bluuebunny/crossref_metadata_2025_split huggingface dataset:
How to achieve resilience as an older widower: turning points or gradual change?
Authors: BENNETT KATE M. 
Published: January 2010

ABSTRACTThe paper draws together two conceptualisations of resilience in bereavement and widowhood that were developed by Bonanno (2004) and Moore and Stratton (2003), both using North American data. This paper has re-examined data from two United Kingdom studies of widowerhood. Among an aggregate sample of 60 widowers, 38 per cent showed resilience in the face of the exacting challenges that late-life widowhood brings. Resilient men were seen as having a positively viewed biography, were participating in relationships and activities, and had returned to a life that had meaning and brought satisfaction. Four broad categories among the resilient widowers were identified. The first had been resilient consistently throughout their widowhood. The second group achieved resilience gradually, and the third following a turning point. Finally, a small group of men demonstrated both gradual and turning point pathways towards resilience. Personal characteristics had been particularly influential for those in the first group, while for the last group, social support had made an important contribution to achieving resilience and had two forms: informal and formal. The paper concludes with a discussion of the implications of the differentiation of resilience for adaptation to bereavement amongst older men.
Time and money volunteering among older adults: the relationship between past and current volunteering and correlates of change and stability
Authors: CHOI NAMKEE G. , CHOU RITA JING-ANN 
Published: January 2010

ABSTRACTUsing data from the first and second waves of the Survey of Midlife Development in the United States – MIDUS1 1995–1996 and MIDUS2 2004–2006, this paper examines the relationship between the extent of time and money volunteering among people aged 55 or more years at baseline and those of the same age nine years later. Following an analysis of the changes and stability in volunteering status, the paper examines the relationships between change or stability in volunteering and various socio-demographic attributes of the respondents and measures of their human capital, cultural capital and social capital. A majority of older volunteers of time and/or money were repeat volunteers, and the extent of volunteering at the start of the studied period was one of the most significant predictors of the extent of volunteering nine years later. The level of education was a consistent predictor of the extent of both time and money volunteering and of new engagement and stability in volunteering. Social network size, or social connectedness, represented by the number of various meetings attended, was a significant predictor not only of the hours of time volunteering, but also of new engagement and stability in both time and money volunteering. A high degree of religious identification also appeared to be a motivation for money volunteering and to affect the value of donations. The paper concludes by discussing the implications of the findings for the recruitment and retention of volunteers.
Perceptions and expectations of pension savings adequacy: a comparative study of Dutch and American workers
Authors: VAN DALEN HENDRIK P. , HENKENS KÈNE , HERSHEY DOUGLAS A. 
Published: January 2010

ABSTRACTWhat drives the perceptions of pension savings adequacy and what do workers expect to receive when they retire? These questions are assessed among married workers using an identical survey distributed to Dutch and American workers in 2007. Despite marked differences in expected pension replacement rates – where the Dutch replacement rates are systematically higher than the American rates – the perceived savings adequacy is more or less the same across Dutch and American workers. In both countries, about half of the respondents were confident they had amassed sufficient retirement savings. Individuals' perceived savings adequacy was found to be influenced by three groups of factors: trust in pension institutions (pension funds, banks, insurance companies and governments), social forces and psychological dispositions. This study shows that differences in the dispositions of workers (with respect to future orientation and financial planning) played a far larger role in explaining differences in perceptions of savings adequacy in the United States than in The Netherlands. Dutch workers rely and trust their pension fund and seem to leave thinking about and planning for retirement to its managers.
Relativistic and ponderomotive effects on evolution of laser beam in a non-uniform plasma channel
Authors: Gill T.S. , Mahajan R. , Kaur R. 
Published: January 2010

