bluuebunny/crossref_metadata_2025_split huggingface dataset:
Potential role of tillage to increase soil organic carbon sequestration.
Authors: Chan K. Y. 
Published: May 2008

Abstract
The importance of soil organic carbon (SOC) in maintaining soil quality is well recognized and more recently there has been much interest in the role of soil as a carbon (C) sink for combating climate change. The impact of tillage on SOC sequestration is reviewed in the context of current knowledge of SOC stabilization mechanisms and soil structure relationships. The current tendency to make comparisons between no-tillage (NT) and conventional tillage of the surface soil, with the latter often ill-defined, is an oversimplification and neglects the potential role of tillage in increasing SOC storage. Research is needed to develop tillage practices that avoid/minimize SOC losses and increase the potential of SOC sequestration in protected forms, particularly in the subsoil layers. To advance this, the development of novel tillage implementation and practices in the context of managing SOC storage of whole soil profile are needed.
Heat stress in feedlot cattle.
Authors: Brown-Brandl T. M. 
Published: May 2008

Abstract
Heat stress in feedlot cattle is a common summertime occurrence in cattle-producing parts of the world (USA, Australia, Brazil, etc.). The impact of heat stress on feedlot animals is quite varied: from little to no effect in a brief exposure; to causing reductions in feed intake, growth, and well-being of the cattle in a moderate event; to death of vulnerable animals during an extreme event. The level of heat stress an animal experiences can be broken down into three primary factors: animal susceptibility, environmental conditions and management strategies. Each of these factors can also be broken down into different elements. This paper describes the physical and physiological processes that describe homeostasis along with factors affecting animal susceptibility, methods of summarizing environmental conditions and some management strategies that can be used to relieve stress.
Assessment and maintenance of soil fertility in temperate organic agriculture.
Authors: Watson C. A. , Stockdale E. A. , Rees R. M. 
Published: May 2008

Abstract
The maintenance of soil fertility is a key tenet of organic farming and can be broadly defined as the ability of the soil to support the productivity of the system. The central concept of soil fertility in these systems is the use of legume-based multi-annual rotations together with the judicious use of on-farm manures. Rotations provide the opportunity for nutrient elements to be replenished, usually within a grass-clover ley phase with inputs of carbon and nitrogen (by the biological processes of photosynthesis and nitrogen fixation). We review evidence that shows that this 'building phase' of the rotations is also associated with increased biological activity and changes to the soil's physical characteristics. The sequence of crops within a rotation is designed to utilize changing levels of fertility and optimize the utilization of nutrient resources over the period of the rotation. Crops with high nutrient demand would therefore normally be placed at a point following the incorporation of a nutrient-rich ley phase. In some circumstances cover crops or undersown vegetation are appropriate to conserve nutrients and reduce losses at particular times within the cropping sequence. Where necessary, a small range of carefully controlled external inputs are allowed. The best methods of assessing soil fertility in organic farming depend upon longer-term and integrative assessments of the system such as crop yields or long-term changes in soil quality and organic matter rather than snapshot measurements of individual nutrient pools.
Transgenic approaches to mastitis.
Authors: Maga E. A. 
Published: May 2008

Abstract

Mastitis is an important disease affecting the dairy industry both in terms of animal welfare and the costs associated with treating the illness. Many mastitis prevention procedures are in place such as teat dipping, line cleaning and dry cow antibiotic treatments, yet mastitis is still common in most herds. The use of antibiotics to treat infected cows also poses concerns of having antibiotic residues in milk and the development of antibiotic resistance. In fact, one of the major mastitis-causing pathogens,
Staphylococcus aureus
, is resistant to treatment. To date, efforts have been focused on producing vaccines to combat mastitis but have yet to be successful. Another approach to fight mastitis is the use of genetic engineering to produce antimicrobial compounds in the mammary gland. Work along this line has been going on since the early 1990s, starting in mouse models and leading to the report of the production of transgenic cattle resistant to
S. aureus
mastitis in 2005. This review will focus on the past and present works conducted with transgenic animals and their potential and hurdles as a novel approach to fight mastitis.
MAPPING EUROPEAN IDEOSCAPES
Authors: Mihelj Sabina , Koenig Thomas , Downey John , Štetka Václav 
Published: May 2008

