bluuebunny/crossref_metadata_2025_split huggingface dataset:
Visualization of ATP with Luciferin-Luciferase Reaction in Mouse Skeletal Muscles Using an “In Vivo Cryotechnique”
Authors: Terada N. , Saitoh Y. , Saitoh S. , Ohno N. , Fujishita K. , Koizumi S. , Ohno S. 
Published: October 2012

AbstractAdenosine triphosphate (ATP) is a well-known energy source for muscle contraction. In this study, to visualize localization of ATP, a luciferin-luciferase reaction (LLR) was performed in mouse skeletal muscle with an “in vivo cryotechnique” (IVCT). First, to confirm if ATP molecules could be trapped and detected after glutaraldehyde (GA) treatment, ATP was directly attached to glass slides with GA, and LLR was performed. The LLR was clearly detected as an intentional design of the ATP attachment. The intensity of the light unit by LLR was correlated with the concentration of the GA-treated ATP in vitro. Next, LLR was evaluated in mouse skeletal muscles with IVCT followed by freeze-substitution fixation (FS) in acetone-containing GA. In such tissue sections the histological structure was well maintained, and the intensity of LLR in areas between muscle fibers and connective tissues was different. Moreover, differences in LLR among muscle fibers were also detected. For the IVCT-FS tissue sections, diaminobenzidine (DAB) reactions were clearly detected in type I muscle fibers and erythrocytes in capillaries, which demonstrated flow shape. Thus, it became possible to perform microscopic evaluation of the numbers of ATP molecules in the mouse skeletal muscles with IVCT, which mostly reflect living states.
Aging Increases Nuclear Chromatin Entropy of Erythroid Precursor Cells in Mice Spleen Hematopoietic Tissue
Authors: Pantic Igor , Pantic Senka , Paunovic Jovana 
Published: October 2012

AbstractDespite recent advances in hematopoietic tissue research, effects of aging on hematopoietic erythroid precursor (EP) cells are unclear. In this article we present results suggesting that chromatin textural entropy of EP cells in mouse spleen increases with age, while chromatin homogeneity decreases. The experiment was conducted on a total of 32 male Swiss white mice. Spleen tissue was acquired from four age groups: 10 days, 1 month, 4 months, and 7 months old mice. A total of 640 randomly selected, nonoverlapping EP cell nuclei (20 per animal) were analyzed using the gray level co-occurrence matrix method. There was statistically highly significant difference between the age groups, both in chromatin entropy (ANOVA,F= 12.99,p< 0.0001) and in homogeneity (ANOVA,F= 7.05,p< 0.001). When the individual groups were compared (ANOVApost hoctest), statistical difference was detected in all group pairs, except between the animals 4 months and 7 months old, either in chromatin entropy or homogeneity. The detected increase of chromatin disorder in mouse juvenile period/early adulthood suggests that cell intrinsic factors such as epigenetic dysregulation and DNA damage accumulation may have an important role in EP cell aging.
Improving Fabrication and Application of Zach Phase Plates for Phase-Contrast Transmission Electron Microscopy
Authors: Hettler Simon , Gamm Björn , Dries Manuel , Frindt Nicole , Schröder Rasmus R. , Gerthsen Dagmar 
Published: October 2012

AbstractZach phase plates (PPs) are promising devices to enhance phase contrast in transmission electron microscopy. The Zach PP shifts the phase of the zero-order beam by a strongly localized inhomogeneous electrostatic potential in the back focal plane of the objective lens. We present substantial improvements of the Zach PP, which overcome previous limitations. The implementation of a microstructured heating device significantly reduces contamination and charging of the PP structure and extends its lifetime. An improved production process allows fabricating PPs with reduced dimensions resulting in lower cut-on frequencies as revealed by simulations of the electrostatic potential. Phase contrast with inversion of PbSe nanoparticles is demonstrated in a standard transmission electron microscope with LaB6cathode by applying different voltages.
ON THIN OR SLENDER BODIES
Authors: TUCK E. O. , STOKES Y. M. 
Published: October 2012

