bluuebunny/crossref_metadata_2025 huggingface dataset:
Tropical Rainfall Variability on Interannual-to-Interdecadal and Longer Time Scales Derived from the GPCP Monthly Product
Authors: Gu Guojun , Adler Robert F. , Huffman George J. , Curtis Scott
Published: August 2007

Global and large regional rainfall variations and possible long-term changes are examined using the 27-yr (1979–2005) Global Precipitation Climatology Project (GPCP) monthly dataset. Emphasis is placed on discriminating among variations due to ENSO, volcanic events, and possible long-term climate changes in the Tropics. Although the global linear change of precipitation in the dataset is near zero during the time period, an increase in tropical rainfall is noted in the dataset, with a weaker decrease over Northern Hemisphere middle latitudes. Focusing on the Tropics (25°S–25°N), the dataset indicates an upward linear change (0.06 mm day−1 decade−1) and a downward linear change (−0.01 mm day−1 decade−1) over tropical ocean and land, respectively. This corresponds to an about 5.5% increase (ocean) and 1% decrease (land) during the entire 27-yr time period. The year 2005 has the largest annual tropical total precipitation (land plus ocean) for the GPCP record. The five highest years are (in descending order) 2005, 2004, 1998, 2003, and 2002. For tropical ocean the five highest years are 1998, 2004, 2005, 2002, and 2003.

Techniques are applied to isolate and quantify variations due to ENSO and two major volcanic eruptions during the time period (El Chichón, March 1982; Mount Pinatubo, June 1991) in order to examine longer-time-scale changes. The ENSO events generally do not impact the tropical total rainfall, but rather induce significant anomalies with opposite signs over tropical land and ocean. The impact of the two volcanic eruptions is estimated to be about a 5% reduction in tropical rainfall over both land and ocean. A modified dataset (with ENSO and volcano effects removed) retains the same approximate linear change slopes, but with reduced variances, thereby increasing the statistical significance levels associated with the long-term rainfall changes in the Tropics. However, although care has been taken to ensure that this dataset is as homogeneous as possible, firm establishment of the existence of the discussed changes as long-term trends may require continued analysis of the input datasets and a lengthening of the observation period.
Statistical Tropical Cyclone Wind Radii Prediction Using Climatology and Persistence
Authors: Knaff John A. , Sampson Charles R. , DeMaria Mark , Marchok Timothy P. , Gross James M. , McAdie Colin J.
Published: August 2007

An operational model used to predict tropical cyclone wind structure in terms of significant wind radii (i.e., 34-, 50-, and 64-kt wind radii, where 1 kt = 0.52 m s−1) at the National Oceanic and Atmospheric Administration/National Hurricane Center (NHC) and the Department of Defense/Joint Typhoon Warning Center (JTWC) is described. The statistical-parametric model employs aspects of climatology and persistence to forecast tropical cyclone wind radii through 5 days. Separate versions of the model are created for the Atlantic, east Pacific, and western North Pacific by statistically fitting a modified Rankine vortex, which is generalized to allow wavenumber-1 asymmetries, to observed values of tropical cyclone wind radii as reported by NHC and JTWC. Descriptions of the developmental data and methods used to formulate the model are given. A 2-yr verification and comparison with operational forecasts and an independently developed wind radii forecast method that also employs climatology and persistence suggests that the statistical-parametric model does a good job of forecasting wind radii. The statistical-parametric model also provides reliable operational forecasts that serve as a baseline for evaluating the skill of operational forecasts and other wind radii forecast methods in these tropical cyclone basins.
The Trouble with Burawoy: An Analytic, Synthetic Alternative
Authors: McLaughlin Neil , Turcotte Kerry
Published: August 2007

As American Sociological Association (ASA) president in 2004, Michael Burawoy argued `for public sociology', sparking impassioned debate focused almost exclusively on the normative issues raised by his prescription for a more public sociology. Nearly absent from the literature is an analytical critique of his underlying model of the structure of sociological practice. The model is flawed in three ways: (1) the core concepts are ambiguous; (2) the model provides little leverage for understanding the institutional context of sociology as a discipline; and (3) comparative understanding of sociologies in different countries or between public engagement in distinct academic disciplines is not facilitated. In this article, we propose a synthetic means of relating academics, disciplines, audiences and institutional environments that forms the basis for movement toward an empirical agenda on public academics more generally.
Towards Postsecular Sociology?
Authors: McLennan Gregor
Published: August 2007