ABSTRACT
Despite embracing the rhetoric of transnational flows and networks, comparative research on media content continues to fall prey to methodological nationalism. When it comes to empirical measurement, researchers often, despite their best intentions, fall back on techniques that assume that the discourses circulating within particular nationally bounded communicative spaces are homogenous. In this article, we developed a set of propositions and analytical approaches that should help to overcome this impasse, and used them to examine the newspaper debates on the EU Constitutional Treaty in seven European states: the Czech Republic, Germany, France, the Slovak Republic, Slovenia, Switzerland, and the UK. We suggested that instead of focusing solely on comparisons between nationally bounded communicative spheres, we should also look at differences between class-related communicative spaces. By adopting such an approach, we can acknowledge both sub-national segmentations of communicative spaces and transnational linkages, while at the same time not losing sight of the importance of the national. The results support our initial contention that the research on European mass communication ought to move beyond comparisons between national units and the levels of their respective Europeanization, and examine how European issues are conveyed in media catering to different social classes.
Swelfe: a detector of internal repeats in sequences and structures
Authors: Abraham Anne-Laure , Rocha Eduardo P. C. , Pothier Joël 
Published: May 2008

Abstract
Summary: Intragenic duplications of genetic material have important biological roles because of their protein sequence and structural consequences. We developed Swelfe to find internal repeats at three levels. Swelfe quickly identifies statistically significant internal repeats in DNA and amino acid sequences and in 3D structures using dynamic programming. The associated web server also shows the relationships between repeats at each level and facilitates visualization of the results.
Availability: http://bioserv.rpbs.jussieu.fr/swelfe
Contact: annela@abi.snv.jussieu.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
Penalized estimation of haplotype frequencies
Authors: Ayers Kristin L. , Lange Kenneth 
Published: May 2008

AbstractMotivation: Low haplotype diversity and linkage disequilibrium are the rule in short genomic segments. This fact suggests that parsimony should be enforced in estimation of haplotype frequencies. The current article introduces a diversity penalty that automatically discards potential haplotypes with low explanatory power. The standard EM algorithm for haplotype frequency estimation can accommodate the penalty if one passes over to a more general minorize–maximize (MM) scheme for estimation.Results: Our new MM algorithm converges in fewer iterations, eliminates marginal haplotypes from further consideration and reduces the computational complexity of each iteration. Estimation by the MM algorithm also improves haplotyping and genotype imputation compared to naive application of the EM algorithm. Thus, the MM algorithm is a useful substitute for the EM algorithm. Compared to the most sophisticated current methods of haplotyping and genotype imputation, the MM algorithm is slightly less accurate but at least an order of magnitude faster.Availability: Our software will be made available in the next release the program Mendel at http://www.genetics.ucla.edu/software/.Contact: kayers@ucla.edu
Prerecruit survival and recruitment of northern Gulf of St Lawrence Atlantic cod
Authors: Duplisea Daniel E. , Robert Dominique 
Published: May 2008

Abstract
Duplisea, D. E., and Robert, D. 2008. Prerecruit survival and recruitment of northern Gulf of St Lawrence Atlantic cod. – ICES Journal of Marine Science, 65: 946–952. Recruitment (R) of exploited marine fish populations is usually modelled exclusively as a function of spawning-stock biomass (SSB). A problem arising when modelling over long time-series is that the nature of the R–SSB relationship is unlikely to be stationary. Changes are often interpreted as productivity regime shifts and are linked to alterations in prerecruit survival rate. We examine the role of environment and predation by fish and harp seals as factors affecting the R–SSB relationship in the northern Gulf of St Lawrence cod, by fitting linear models using combinations of covariates to explain cod prerecruit survival. The most parsimonious model (based on a Bayesian Information Criterion, BIC) included cod, mackerel, and temperature, whereas redfish and seals did not appear in any of the best-fit models. Recruitment models derived from this analysis could be used in operating models for management strategy evaluation simulations for northern Gulf cod, so one could develop harvest control rules that are robust to changes in recruitment productivity regimes.
Methane, oxygen, photosynthesis, rubisco and the regulation of the air through time
Authors: Nisbet Euan G , Nisbet R. Ellen R 
Published: May 2008

Rubisco I's specificity, which today may be almost perfectly tuned to the task of cultivating the global garden, controlled the balance of carbon gases and O
2
in the Precambrian ocean and hence, by equilibration, in the air. Control of CO
2
and O
2
by rubisco I, coupled with CH
4
from methanogens, has for the past 2.9 Ga directed the global greenhouse warming, which maintains liquid oceans and sustains microbial ecology.