AbstractThis is a review of thin-body and slender-body theories, with indications of some new applications. Topics discussed include bodies with near-constant surface pressure, subsonic and supersonic aerodynamics, ship hydrodynamics, slender bodies in Stokes flow, slender footings in elastic media, and slender moonpools. Mathematical features of the thin- and slender-body approximations are also discussed, especially nonlocal convolution terms modelling three-dimensionality in the otherwise two-dimensional near field, end effects, and the role of the logarithm of the slenderness ratio. This review was presented by the first author as the IMA Lighthill Memorial Lecture at the British Applied Mathematics Colloquium (BAMC) 2004.
The 2010 U.S. health care reform: approaching and avoiding how other countries finance health care
Authors: White Joseph 
Published: October 2012

AbstractThis article describes and analyzes the U.S. health care legislation of 2010 by asking how far it was designed to move the U.S. system in the direction of practices in all other rich democracies. The enacted U.S. reform could be described, extremely roughly, as Japanese pooling with Swiss and American problems at American prices. Its policies are distinctive, yet nevertheless somewhat similar to examples in other rich democracies, on two important dimensions: how risks are pooled and the amount of funds redistributed to subsidize care for people with lower incomes. Policies about compelling people to contribute to a finance system would be further from international norms, as would the degree to which coverage is set by clear and common substantive standards – that is, standardization of benefits. The reform would do least, however, to move the United States toward international practices for controlling spending. This in turn is a major reason why the results would include less standard benefits and incomplete coverage. In short, the United States would remain an outlier on coverage less because of a failure to make an effort to redistribute – a lack of solidarity – than due to a failure to control costs.
Geologic heterogeneity can produce aseismic slip transients
Authors: Skarbek R. M. , Rempel A. W. , Schmidt D. A. 
Published: October 2012

Slow slip and tectonic tremor in subduction zones take place at depths where there is abundant evidence for distributed shear over broad zones (∼10–103 m) composed of rocks with marked differences in mechanical properties. Here we model quasi‐dynamic rupture along faults composed of material mixtures characterized by different rate‐and‐state‐dependent frictional properties to determine the parameter regime capable of producing slow slip in an idealized subduction zone setting. Keeping other parameters fixed, the relative proportions of velocity‐weakening (VW) and velocity‐strengthening (VS) materials control the sliding character (stable, slow, or dynamic) along the fault. The stability boundary between slow and dynamic is accurately described by linear analysis of a double spring‐slider system with VW and VS blocks. Our results place bounds on the volume fractions of VW material present in heterogeneous geological assemblages that host slow slip and tremor in subduction zones.
Towards the use of cloud microphysical properties to simulate IASI spectra in an operational context
Authors: Faijan François , Lavanant Lydie , Rabier Florence 
Published: October 2012

Capabilities and limitations of two fast radiative transfer models simulating cloudy spectra of the Infrared Atmospheric Sounding Interferometer (IASI) have been investigated in this paper. These models include a better modeling of the clouds than current operational fast forward models, such as scattering effects of the radiation in the cloud layer. An accurate simulation of the IASI spectra in the presence of ice clouds or for vertically extended clouds is a necessary step toward the use of these cloud‐affected radiances in an operational context. Through a collocation of IASI observations with an independent data set from the Lindenberg ground‐based station and the A‐Train space‐borne active instruments, this study first examines the accuracy of the fast radiative transfer models to simulate the cloudy spectra and provides some indications of confidence in the use of the cloud microphysical and optical properties. This first step shows the high sensitivity toward the cloudy inputs (crystal shapes, particle size, and cloud water content) which can reach several kelvins. It also provides a screening method to process cloudy radiances and to deal with the strong sensitivity of the fast radiative transfer model. The performance of the scattering fast radiative transfer models is then assessed in a global operational through simulations during a one week period over the globe, with the profiles of cloud variables from the ECMWF forecast used to compute the radiances. The applied screening method has reduced the standard deviation between simulated and observed spectra from 9 to 3 K.
Design of a heterotetravalent synthetic allergen that reflects epitope heterogeneity and IgE antibody variability to study mast cell degranulation
Authors: Handlogten Michael W. , Kiziltepe Tanyel , Bilgicer Basar 
Published: October 2012