AbstractThe nonlinear parabolic partial differential equation governing the evolution of the complex envelope in the slowly varying envelope approximation is solved using the variational approach. The basic nonlinear phenomena of relativistic and ponderomotive self-focusing in a plasma channel are taken into account. Self-focusing, self-phase modulation as well as self-trapping of laser beam is studied in a variety of situations. Further, in the absence of dissipation mechanisms, the stability of the beam is also studied.
Generation of attosecond X-ray pulses via Thomson scattering of counter-propagating laser pulses
Authors: Liu L. , Xia C.-Q. , Liu J.-S. , Wang W.-T. , Cai Y. , Wang C. , Li R.-X. , Xu Z.-Z. 
Published: January 2010

AbstractIt is proposed that single attosecond pulses be generated via electron's Thomson scattering of two counter-propagating laser pulses. In the case of linear polarization, the generation of a single attosecond pulse is highly sensitive to the carrier envelope phase (CEP). However, in the case of circular polarization, it is completely independent on the CEP, which will make circular polarization favorable to generate a stable attosecond X-ray pulse. For either linear or circular polarization, the radiation obtained by using two counter-propagating pulses can be much more intense than that obtained by only using one of these two pulses.
Radiative reaction effect on electron dynamics in an ultra intense laser field
Authors: Mao Q.Q. , Kong Q. , Ho Y.K. , Che H.O. , Ban H.Y. , Gu Y.J. , Kawata S. 
Published: January 2010

AbstractThe radiative reaction effect of an electron is usually very small and can be neglected in most cases. But for an ultra intensity laser-electron interaction region, the radiation can become large. The influence of the radiative reaction effect of an electron interacting with an ultra intense laser pulses in vacuum on electron dynamics is investigated within the classical relativistic Lorentz-Dirac approach. A predictor-corrector method is proposed to numerically solve the equation of motion with the electron radiative reaction included. We study the counter-propagating case (for Thomson scattering scheme) and the same direction propagating cases (for laser acceleration). Our simulation results show that radiation can have great effect in the counter-propagating case. But in the vacuum laser electron acceleration regime, both the ponderomotive acceleration scenario case and the capture and acceleration scenario, radiative reaction effect can totally be ignored for laser intensity available presently or in the near-future.
Comparison of the anaerobic microbiota of deep-water Geodia spp. and sandy sediments in the Straits of Florida
Authors: Brück Wolfram M , Brück Thomas B , Self William T , Reed John K , Nitecki Sonja S , McCarthy Peter J 
Published: January 2010

Abstract
Marine sediments and sponges may show steep variations in redox potential, providing niches for both aerobic and anaerobic microorganisms. Geodia spp. and sediment specimens from the Straits of Florida were fixed using paraformaldehyde and 95% ethanol (v/v) for fluorescence in situ hybridization (FISH). In addition, homogenates of sponge and sediment samples were incubated anaerobically on various cysteine supplemented agars. FISH analysis showed a prominent similarity of microbiota in sediments and Geodia spp. samples. Furthermore, the presence of sulfate-reducing and annamox bacteria as well as other obligate anaerobic microorganisms in both Geodia spp. and sediment samples were also confirmed. Anaerobic cultures obtained from the homogenates allowed the isolation of a variety of facultative anaerobes, primarily Bacillus spp. and Vibrio spp. Obligate anaerobes such as Desulfovibrio spp. and Clostridium spp. were also found. We also provide the first evidence for a culturable marine member of the Chloroflexi, which may enter into symbiotic relationships with deep-water sponges such as Geodia spp. Resuspended sediment particles, may provide a source of microorganisms able to associate or form a symbiotic relationship with sponges.
Experimental factors affecting PCR-based estimates of microbial species richness and evenness
Authors: Engelbrektson Anna , Kunin Victor , Wrighton Kelly C , Zvenigorodsky Natasha , Chen Feng , Ochman Howard , Hugenholtz Philip 
Published: January 2010