Both rubisco compensation controls and the danger of greenhouse runaway (e.g. glaciation) put limits on biological productivity. Rubisco may sustain the air in either of two permissible stable states:
either
an anoxic system with greenhouse warming supported by both high methane mixing ratios as well as carbon dioxide,
or
an oxygen-rich system in which CO
2
largely fulfils the role of managing greenhouse gas, and in which methane is necessarily only a trace greenhouse gas, as is N
2
O. Transition from the anoxic to the oxic state risks glaciation. CO
2
build-up during a global snowball may be an essential precursor to a CO
2
-dominated greenhouse with high levels of atmospheric O
2
.

Photosynthetic and greenhouse-controlling competitions between marine algae, cyanobacteria, and terrestrial C3 and C4 plants may collectively set the CO
2
: O
2
ratio of the modern atmosphere (last few million years ago in a mainly glacial epoch), maximizing the productivity close to rubisco compensation and glacial limits.
SOMNUS, a CCCH-Type Zinc Finger Protein inArabidopsis, Negatively Regulates Light-Dependent Seed Germination Downstream of PIL5
Authors: Kim Dong Hwan , Yamaguchi Shinjiro , Lim Soohwan , Oh Eunkyoo , Park Jeongmu , Hanada Atsushi , Kamiya Yuji , Choi Giltsu 
Published: May 2008

AbstractLight absorbed by seed phytochromes of Arabidopsis thaliana modulates abscisic acid (ABA) and gibberellic acid (GA) signaling pathways at least partly via PHYTOCHROME-INTERACTING FACTOR3-LIKE5 (PIL5), a phytochrome-interacting basic helix-loop-helix transcription factor. Here, we report a new mutant, somnus (som), that germinates in darkness, independently of various light regimens. SOM encodes a nucleus-localized CCCH-type zinc finger protein. The som mutant has lower levels of ABA and elevated levels of GA due to expressional changes in ABA and GA metabolic genes. Unlike PIL5, however, SOM does not regulate the expression of GA-INSENSITIVE and REPRESSOR OF GA1 (RGA/RGA1), two DELLA genes encoding GA negative signaling components. Our in vivo analysis shows that PIL5 activates the expression of SOM by binding directly to its promoter, suggesting that PIL5 regulates ABA and GA metabolic genes partly through SOM. In agreement with these results, we also observed that the reduced germination frequency of a PIL5 overexpression line is rescued by the som mutation and that this rescue is accompanied by expressional changes in ABA and GA metabolic genes. Taken together, our results indicate that SOM is a component in the phytochrome signal transduction pathway that regulates hormone metabolic genes downstream of PIL5 during seed germination.
Are there genetic influences on addiction: evidence from family, adoption and twin studies
Authors: Agrawal Arpana , Lynskey Michael T. 
Published: May 2008

ABSTRACTAims  In this exciting era of gene discovery, we review evidence from family, adoption and twin studies that examine the genetic basis for addiction. With a focus on the classical twin design that utilizes data on monozygotic and dizygotic twins, we discuss support in favor of heritable influences on alcohol, nicotine, cannabis and other illicit drug dependence.Methods  We review whether these genetic factors also influence earlier stages (e.g. experimentation) of the addictive process and whether there are genetic influences specific to each psychoactive substance.Results  Converging evidence from these studies supports the role of moderate to high genetic influences on addiction with estimates ranging from 0.30 to 0.70. The changing role of these heritable factors as a function of gender, age and cultural characteristics is also discussed. We highlight the importance of the interplay between genes and the environment as it relates to risk for addiction and the utility of the children‐of‐twins design for emerging studies of gene–environment interaction is presented.Conclusions  Despite the advances being made by low‐cost high‐throughput whole genome association assays, we posit that information garnered from twin studies, especially extended twin designs with power to examine gene–environment interactions, will continue to form the foundation for genomic research.
Contingency management reduces drug‐related human immunodeficiency virus risk behaviors in cocaine‐abusing methadone patients
Authors: Hanson Tressa , Alessi Sheila M. , Petry Nancy M. 
Published: May 2008