The present paper describes the design of a HtTA (heterotetravalent allergen) as a multi-component experimental system that enables an integrative approach to study mast cell degranulation. The HtTA design allows presentation of two distinct haptens, each with a valency of 2, thereby better reflecting the complexity of natural allergens by displaying epitope heterogeneity and IgE antibody variability. Using the HtTA design, synthetic allergens HtTA-1 and HtTA-2 were synthesized to model a combination of epitope/IgE affinities. HtTA-1 presented DNP (2,4-dinitrophenyl) and dansyl haptens (Kd=22 and 54 nM for IgEDNP and IgEdansyl respectively) and HtTA-2 presented dansyl and the weak-affinity DNP-Pro (DNP-proline) haptens (Kd=550 nM for IgEDNP). Both HtTAs effectively induced degranulation when mast cells were primed with both IgEDNP and IgEdansyl antibodies. Interestingly tetravalent DNP-Pro or bivalent dansyl were insufficient in stimulating a degranulation response, illustrating the significance of valency, affinity and synergy in allergen–IgE interactions. Importantly, maximum degranulation with both HtTA-1 and HtTA-2 was observed when only 50% of the mast cell-bound IgEs were hapten-specific (25% IgEdansyl and 25% IgEDNP). Taken together, results of the present study establish the HtTA system as a physiologically relevant experimental model and demonstrates its utility in elucidating critical mechanisms of mast cell degranulation.
Ribavirin-induced intracellular GTP depletion activates transcription elongation in coagulation Factor VII gene expression
Authors: Suzuki Atsuo , Miyawaki Yuhri , Okuyama Eriko , Murata Moe , Ando Yumi , Kato Io , Takagi Yuki , Takagi Akira , Murate Takashi , Saito Hidehiko , Kojima Tetsuhito 
Published: October 2012

Coagulation FVII (Factor VII) is a vitamin K-dependent glycoprotein synthesized in hepatocytes. It was reported previously that FVII gene (F7) expression was up-regulated by ribavirin treatment in hepatitis C virus-infected haemophilia patients; however, its precise mechanism is still unknown. In the present study, we investigated the molecular mechanism of ribavirin-induced up-regulation of F7 expression in HepG2 (human hepatoma cell line). We found that intracellular GTP depletion by ribavirin as well as other IMPDH (inosine-5′-monophosphate dehydrogenase) inhibitors, such as mycophenolic acid and 6-mercaptopurine, up-regulated F7 expression. FVII mRNA transcription was mainly enhanced by accelerated transcription elongation, which was mediated by the P-TEFb (positive-transcription elongation factor b) complex, rather than by promoter activation. Ribavirin unregulated ELL (eleven-nineteen lysine-rich leukaemia) 3 mRNA expression before F7 up-regulation. We observed that ribavirin enhanced ELL3 recruitment to F7, whereas knockdown of ELL3 diminished ribavirin-induced FVII mRNA up-regulation. Ribavirin also enhanced recruitment of CDK9 (cyclin-dependent kinase 9) and AFF4 to F7. These data suggest that ribavirin-induced intracellular GTP depletion recruits a super elongation complex containing P-TEFb, AFF4 and ELL3, to F7, and modulates FVII mRNA transcription elongation. Collectively, we have elucidated a basal mechanism for ribavirin-induced FVII mRNA up-regulation by acceleration of transcription elongation, which may be crucial in understanding its pleiotropic functions in vivo.
BELIEVING AND BELONGING IN EUROPE
Authors: Reitsma Jan , Pelzer Ben , Scheepers Peer , Schilderman Hans 
Published: October 2012

ABSTRACT
This paper investigates (trends and determinants of) individual combinations of religious believing and belonging in Europe from a cross-national and longitudinal perspective. Individual level data for the period 1981–2007 in 42 countries derived from the European Values Survey and the European Social Survey are harmonised and enriched with contextual characteristics, constituting a more comprehensive data base for Europe than any previous research. Complementary hypotheses from modernisation and market theories are derived systematically and tested rigorously. We find differential trends. In western societies, the popularity of secularity and consistent religiosity has persisted. In former communist societies, the popularity of consistent religiosity has increased whereas secularity has decreased. In both western and former communist societies, solitary religiosity has been a clear yet small phenomenon, somewhat increasing in western societies and somewhat decreasing in former communist societies. A crucial hypothesis derived from modernisation theories, stating that financial and social security would decrease consistent religiosity, is empirically supported.
Exploring the processes involved in long‐term recovery from chronic alcohol addiction within an abstinence‐based model: Implications for practice
Authors: Gubi Peter Madsen , Marsden-Hughes Howard 
Published: October 2012

