavior right after training and 1 year later. As expected, motivation to transfer and organizational support predict behavioral transfer immediately after training and 1 year later. Moreover, behavioral transfer after the training predicts job performance 1 year later.
To Belong or Not to Belong
Authors: Peters Kim , Ryan Michelle , Haslam S. Alexander , Fernandes Helen
Published: July 2012

Women continue to be underrepresented in traditionally masculine occupations. We argue that this may be explained in part by women’s perceptions that they do not fit in with the dominant identities in these occupations, contributing to occupational disidentification and an inclination to “opt out.” We tested this argument in two samples of trainee surgeons. Study 1 (N = 129 female trainees) showed that women perceived a lack of fit with the masculine surgeon prototype and that, as expected, this perception was associated with a reduction in occupational identification and an increased desire to opt out. Study 2 (N = 216 male and female trainees) showed that women’s perceived lack of fit with the surgeon prototype was greater than men’s, and that this accounted for women’s relative disidentification.
On the interpretation of constrained climate model ensembles
Authors: Sanderson Benjamin M. , Knutti Reto
Published: July 2012

An ensemble of models can be interpreted in two ways. The first treats each model as an approximation of the true system with some random error. Alternatively, the true system can be interpreted as a sample drawn from a distribution of models, such that model and truth are statistically indistinguishable. Both interpretations are ubiquitous and have different consequences for the uncertainty of model projections, but are rarely defended. Here we argue that the two seemingly conflicting views are in fact complementary, and the interpretation of the ensemble may evolve seamlessly from the former to the latter. We show some ‘truth plus error’ like properties exist for historical and present day climate simulations in the CMIP archive, and that they can be explained by the ensemble design and tuning to observations, although both models and tuning are imperfect. For future projections, structural differences in model response arise which are independent of the present day state and thus the ‘indistinguishable’ interpretation is increasingly favored. Our inability to define performance metrics that identify ‘good’ and ‘bad’ models can be explained by the models having largely exploited the available observations. The remaining model error is largely structural and the observations are often uninformative to further reduce model biases or reduce the range of projections covered by the ensemble. The discussion here is motivated by the use of multi model ensembles in climate projections, but the arguments are generic to any situation where multiple different models constrained by observations are used to describe the same system.
Trends in Arctic sea ice extent from CMIP5, CMIP3 and observations
Authors: Stroeve Julienne C. , Kattsov Vladimir , Barrett Andrew , Serreze Mark , Pavlova Tatiana , Holland Marika , Meier Walter N.
Published: July 2012

The rapid retreat and thinning of the Arctic sea ice cover over the past several decades is one of the most striking manifestations of global climate change. Previous research revealed that the observed downward trend in September ice extent exceeded simulated trends from most models participating in the World Climate Research Programme Coupled Model Intercomparison Project Phase 3 (CMIP3). We show here that as a group, simulated trends from the models contributing to CMIP5 are more consistent with observations over the satellite era (1979–2011). Trends from most ensemble members and models nevertheless remain smaller than the observed value. Pointing to strong impacts of internal climate variability, 16% of the ensemble member trends over the satellite era are statistically indistinguishable from zero. Results from the CMIP5 models do not appear to have appreciably reduced uncertainty as to when a seasonally ice‐free Arctic Ocean will be realized.
Intercomparison of pressure standards (Au, Pt, Mo, MgO, NaCl and Ne) to 2.5 Mbar
Authors: Dorfman S. M. , Prakapenka V. B. , Meng Y. , Duffy T. S.
Published: July 2012