This article identifies four articulations of the growing `postsecular' condition of social and political thought, and places the idea of sociology in relation to them. I identify and critically engage with those aspects of poststructuralist vitalism, transcendental realism, multiculturalist thinking, and the recent `dialogical' sentiments of Habermas that might undermine sociology's definitive (but broadly conceived) secularism/naturalism. This implies that if we are concerned about advancing the role of `public sociology' then we should be actively engaged in countering anti-secular and anti-naturalistic elements of the postsecular climate.Yet we must avoid anthropomorphizing sociology as a public player, and accept too that the postsecular reconsideration of `faith versus reason' stretches beyond the confines of epistemological and explanatory considerations per se.
The Coming Crisis of Empirical Sociology
Authors: Savage Mike , Burrows Roger
Published: August 2007

This ar ticle argues that in an age of knowing capitalism, sociologists have not adequately thought about the challenges posed to their expertise by the proliferation of `social' transactional data which are now routinely collected, processed and analysed by a wide variety of private and public institutions. Drawing on British examples, we argue that whereas over the past 40 years sociologists championed innovative methodological resources, notably the sample survey and the in-depth interviews, which reasonably allowed them to claim distinctive expertise to access the `social' in powerful ways, such claims are now much less secure. We argue that both the sample survey and the in-depth interview are increasingly dated research methods, which are unlikely to provide a robust base for the jurisdiction of empirical sociologists in coming decades. We conclude by speculating how sociology might respond to this coming crisis through taking up new interests in the `politics of method'.
Social Divisions, Social Mobilities and Social Research: Methodological Issues after 40 Years
Authors: Payne Geoff
Published: August 2007

As sociology diversified, and under other academic pressures, British sociologists became `hyper-specialized' in subject expertise and methodology. Exploring multidimensional social life requires knowing about more than one field and having skills in more than one method. The retreat from quantitative methods, however good our qualitative methods, loses opportunities to contribute to important issues, particularly those in the public arena, at the boundaries of the discipline, or which take numerical form. This argument is developed through three recent examples: a critique of Erikson's view of British sociology and the BSA; the socio-economic circumstances of minority ethnic groups; and the isolation of social mobility analysis from political discourse. An approach based on an integrated view of social divisions and expanded methodological pluralism, in which we moderate our claims to sociological generalization, is proposed as a way forward.
Groundhog Day? The Strange Case of Sociology, Race and `Science'
Authors: Skinner David
Published: August 2007

Discussion of the natural sciences had a foundational role in the development of the sociology of race and racism, underpinning the claim that races should, if at all, be studied as social rather than natural phenomena. Whatever its strengths, the position on race and science that sociologists established had important limitations both as an account of science and society and as a solution to sociological problems. These limitations have been thrown into sharp relief by new forms of biological knowledge and practice that have the potential to disorder and reorder categories, disciplinary boundaries and the politics of difference. These developments require sociologists to rethink how they engage with academic and public discussion of race and biology.
Confusing Confucius in Asian Values? A Constructivist Critique
Authors: Tamaki Taku
Published: August 2007

It is tempting to interpret Confucius as a Realist who believes in coercion as a means of achieving good governance. Parallels can readily be drawn between him and Machiavelli, with ren fusing with virtú to represent Confucius as obsessed with power and authority. Southeast Asian leaders compound the problem by misappropriating the Sage to justify their intolerance for dissent within the `Asian values' discourse. This article seeks to reveal a glimpse of Confucius that has been missing in IR literature: that of Confucius as a Constructivist. I argue that ren needs to be translated as honesty — a behavioural norm required of a responsible member of society. Applied to IR, ren not only espouses normative presumptions, but also a realisation of the crucial role played by intersubjectivity in social interactions. This article then uses `Confucian' Constructivism to critique `Asian values'.
Debt and Power: The United States' Debt in Historical Perspective
Authors: Thompson Helen
Published: August 2007