AbstractBackground: There is little consensus at policy or treatment level as to what defines ‘recovery’ in the alcohol addiction field. Aim: From interviewing a cohort of eight severely alcohol‐dependent people who fulfilled all categories of DSM‐IV and ICD 10 diagnostic criteria and had achieved long‐term recovery (LTR) of between 8 and 48 years, and who are long‐term AA members, a definition of recovery that is inclusive, and achievable, was sought from their lived experiences. Methodology: Interpretative Phenomenological Analysis was used. Findings: This research uncovers the processes involved in long‐term recovery, and identifies them as: sober; maintaining sobriety; and recovery. It suggests a move away from the acute model of cure by brief, time‐limited therapy, towards a model of sustained, on‐going and life‐long recovery management, combined with pro‐social aid resources. Individuals need to observe, and hear, the success narratives of others, and the therapeutic conditions of empathy, unconditional positive regard and congruence need to be strongly experienced by the individual.
Upper body force production after a low‐volume static and dynamic stretching
Authors: Leone D. C. P. G. , Pezarat P. , Valamatos M. J. , Fernandes O. , Freitas S. , Moraes A. C. 
Published: October 2012

AbstractThis study investigated the acute effect of a low‐volume static and dynamic stretching on maximal isometric peak force (MIPF), time to maximal isometric force (TMIF), rate of force production (RFP) and average amplitude of the surface EMG (AvgEMG) of the main agonist muscles acting on the bench press maximum isometric force exercise. Thirty subjects were randomly divided into three groups: static stretch (SG: 22.8±5.6 years, 176.6±3.5 cm, 74.4±5.9 kg), dynamic stretch (DG: 21.4±3.9 years, 178.4±7.2 cm, 71.7±8.2 kg) and control group (CG: 20.4±3.6 years, 179.8±5.8 cm, 74.4±9.8 kg). SG performed two 30‐s repetitions and DG performed 10 repetitions of each of the two different exercises for the pectoralis major and triceps brachii. The MIPF, TMIF, RFP and AvgEMG of the pectoralis major (sternocostal part) and triceps brachii (long and lateral head) were measured before and immediately after the stretching protocols. A significant decrease in the MIPF from pre‐ to post‐stretching was observed in both SG (p <0.001) and DG (p <0.05). No significant differences were found in the CG for all force parameters. No significant differences in the TMIF and RFP from pre‐ to post‐stretching were found in the three groups. The SG showed a significant (p <0.05) decrease in the AvgEMG of the three muscles, whereas no significant differences were found for the DG and CG. These findings suggest that a low‐volume static and dynamic stretching adversely affects efforts of muscle maximal strength of the upper limb muscles studied, but it does not seem to affect TMIF or RFP.
Length, width and centroid distance as measures of teams tactical performance in youth football
Authors: Folgado Hugo , Lemmink Koen A. P. M. , Frencken Wouter , Sampaio Jaime 
Published: October 2012

AbstractSmall‐sided games are commonly used in training and teaching contexts of football. However, few studies have focused on the tactical implications of this type of drills. The aim of this study is to identify how tactical collective behaviour varies with age in different small‐sided game formats. We investigated the in‐game field position in three different age groups of youth football players [under‐9 (n=10; age = 8.5±0.53), under‐11 (n=10; age = 10.4±0.52) and under‐13 (n=10; age = 12.7±0.48)], participating in two different small‐sided game conditions (GK + 3×3 + GK and GK + 4×4 + GK). A team variable was created based on the players’ length per width ratio (lpwratio), and a match variable was calculated as the distance between the centroid of the two teams. Results show that team variable values were influenced by the age of the players, as younger teams tend to present a higher value of lpwratio in their dispersion on the pitch. The variability of this variable also showed a decrease for teams with older players, suggesting a more consistent application of the width (stretching and creating space) and concentration (compressing into a confined area) principles of play and reflecting a higher level of collective tactical behaviour. Match variable showed a larger centroid distance for the older age groups in comparison with the younger players in the GK + 3×3 + GK, while all age groups demonstrated similar large centroid distances in the GK + 4×4 + GK game format. These results suggest that length and width ratio and centroid distance are useful measures of tactical performance in small‐sided games in youth football.
Opportunities for Building Social-Ecological Resilience in New Mexico Forest Communities
Authors: Roybal M. A. , Benson M. H. 
Published: October 2012