We have performed a series of co‐compression experiments on Au, Pt, Mo, MgO and NaCl to extend internally consistent pressure calibration and characterize shear strength of pressure media to 2.5 Mbar. Measured unit cell volumes of calibrants show differences between existing pressure scales of ∼10% above 2 Mbar. A new comprehensive pressure scale is proposed in good agreement with recent reduced shock isotherms for Au, Mo and Pt and with internal agreement to 3% at Mbar pressures. Deviatoric stresses were analyzed for each material based on diffraction line broadening and line shifts due to anisotropic strain. The measured strength of Ne at 2.5 Mbar is 8 GPa. Diffraction line width analysis suggests that deviatoric stress conditions at 2.5 Mbar are similar for He and Ne media.
Lambert albedo retrieval and analyses over Aram Chaos from OMEGA hyperspectral imaging data
Authors: Liu Yang , Arvidson Raymond E. , Wolff Michael J. , Mellon Michael T. , Catalano Jeffrey G. , Wang Alian , Bishop Janice L.
Published: July 2012

The DISORT radiative transfer model was used to retrieve Lambert albedos from 0.4 to 4.0 μm over hydrated sulfate deposits in Aram Chaos for the Mars Express OMEGA instrument. Albedos were also retrieved for a relatively anhydrous area to the north to use as a control for comparison to the hydrated sulfate spectra. Atmospheric gases and aerosols were modeled, along with both solar and thermal radiance contributions and retrieved Lambert albedos are similar for multiple OMEGA observations over the same areas. The Lambert albedo spectra show that the control area is dominated by electronic transition bands due to nanophase iron oxides and low‐calcium orthopyroxenes, together with the ubiquitous 2.98μm band due in part to water adsorbed onto particle surfaces. The retrieved Lambert albedos for Aram Chaos show an enhanced 2.98 μm water band and bands located at 0.938, 1.46, 1.96, and 2.41 μm. We infer the presence of nanophase iron oxides, schwertmannite, and starkeyite based on consideration of these band locations, inferred electronic and vibrational absorptions, stability under Mars conditions, and pathways for formation. This mineral assemblage, together with gray, crystalline hematite previously detected from TES data (Glotch and Christensen, 2005), can be explained as a result of iron oxidation and evaporation of iron‐, magnesium‐, and sulfur‐rich fluids during periods of rising groundwater.
Shape and evolution of the fundamental niche in marine Vibrio
Authors: Materna Arne C , Friedman Jonathan , Bauer Claudia , David Christina , Chen Sara , Huang Ivy B , Gillens April , Clarke Sean A , Polz Martin F , Alm Eric J
Published: July 2012

Hutchinson’s fundamental niche, defined by the physical and biological environments in which an organism can thrive in the absence of inter-species interactions, is an important theoretical concept in ecology. However, little is known about the overlap between the fundamental niche and the set of conditions species inhabit in nature, and about natural variation in fundamental niche shape and its change as species adapt to their environment. Here, we develop a custom-made dual gradient apparatus to map a cross-section of the fundamental niche for several marine bacterial species within the genus Vibrio based on their temperature and salinity tolerance, and compare tolerance limits to the environment where these species commonly occur. We interpret these niche shapes in light of a conceptual model comprising five basic niche shapes. We find that the fundamental niche encompasses a much wider set of conditions than those strains typically inhabit, especially for salinity. Moreover, though the conditions that strains typically inhabit agree well with the strains’ temperature tolerance, they are negatively correlated with the strains’ salinity tolerance. Such relationships can arise when the physiological response to different stressors is coupled, and we present evidence for such a coupling between temperature and salinity tolerance. Finally, comparison with well-documented ecological range in V. vulnificus suggests that biotic interactions limit the occurrence of this species at low-temperature—high-salinity conditions. Our findings highlight the complex interplay between the ecological, physiological and evolutionary determinants of niche morphology, and caution against making inferences based on a single ecological factor.
A dietary source of coenzyme Q is essential for growth of long-lived
Caenorhabditis elegans clk-1
mutants
Authors: Jonassen Tanya , Larsen Pamela L. , Clarke Catherine F.
Published: July 2012