The United States' borrowing poses a potential threat to its long-term external power. This is not because the United States' fiscal debt is large in relative terms, or because rising debt necessarily threatens a state's power, but because the United States has now indebted itself to China, and this financial relationship fundamentally changes the political terms on which the United States has borrowed since the 1960s. The consequences of that change may force American presidents to consider questions about the domestic viability of their foreign policy in a way that has not been necessary since the beginnings of the Cold War. Neither liberals nor realists are equipped to understand the significance of this change, because of the way in which they conceive power in relation to the interaction between domestic and international politics.
CHAID-based Segmentation: International Visitors' Trip Characteristics and Perceptions
Authors: Hsu Cathy H.C. , Kang Soo K.
Published: August 2007

This study segments inbound travelers to Hong Kong with aCH i-squareA utomaticI dentificationD etector (CHAID) technique. Seven predictors are used to derive market segments based on their likelihood of revisiting Hong Kong. The CHAID analysis produces six segments based on respondents' travel purpose, age, income, and repeat visit status. Each segment is described according to trip characteristics, including length of stay, travel party size, total expenditure, frequency of visits, mode of travel, and post-trip perceptions. Suggestions are made based on findings from the study, and marketing implications for resultant segments are discussed.
Perceived Risk and the Non-Institutionalized Tourist Role: The Case of Israeli Student Ex-Backpackers
Authors: Reichel Arie , Fuchs Galia , Uriely Natan
Published: August 2007

While backpacking is often associated with a propensity for risk-taking, the literature lacks quantitative analyses of backpackers' perceived risk. The current study attempts to fill this gap by exploring risk perceptions of 579 Israeli students who were backpackers. The study findings indicate that perceived risk of the backpackers' experience is a multidimensional phenomenon, which includes factors of risk similar to those mentioned in both the consumer behavior literature and in studies on perceived risk in tourism. This finding supports the thesis that backpacking is becoming more institutionalized and less distinct from conventional mass tourism. In addition, the study reveals that perceptions of risk involved in the backpacking experience vary across the individual's characteristics, such as gender, past backpacking experience, and preference for fellow travelers. This is congruent with the contemporary notion of backpacking as a heterogeneous tourist experience.
Une ontologie réaliste pour la sociologie: système, morphogenèse et collectifs
Authors: Vandenberghe Frédéric
Published: August 2007

English

After presenting French readers with the main ideas of Roy Bhaskar's critical realism and of Margaret Archer's morphogenetic theory, the article sets out a complex and stratified ontology for sociology that makes it possible to displace, if not surpass, the former opposition between individualism and collectivism, while avoiding the twin stumbling blocks of reification and reduction. The article next introduces collective actors into society and thus develops a realistic dialectical analysis of collective subjectivity. Symbolic identification, socio-technical mediation and political representation are identified as three stages of group structuration, which gradually transform categories into structured, mobilisable groups capable of action.

French

Tout en présentant les lignes de force du réalisme critique de Roy Bhaskar et de la théorie morphogénétique de Margaret Archer aux lecteurs francophones, l’article propose une ontologie complexe et stratifiée pour la sociologie qui permet de déplacer, si ce n’est de dépasser, l’ancienne opposition entre l’individualisme et le collectivisme en évitant le double écueil de la réification et de la réduction. En introduisant, ensuite, les acteurs collectifs dans la société, l’article développe une analyse réaliste et dialectique des subjectivités collectives. L’identification symbolique, la médiation sociotechnique et la représentation politique sont identifiées comme trois moments de la structuration des collectifs qui transforment progressivement les catégories en groupes structurés, mobilisables et capables d’action.
Everyday Moments
Authors: Kremer-Sadlik Tamar , Paugh Amy L.
Published: August 2007

American popular and academic discourses suggest that `quality time' — conceived as unstressed, uninterrupted special time with children — is important for family well-being. However, such discourses often engender stress and guilt among working parents, who have difficulty finding time for `quality time'. This article explores the concept of `quality time' in academic and popular literature (such as websites) and then draws on interviews and ethnographic video recordings of 32 dual-earner, two-parent American families to explore both perceived and lived experiences of family time. It proposes that everyday activities (like household chores or running errands) may afford families quality moments, unplanned, unstructured instances of social interaction that serve the important relationship-building functions that parents seek from `quality time'.
Parapublic Underpinnings of International Relations: The Franco-German Construction of Europeanization of a Particular Kind
Authors: Krotz Ulrich
Published: August 2007