AbstractThe forest lands of northern New Mexico are a contested landscape fraught with conflicts over ownership, resource exploitation and land fraud. Partly in recognition of this, the US Forest Service established the Vallecitos Federal Sustained Yield in 1948 under the relatively obscure Sustained Yield Forest Management Act of 1944 to promote the “stability” of rural Hispano communities and the sustained yield of forest products. The Unit, however, has failed to live up to its promise. This paper explores the concept of resilience as a new way of looking at this ongoing conflict and examines its potential to support future policies for management of the Unit and other public lands.
Climate Change and Human Capital Accumulation: Educational Decisions under Resource Scarcity and Uncertainty
Authors: Ranjan Ram 
Published: October 2012

Abstract
Climate change is forcing large scale structural changes in agrarian sectors in the developing world by adversely affecting water resources and threatening the viability of future agriculture. In the most drought affected regions, farmers must explore alternative skills for themselves and their children when faced with unsustainable livelihoods. In this paper, a stylized decision model of skill acquisition is developed in which farmers face the risk of an irreversible loss of groundwater due to climate change. Findings indicate that the risk of groundwater loss promotes higher efforts towards skill acquisition, in general, but skill seeker's own learning capabilities play an important role in determining the eventual outcome. Additionally, groundwater resources are depleted to fund skill acquisition through education, but when rate of skill depreciation is large or differences between skilled wages and agricultural income are small, groundwater depletion is delayed. A non-linear relationship between skill acquisition and groundwater sustainability emerges.
Adaptive Management and Scale in a Flood-Pulsed Ecosystem—the Case of the Okavango Delta Management Plan, Botswana
Authors: Motsumi Sekgowa , Cassidy Lin 
Published: October 2012

AbstractThe flood pulse, as the main driver of Botswana's Okavango Delta system, creates variable responses in terms of its biophysical, socioeconomic aspects which presents challenges for its management. This, along with the perturbation caused by substantially increased human impacts in the last few decades, has led to the initiation of a systematic framework for management, the Okavango Delta Management Plan (ODMP). This paper analyses the extent to which the ODMP accommodates adaptive management principles in its implementation, and focuses on the scale aspects of institutional arrangements, still founded on administrative, not social-ecological, boundaries. Specifically, we examine the hierarchy of decision-making and highlight the challenges associated with scale mismatch. Centralized sectoral decision-making has prevented the ODMP being adopted as all parties' responsibility. Scale effects compound this, because decision-making at the national level challenges the implementing district level's efforts at transdisciplinary responses. Nevertheless, capacity-building on the ground means that district officers are increasingly adopting integrated, collaborative responses to management issues.
CLEVER: clique-enumerating variant finder
Authors: Marschall Tobias , Costa Ivan G. , Canzar Stefan , Bauer Markus , Klau Gunnar W. , Schliep Alexander , Schönhuth Alexander 
Published: October 2012

Abstract
Motivation: Next-generation sequencing techniques have facilitated a large-scale analysis of human genetic variation. Despite the advances in sequencing speed, the computational discovery of structural variants is not yet standard. It is likely that many variants have remained undiscovered in most sequenced individuals.
Results: Here, we present a novel internal segment size based approach, which organizes all, including concordant, reads into a read alignment graph, where max-cliques represent maximal contradiction-free groups of alignments. A novel algorithm then enumerates all max-cliques and statistically evaluates them for their potential to reflect insertions or deletions. For the first time in the literature, we compare a large range of state-of-the-art approaches using simulated Illumina reads from a fully annotated genome and present relevant performance statistics. We achieve superior performance, in particular, for deletions or insertions (indels) of length 20–100 nt. This has been previously identified as a remaining major challenge in structural variation discovery, in particular, for insert size based approaches. In this size range, we even outperform split-read aligners. We achieve competitive results also on biological data, where our method is the only one to make a substantial amount of correct predictions, which, additionally, are disjoint from those by split-read aligners.
Availability: CLEVER is open source (GPL) and available from http://clever-sv.googlecode.com.
Contact: as@cwi.nl or tm@cwi.nl
Supplementary information: Supplementary data are available at Bioinformatics online.