Mutations in the
clk-1
gene of the nematode
Caenorhabditis elegans
result in slowed
development, sluggish adult behaviors, and an increased lifespan. CLK-1
is a mitochondrial polypeptide with sequence and functional
conservation from human to yeast. Coq7p, the
Saccharomyces
cerevisiae
homologue, is essential for ubiquinone (coenzyme Q
or Q) synthesis and therefore respiration. However, based on assays of
respiratory function, it has been reported that the primary defect in
the
C. elegans clk-1
mutants is not in Q biosynthesis.
How do the
clk-1
mutant worms have essentially normal
rates of respiration, when biochemical studies in yeast suggest a Q
deficiency? Nematodes are routinely fed
Escherichia coli
strains containing a rich supply of Q. To study the Q synthesized by
C. elegans
, we cultured worms on an
E.
coli
mutant that lacks Q and found that
clk-1
mutants display early developmental arrest from eggs, or sterility
emerging from dauer stage. Provision of Q-replete
E.
coli
rescues these defects. Lipid analysis showed that
clk-1
worms lack the nematode Q
9
isoform and
instead contain a large amount of a metabolite that is slightly more
polar than Q
9
. The
clk-1
mutants also have
increased levels of Q
8
, the
E. coli
isoform,
and rhodoquinone-9. These results show that the
clk-1
mutations result in Q auxotrophy evident only when Q is removed from
the diet, and that the aging and developmental phenotypes previously
described are consistent with altered Q levels and distribution.
Loss of imprinting of the insulin-like growth factor II gene occurs by biallelic methylation in a core region of
H19
-associated CTCF-binding sites in colorectal cancer
Authors: Nakagawa Hidewaki , Chadwick Robert B. , Peltomäki Päivi , Plass Christoph , Nakamura Yusuke , de la Chapelle Albert
Published: July 2012

We hypothesize that loss of imprinting (LOI) of the insulin-like
growth factor II (
IGF2
) gene is associated with a
predisposition to sporadic colorectal cancer. We confirmed a previously
known strong correlation between LOI and microsatellite instability and
showed that LOI was not a consequence of microsatellite instability or
mismatch repair deficiency. LOI of
IGF2
correlated
strongly with biallelic hypermethylation of a core of five CpG sites in
the insulator region of
IGF2/H19
, which is a known
CTCF-binding element. As this methylation-dependent LOI was present in
both tumors and normal colonic mucosa, it is possible that
hypermethylation creates a field defect predisposing to cancer.
Allelic exclusion and differentiation by protein kinase C-mediated signals in immature thymocytes
Authors: Michie Alison M. , Soh Jae-Won , Hawley Robert G. , Weinstein I. Bernard , Zúñiga-Pflücker Juan Carlos
Published: July 2012

Pre-T cell receptor (preTCR)-derived signals mediate the transition
of thymocytes from the CD4
−
CD8
−
double-negative (DN) to CD4
+
CD8
+
double-positive stage of T lymphocyte development. This progression,
termed β-selection, is limited to thymocytes that have generated a
functional TCR-β chain able to associate with pTα to form the
preTCR complex. Formation of the preTCR complex not only induces
differentiation, survival, and proliferation of DN thymocytes; it also
inhibits further TCR-β gene rearrangement through an ill-defined
process known as allelic exclusion. The signaling pathways controlling
this critical developmental checkpoint have not been characterized.
Here we demonstrate that formation of the preTCR complex leads to the
activation of protein kinase C (PKC), and that activation of PKC is
necessary for the differentiation and expansion of DN thymocytes.
Importantly, we also show that allelic exclusion at the TCR-β gene
loci is enforced by PKC-mediated signals. These results define PKC as a
central mediator of both differentiation and allelic exclusion during
thymocyte development.
Reproduction-related behaviors of Swiss–Webster female mice living in a cold environment
Authors: Chan Johnny , Ogawa Sonoko , Pfaff Donald W.
Published: July 2012