Parapublic underpinnings of international relations are cross-border interactions that belong neither to the public world of states nor to the private world of societies. They underpin relations among specific states and construct social purpose in the international realm. Focusing on Franco-German parapublic underpinnings reveals a particular and neglected kind of `Europeanization'. Such parapublic activity includes massive state-financed youth exchanges, some two thousand municipal partnerships, and a host of institutes and associations. In their entirety, these parapublic interactions have developed into structural components of the European polity. Rather than directly affecting domestic political affairs, this kind of Europeanization connects French and Germans in a certain way. It makes Europeans more European, but without making them less national. This article contributes a concept to properly capture a distinct and substantial type of international activity and to identify its characteristic effects and limitations.
Duverger's Law and the Size of the Indian Party System
Authors: Diwakar Rekha
Published: August 2007

Duverger's law postulates that single-member plurality electoral systems lead to two-party systems. Existing scholarship regards India as an exception to this law at national level, but not at district level. This study tests the latter hypothesis through analysis of a comprehensive dataset covering Indian parliamentary elections in the period 1952—2004. The results show that a large number of Indian districts do not conform to the Duvergerian norm of two-party competition, and that there is no consistent movement towards the Duvergerian equilibrium. Furthermore, inter-region and inter-state variations in the size of district-level party systems make it difficult to generalize about the application of Duverger's law to the Indian case. The study concludes that a narrow focus on electoral rules is inadequate, and that a more comprehensive set of explanatory variables is needed to explain the size of the Indian party system even at the district level.
Committee Decision-making in the Council of the European Union
Authors: Häge Frank M.
Published: August 2007

Committees of national officials play a major role in the decision-making of the European Union's main legislative body, the Council of Ministers. The study investigates the conditions under which bureaucrats decide on legislative dossiers without direct involvement of ministers. A statistical analysis is performed to examine this question, using an original data set of 439 legislative proposals. The results of the analysis indicate that formal institutional features such as the voting rule in the Council and the involvement of the European Parliament affect committee decision-making, whereas no effects of committee socialization and preference divergence among member states are identified. The results diminish concerns about the democratic legitimacy of Council decision-making to some extent, as the findings demonstrate that bureaucrats tend to decide only the less salient and more complex proposals.
Institutional Context, Organizational Resources and Strategic Choices
Authors: Eising Rainer
Published: August 2007

Drawing on a survey of 800 business associations, the article seeks to explain why interest groups lobby the EU institutions and what groups maintain contacts with them. Rooted in organizational theory, it argues that four main dimensions influence access patterns — institutional context, resource dependencies, interest group organization, and strategic choices. The empirical analysis demonstrates that all dimensions are relevant. Nonetheless, contacts between EU policy-makers and interest groups display only a few general traits: they are shaped by the political mobilization of groups in response to EU regulation, the division of labour among EU and national associations and the importance of organizational resources. Beyond these general influences, the interactions vary profoundly in the segmented institutional context.
Effects of arc distance on angular distortion by asymmetrical double sided arc welding
Authors: Zhang H. J. , Zhang G. J. , Wu L.
Published: August 2007

Permanent angular distortion of the welded structure is developed because of non-uniform transverse shrinkage on thickness. Reducing and controlling residual angular deformation from the welding processes is extremely important in the manufacturing industry. A new method, asymmetrical double sided arc welding (A-DSAW), is studied due to controlling residual angular distortion. But it is not clear about the effects of arc distance on the angular distortions. In this paper, the effects of arc distance on angular deformation are researched through developing finite element model of A-DSAW at different arc distances. To verify the calculated results, the temperature and angular distortion are measured. Numerical and experimental results indicate that angular distortion v. arc distance appears non-linear relationship and the effect mechanism of arc distance on angular distortion of A-DSAW is further analysed.
Friend retrovirus infection of myeloid dendritic cells impairs maturation, prolongs contact to naïve T cells, and favors expansion of regulatory T cells
Authors: Balkow Sandra , Krux Frank , Loser Karin , Becker Jan U. , Grabbe Stephan , Dittmer Ulf
Published: August 2007