ABSTRACTAim  Contingency management (CM) is efficacious in reducing drug use. This study examined whether CM also reduces human immunodeficiency virus (HIV) risk behaviors and if these effects are mediated by longest duration of abstinence achieved during treatment.Design  Data were analyzed from a subset of participants in a combined data set of three published randomized controlled trials of CM treatments.Setting  A community‐based methadone maintenance clinic.Participants  One‐hundred and sixty‐five cocaine‐abusing methadone maintenance patients.Intervention  Participants received either standard methadone treatment or standard methadone treatment with CM for 3 months.Measurements  The HIV Risk Behavior Scale (HRBS) was administered prior to randomization to a study condition and 3 months after the study treatments ended. The primary objective indicator of drug use was longest duration of cocaine and opioid abstinence achieved during treatment.Findings  Relative to those assigned to standard care, participants receiving CM significantly decreased overall HIV risk behaviors and injection drug use risk behaviors. CM participants also achieved longer durations of consecutive cocaine and opioid abstinence during treatment. Duration of abstinence achieved mediated the relationship between treatment condition and HRBS difference scores.Conclusions  These results suggest that CM treatment reduces HIV drug use risk behaviors in cocaine‐abusing methadone maintenance patients.
Effects of behavioral intervention on substance use among people living with HIV: the Healthy Living Project randomized controlled study
Authors: Wong F. Lennie , Rotheram‐Borus Mary Jane , Lightfoot Marguerita , Pequegnat Willo , Comulada W. Scott , Cumberland William , Weinhardt Lance S. , Remien Robert H. , Chesney Margaret , Johnson Mallory ,   Healthy Living Trial Group
Published: May 2008

ABSTRACTAim  Reductions in substance use were examined in response to an intensive intervention with people living with human immunodeficiency virus (HIV) (PLH).Design, setting and participants  A randomized controlled trial was conducted with 936 PLH who had recently engaged in unprotected sexual risk acts recruited from four US cities: Milwaukee, San Francisco, New York and Los Angeles. Substance use was assessed as the number of days of use of 19 substances recently (over the last 90 days), evaluated at 5‐month intervals over 25 months.Intervention  A 15‐session case management intervention was delivered to PLH in the intervention condition; the control condition received usual care.Measurements  An intention‐to‐treat analysis was conducted examining reductions on multiple indices of recent substance use calculated as the number of days of use.Findings  Reductions in recent substance use were significantly greater for intervention PLH compared to control PLH: alcohol and/or marijuana use, any substance use, hard drug use and a weighted index adjusting for seriousness of the drug. While the intervention‐related reductions in substance use were larger among women than men, men also reduced their use. Compared to controls, gay and heterosexual men in the intervention reduced significantly their use of alcohol and marijuana, any substance, stimulants and the drug severity‐weighted frequency of use index. Gay men also reduced their hard drug use significantly in the intervention compared to the control condition.Conclusions  A case management intervention model, delivered individually, is likely to result in significant and sustained reductions in substance use among PLH.
The search for reference conditions for stream vegetation in northern Europe
Authors: BAATTRUP‐PEDERSEN ANNETTE , SPRINGE GUNTA , RIIS TENNA , LARSEN SØREN E. , SAND‐JENSEN KAJ , KJELLERUP LARSEN LARS M. 
Published: May 2008