Abstract
Pyrosequencing of 16S rRNA gene amplicons for microbial community profiling can, for equivalent costs, yield more than two orders of magnitude more sensitivity than traditional PCR cloning and Sanger sequencing. With this increased sensitivity and the ability to analyze multiple samples in parallel, it has become possible to evaluate several technical aspects of PCR-based community structure profiling methods. We tested the effect of amplicon length and primer pair on estimates of species richness (number of species) and evenness (relative abundance of species) by assessing the potentially tractable microbial community residing in the termite hindgut. Two regions of the 16S rRNA gene were sequenced from one of two common priming sites, spanning the V1–V2 or V8 regions, using amplicons ranging in length from 352 to 1443 bp. Our results show that both amplicon length and primer pair markedly influence estimates of richness and evenness. However, estimates of species evenness are consistent among different primer pairs targeting the same region. These results highlight the importance of experimental methodology when comparing diversity estimates across communities.
Implementation Methods for Estimating Haplotypes with Grid Computing Technology
Authors: Muhammad Zafri , KC Sanjaya , Kia Kien Phua 
Published: January 2010

AbstractIntroduction: PHASE is a software for haplotype reconstruction and recombination rate estimation from population data and implements the methods for estimating haplotypes from population genotype data. This software require enormous computing power due to the complexity algorithms used. Recent advancement in grid computing and multi-core processing technology has resulted in the creating of virtual supercomputers (that are capable of massive parallel computations).
Method:
PHASE version 2.0 was downloaded from PHASE’s homepage (http://stephenslab.uchicago.edu/software.html), and installed on 10 Apple iMac computers (20 CPUs) running Mac OS 10.5 using Apple™ Xserve as a controller. A PHP web-based application was developed to enable easy job submission and result retrieval. Haplotype estimation jobs for PHASE were submitted using a web browser running either from Windows®, Linux® or Macintosh™ OS 10.5 operating systems. Jobs consisting of 20 input files of genomic loci (SNPs) were submitted to the Xgrid via the controller and the job completion time for each run were recorded and compared.

Results:
The job completion time for estimating 20 input files and returning the results to the controller using XGrid (20 CPUs) took 4,980 seconds compared with 58,800 seconds using a single computer (2 CPUs), representing 91.5% reduction in computing time.
Impacts of Minimum Quality Standards Imposed Through Marketing Orders or Related Producer Organizations
Authors: Saitone Tina L. , Sexton Richard J. 
Published: January 2010

AbstractWe analyze the impacts of minimum quality standards (MQS) imposed by producers acting collectively through a producer organization, such as a marketing order. MQS imposed in a competitive market can never enhance social welfare because in general an MQS creates two deadweight losses—one due to inefficient enhancement of product quality and a second due to wastage of the low‐quality product. Any MQS that a competitive industry implements based upon a profit criterion causes all consumers in the market to be harmed. However, an MQS may be preferred relative to supply control as a second‐best instrument for transferring income to producers.
Do Economic Variables Follow Scale or Location‐Scale Distributions?
Authors: Antle John M. 
Published: January 2010

AbstractEconomics researchers often assume that random variables are drawn from distributions that are members of scale or location‐scale families of distributions. This article generalizes earlier results in the literature on the bias in least squares estimates of multiplicative error models, and uses those results to construct a test of the scale and location‐scale hypotheses. A Monte Carlo simulation shows that the test is powerful in large samples. The empirical relevance of these findings is illustrated with estimates of a supply function for U.S. wheat production. Implications for applied economics research are discussed.
Estimating Griliches' k‐Shifts
Authors: Fulginiti Lilyan E. 
Published: January 2010

AbstractGriliches' k‐shift, a crucial parameter in the welfare evaluation of technological change, is shown to be equal to the radial rate of technological change plus a vector of commodity bias parameters obtained from the distance function. The analysis permits decomposition of sectoral productivity growth into productivity growth by commodity. The k‐shifts estimated for wheat, corn, soybeans, and beef in U.S. agriculture indicate a decrease in the marginal cost of production of corn, soybeans, and wheat during the 1950–1993 years.
Producer Protection Legislation and Termination Damages in the Presence of Contracting Frictions
Authors: Wu Steven Y. 
Published: January 2010