Based on a molecular neuroendocrine theory about cold environments,
thyroid hormone levels, and liganded thyroid hormone receptor
interference with estrogen receptor function, experiments were designed
to test female mouse reproductive behaviors in the cold. Because
natural seasonal temperature declines would usually be associated with
decreased photoperiods and reduced food supplies, we combined cold
temperatures with short days and metabolic challenge. The simplest
hypothesis was that lordosis quotients would be significantly reduced
as a result of cold temperatures. That hypothesis was denied. Instead,
female approaches to the stud male declined. Because cold temperatures
also led to significant reductions of activity in locomotor wheels, a
straightforward reduction of activity could explain the female's
behavior during mating tests. We suggest that cold temperatures
accompanied by reduced photoperiod and reduced metabolic fuel can
reduce overall activity in female mice, thus indirectly blocking
untimely reproductive behaviors.
A mechanism for ATP-sensitive potassium channel diversity: Functional coassembly of two pore-forming subunits
Authors: Cui Yi , Giblin Jonathan P. , Clapp Lucie H. , Tinker Andrew
Published: July 2012

ATP-sensitive potassium channels are an octomeric complex of
four pore-forming subunits of the Kir 6.0 family and four sulfonylurea
receptors. The Kir 6.0 family consists of two known members, Kir 6.1
and Kir 6.2, with distinct functional properties. The tetrameric
structure of the pore-forming domain leads to the possibility that
mixed heteromultimers may form. In this study, we examine this by using
biochemical and electrophysiological techniques after heterologous
expression of these subunits in HEK293 cells. After the coexpression of
Kir 6.1 and Kir 6.2, Kir 6.1 can be coimmunoprecipitated with
isoform-specific Kir 6.2 antisera and vice versa. Coexpression of SUR2B
and Kir 6.2 with Kir 6.1 dominant negatives at a 1:1 expression ratio
and vice versa led to a potent suppression of current. Kir 6.1, and Kir
6.2 dominant negative mutants were without effect on an inwardly
rectifying potassium channel from a different family, Kir 2.1.
Single-channel analysis, after coexpression of SUR2B, Kir 6.1, and Kir
6.2, revealed the existence of five distinct populations with differing
single-channel current amplitudes. All channel populations were
inhibited by glibenclamide. A dimeric Kir 6.1–Kir 6.2 construct
expressed with SUR2B had a single-channel conductance intermediate
between that of either Kir 6.2 or Kir 6.1 expressed with SUR2B. In
conclusion, Kir 6.1 and Kir 6.2 readily coassemble to produce
functional channels, and such phenomena may contribute to the diversity
of nucleotide-regulated potassium currents seen in native tissues.
Accumulation of soluble and wall-bound indolic metabolites in
Arabidopsis thaliana
leaves infected with virulent or avirulent
Pseudomonas syringae
pathovar tomato strains
Authors: Hagemeier Jens , Schneider Bernd , Oldham Neil J. , Hahlbrock Klaus
Published: July 2012

The chemical structures and accumulation kinetics of several
major soluble as well as wall-bound, alkali-hydrolyzable compounds
induced upon infection of
Arabidopsis thaliana
leaves
with
Pseudomonas syringae
pathovar tomato were
established. All identified accumulating products were structurally
related to tryptophan. Most prominent among the soluble substances were
tryptophan, β-
d
-glucopyranosyl indole-3-carboxylic acid,
6-hydroxyindole-3-carboxylic acid
6-
O
-β-
d
-glucopyranoside, and the
indolic phytoalexin camalexin. The single major accumulating wall
component detectable under these conditions was indole-3-carboxylic
acid. All of these compounds increased more rapidly, and camalexin as
well as indole-3-carboxylic acid reached much higher levels, in the
incompatible than in the compatible
P. syringae/A.
thaliana
interaction. The only three prominent phenylpropanoid
derivatives present in the soluble extract behaved differently.
Two kaempferol glycosides remained largely unaffected, and sinapoyl
malate decreased strongly upon bacterial infection with a time course
inversely correlated with that of the accumulating tryptophan-related
products. The accumulation patterns of both soluble and wall-bound
compounds, as well as the disease resistance phenotypes, were
essentially the same for infected wild-type and
tt4
(no
kaempferol glycosides) or
fah1
(no sinapoyl malate)
mutant plants. Largely different product combinations accumulated in
wounded or senescing
A. thaliana
leaves. It seems
unlikely that any one of the infection-induced compounds identified so
far has a decisive role in the resistance response to
P.
syringae
.