Summary1. The European Water Framework Directive provides a framework for improving the ecological quality of stream ecosystems, with deviation from reference used as a measure of ecological status.2. Here we examine the possibility of using less impacted stream sites from Latvia, Lithuania and Poland to establish a Danish reference network for macrophyte assemblages, and as a guiding image for identification of possible references sites within Denmark. Both approaches were evaluated using historical Danish records.3. Four different macrophyte assemblages were identified for mid‐sized streams in the Central and Eastern Lowland ecoregions. Macrophyte assemblages could not be delineated using physical stream site characteristics; however a gradual change in assemblage composition was attributed to differences in alkalinity and human impact.4. Assemblages of contemporary vegetation in Denmark were quite similar to those found in Polish, Latvian and Lithuanian streams (26–35%). However, more importantly, from species‐based predictions we noted higher similarity, particularly with Latvian and Lithuanian streams, before intensive land use commenced in Denmark (c. 1900). These results show that stream sites from these three countries can be considered in a Danish reference network.5. Two of the four macrophyte assemblages comprised species such as Fontinalis antipyretica, Myriophyllum spicatum, Nuphar lutea, Potamogeton alpinus and P. perfoliatus that have a very scattered occurrence in the contemporary vegetation in Denmark. These groups were closely associated with the predictions from historic records, thereby lending support the conjecture that these assemblages could be part of the guiding image for the identification of potential reference sites within Denmark.
Wetlands as barriers: effects of vegetated waterways on downstream dispersal of zebra mussels
Authors: BODAMER BETSY L. , BOSSENBROEK JONATHAN M. 
Published: May 2008

Summary1. Stream flow is a major vector for zebra mussel spread among inland lakes. Veligers have been found tens to hundreds of km from upstream source lakes in unvegetated stream and river systems. It has been suggested, however, that the downstream transport of zebra mussels is restricted by wetland ecosystems. We hypothesized that vegetated waterways, (i.e. wetland streams) would hinder the downstream dispersal of zebra mussels in connected inland lake systems.2. Veliger abundance, recruitment and adult mussels were surveyed in four lake‐wetland systems in southeastern Michigan, U.S.A. from May to August 2006. Sampling was conducted downstream of the lakes invaded by zebra mussels, beginning at the upstream edge of aquatic vegetation and continuing downstream through the wetland streams.3. Veliger abundance decreased rapidly in vegetated waterways compared to previously reported rates of decrease in non‐vegetated streams. Veligers were rarely found more than 1 km downstream from where vegetation began. Newly recruited individuals and adults were extremely rare beyond open water in the wetland systems.4. Densely vegetated aquatic ecosystems limit the dispersal of zebra mussels downstream from invaded sources. Natural, remediated and constructed wetlands may therefore serve as a protective barrier to help prevent the spread of zebra mussels and other aquatic invasive species to other lakes and ecosystems.
Diffraction imaging in depth
Authors: Moser T.J. , Howard C.B. 
Published: May 2008

ABSTRACTHigh resolution imaging is of great value to an interpreter, for instance to enable identification of small scale faults, and to locate formation pinch‐out positions. Standard approaches to obtain high‐resolution information, such as coherency analysis and structure‐oriented filters, derive attributes from stacked, migrated images. Since they are image‐driven, these techniques are sensitive to artifacts due to an inadequate migration velocity; in fact the attribute derivation is not based on the physics of wave propagation. Diffracted waves on the other hand have been recognized as physically reliable carriers of high‐ or even super‐resolution structural information. However, high‐resolution information, encoded in diffractions, is generally lost during the conventional processing sequence, indeed migration kernels in current migration algorithms are biased against diffractions. We propose here methods for a diffraction‐based, data‐oriented approach to image resolution. We also demonstrate the different behaviour of diffractions compared to specular reflections and how this can be leveraged to assess characteristics of subsurface features. In this way a rough surface such as a fault plane or unconformity may be distinguishable on a diffraction image and not on a traditional reflection image.We outline some characteristic properties of diffractions and diffraction imaging, and present two novel approaches to diffraction imaging in the depth domain. The first technique is based on reflection focusing in the depth domain and subsequent filtering of reflections from prestack data. The second technique modifies the migration kernel and consists of a reverse application of stationary‐phase migration to suppress contributions from specular reflections to the diffraction image. Both techniques are proposed as a complement to conventional full‐wave pre‐stack depth migration, and both assume the existence of an accurate migration velocity.