AbstractThis study models producer protection legislation (PPL) that would grant growers the right to claim damages if their contracts are prematurely terminated. In the absence of contracting frictions that prevent contractors from redesigning contracts to accommodate exogenous policy changes, producer protection legislation damages (PPLD) would not be distortionary or redistributive. If contracting frictions exist, then PPLD would have efficiency and redistributive effects, though the direction and magnitude depends on the size of PPL damages vis‐à‐vis expected damages under existing contract law. This study clarifies the conditions under which PPLD would decrease efficiency and protect growers.
Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALS
Authors: Greene Casey S. , Sinnott-Armstrong Nicholas A. , Himmelstein Daniel S. , Park Paul J. , Moore Jason H. , Harris Brent T. 
Published: January 2010

Abstract
Motivation: Epistasis, the presence of gene–gene interactions, has been hypothesized to be at the root of many common human diseases, but current genome-wide association studies largely ignore its role. Multifactor dimensionality reduction (MDR) is a powerful model-free method for detecting epistatic relationships between genes, but computational costs have made its application to genome-wide data difficult. Graphics processing units (GPUs), the hardware responsible for rendering computer games, are powerful parallel processors. Using GPUs to run MDR on a genome-wide dataset allows for statistically rigorous testing of epistasis.
Results: The implementation of MDR for GPUs (MDRGPU) includes core features of the widely used Java software package, MDR. This GPU implementation allows for large-scale analysis of epistasis at a dramatically lower cost than the standard CPU-based implementations. As a proof-of-concept, we applied this software to a genome-wide study of sporadic amyotrophic lateral sclerosis (ALS). We discovered a statistically significant two-SNP classifier and subsequently replicated the significance of these two SNPs in an independent study of ALS. MDRGPU makes the large-scale analysis of epistasis tractable and opens the door to statistically rigorous testing of interactions in genome-wide datasets.
Availability: MDRGPU is open source and available free of charge from http://www.sourceforge.net/projects/mdr.
Contact: jason.h.moore@dartmouth.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes
Authors: Otto Thomas Dan , Catanho Marcos , Tristão Cristian , Bezerra Márcia , Fernandes Renan Mathias , Elias Guilherme Steinberger , Scaglia Alexandre Capeletto , Bovermann Bill , Berstis Viktors , Lifschitz Sergio , de Miranda Antonio Basílio , Degrave Wim 
Published: January 2010

Abstract
Motivation: Many analyses in modern biological research are based on comparisons between biological sequences, resulting in functional, evolutionary and structural inferences. When large numbers of sequences are compared, heuristics are often used resulting in a certain lack of accuracy. In order to improve and validate results of such comparisons, we have performed radical all-against-all comparisons of 4 million protein sequences belonging to the RefSeq database, using an implementation of the Smith–Waterman algorithm. This extremely intensive computational approach was made possible with the help of World Community Grid™, through the Genome Comparison Project. The resulting database, ProteinWorldDB, which contains coordinates of pairwise protein alignments and their respective scores, is now made available. Users can download, compare and analyze the results, filtered by genomes, protein functions or clusters. ProteinWorldDB is integrated with annotations derived from Swiss-Prot, Pfam, KEGG, NCBI Taxonomy database and gene ontology. The database is a unique and valuable asset, representing a major effort to create a reliable and consistent dataset of cross-comparisons of the whole protein content encoded in hundreds of completely sequenced genomes using a rigorous dynamic programming approach.
Availability: The database can be accessed through http://proteinworlddb.org
Contact: otto@fiocruz.br
Protein secondary structure appears to be robust underin silicoevolution while protein disorder appears not to be
Authors: Schaefer Christian , Schlessinger Avner , Rost Burkhard 
Published: January 2010

AbstractMotivation: The mutation of amino acids often impacts protein function and structure. Mutations without negative effect sustain evolutionary pressure. We study a particular aspect of structural robustness with respect to mutations: regular protein secondary structure and natively unstructured (intrinsically disordered) regions. Is the formation of regular secondary structure an intrinsic feature of amino acid sequences, or is it a feature that is lost upon mutation and is maintained by evolution against the odds? Similarly, is disorder an intrinsic sequence feature or is it difficult to maintain? To tackle these questions, we in silico mutated native protein sequences into random sequence-like ensembles and monitored the change in predicted secondary structure and disorder.Results: We established that by our coarse-grained measures for change, predictions and observations were similar, suggesting that our results were not biased by prediction mistakes. Changes in secondary structure and disorder predictions were linearly proportional to the change in sequence. Surprisingly, neither the content nor the length distribution for the predicted secondary structure changed substantially. Regions with long disorder behaved differently in that significantly fewer such regions were predicted after a few mutation steps. Our findings suggest that the formation of regular secondary structure is an intrinsic feature of random amino acid sequences, while the formation of long-disordered regions is not an intrinsic feature of proteins with disordered regions. Put differently, helices and strands appear to be maintained easily by evolution, whereas maintaining disordered regions appears difficult. Neutral mutations with respect to disorder are therefore very unlikely.Contact: schaefer@rostlab.orgSupplementary Information: Supplementary data are available at Bioinformatics online.
NEMO: a tool for analyzing gene and chromosome territory distributions from 3D-FISH experiments
Authors: Iannuccelli E. , Mompart F. , Gellin J. , Lahbib-Mansais Y. , Yerle M. , Boudier T. 
Published: January 2010

Abstract
Summary: Three-dimensional fluorescence in situ hybridization (3D-FISH) is used to study the organization and the positioning of chromosomes or specific sequences such as genes or RNA in cell nuclei. Many different programs (commercial or free) allow image analysis for 3D-FISH experiments. One of the more efficient open-source programs for automatically processing 3D-FISH microscopy images is Smart 3D-FISH, an ImageJ plug-in designed to automatically analyze distances between genes. One of the drawbacks of Smart 3D-FISH is that it has a rather basic user interface and produces its results in various text and image files thus making the data post-processing step time consuming. We developed a new Smart 3D-FISH graphical user interface, NEMO, which provides all information in the same place so that results can be checked and validated efficiently. NEMO gives users the ability to drive their experiments analysis in either automatic, semi-automatic or manual detection mode. We also tuned Smart 3D-FISH to better analyze chromosome territories.
Availability: NEMO is a stand-alone Java application available for Windows and Linux platforms. The program is distributed under the creative commons licence and can be freely downloaded from https://www-lgc.toulouse.inra.fr/nemo
Contact: eddie.iannuccelli@toulouse.inra.fr
Random distance dependent attachment as a model for neural network generation in the Caenorhabditis elegans
Authors: Itzhack Royi , Louzoun Yoram 
Published: January 2010

Abstract
Motivation: The topology of the network induced by the neurons connectivity's in the Caenorhabditis elegans differs from most common random networks. The neurons positions of the C.elegans have been previously explained as being optimal to induce the required network wiring. We here propose a complementary explanation that the network wiring is the direct result of a local stochastic synapse formation process.
Results: We show that a model based on the physical distance between neurons can explain the C.elegans neural network structure, specifically, we demonstrate that a simple model based on a geometrical synapse formation probability and the inhibition of short coherent cycles can explain the properties of the C.elegans' neural network. We suggest this model as an initial framework to discuss neural network generation and as a first step toward the development of models for more advanced creatures. In order to measure the circle frequency in the network, a novel graph-theory circle length measurement algorithm is proposed.
Contact: royi.its@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.