Retroviruses have developed immunmodulatory mechanisms to avoid being attacked by the immune system. The mechanisms of this retrovirus-associated immune suppression are far from clarified. Dendritic cells (DCs) have been attributed a decisive role in these pathogenic processes. We have used the Friend retrovirus (FV) mouse model in order to acquire further knowledge about the role of infection of DCs in virus-induced immunosuppression. About 20% of the myeloid DCs that were generated from the bone marrow of FV-infected mice carried FV proteins. The infection was productive, and infected DCs transmitted the virus in cell culture and in vivo. FV infection of DCs led to a defect in DC maturation, as infected cells expressed very little costimulatory molecules. Live imaging analysis of the cell contact between DCs and T cells revealed prolonged contacts of T cells with infected DCs compared with uninfected DCs. Although naive T cells were still activated by FV-infected DCs, this activation did not result in antigen-specific T-cell proliferation. Interestingly, infected DCs expanded a population of Foxp3+ regulatory T cells with immunosuppressive potential, suggesting that the contact between naive T cells and retrovirus-infected DCs results in tolerance rather than immunity. Thus, retroviral infection of DCs leads to an expansion of regulatory T cells, which might serve as an immune escape mechanism of the virus.
The transcriptional coactivator Maml1 is required for Notch2-mediated marginal zone B-cell development
Authors: Wu Lizi , Maillard Ivan , Nakamura Makoto , Pear Warren S. , Griffin James D.
Published: August 2007

Signaling mediated by various Notch receptors and their ligands regulates diverse biological processes, including lymphoid cell fate decisions. Notch1 is required during T-cell development, while Notch2 and the Notch ligand Delta-like1 control marginal zone B (MZB) cell development. We previously determined that Mastermind-like (MAML) transcriptional coactivators are required for Notchinduced transcription by forming ternary nuclear complexes with Notch and the transcription factor CSL. The 3 MAML family members (MAML1-MAML3) are collectively essential for Notch activity in vivo, but whether individual MAMLs contribute to the specificity of Notch functions is unknown. Here, we addressed this question by studying lymphopoiesis in the absence of the Maml1 gene. Since Maml1−/− mice suffered perinatal lethality, hematopoietic chimeras were generated with Maml1−/−, Maml1+/−, or wild-type fetal liver progenitors. Maml1 deficiency minimally affected T-cell development, but was required for the development of MZB cells, similar to the phenotype of Notch2 deficiency. Moreover, the number of MZB cells correlated with Maml1 gene dosage. Since all 3 Maml genes were expressed in MZB cells and their precursors, these results suggest that Maml1 is specifically required for Notch2 signaling in MZB cells.
Thiamine diphosphate adenylyl transferase from E. coli: functional characterization of the enzyme synthesizing adenosine thiamine triphosphate
Authors: Makarchikov Alexander F , Brans Alain , Bettendorff Lucien
Published: August 2007

Background

We have recently identified a new thiamine derivative, adenosine thiamine triphosphate (AThTP), in E. coli. In intact bacteria, this nucleotide is synthesized only in the absence of a metabolizable carbon source and quickly disappears as soon as the cells receive a carbon source such as glucose. Thus, we hypothesized that AThTP may be a signal produced in response to carbon starvation.

Results

Here we show that, in bacterial extracts, the biosynthesis of AThTP is carried out from thiamine diphosphate (ThDP) and ADP or ATP by a soluble high molecular mass nucleotidyl transferase. We partially purified this enzyme and characterized some of its functional properties. The enzyme activity had an absolute requirement for divalent metal ions, such as Mn2+ or Mg2+, as well as for a heat-stable soluble activator present in bacterial extracts. The enzyme has a pH optimum of 6.5–7.0 and a high K
m for ThDP (5 mM), suggesting that, in vivo, the rate of AThTP synthesis is proportional to the free ThDP concentration. When ADP was used as the variable substrate at a fixed ThDP concentration, a sigmoid curve was obtained, with a Hill coefficient of 2.1 and an S
0.5 value of 0.08 mM. The specificity of the AThTP synthesizing enzyme with respect to nucleotide substrate is restricted to ATP/ADP, and only ThDP can serve as the second substrate of the reaction. We tentatively named this enzyme ThDP adenylyl transferase (EC 2.7.7.65).

Conclusion

This is the first demonstration of an enzyme activity transferring a nucleotidyl group on thiamine diphosphate to produce AThTP. The existence of a mechanism for the enzymatic synthesis of this compound is in agreement with the hypothesis of a non-cofactor role for thiamine derivatives in living cells.
Regionalisation of the mouse visceral endoderm as the blastocyst transforms into the egg cylinder
Authors: Perea-Gomez Aitana , Meilhac Sigolène M , Piotrowska-Nitsche Karolina , Gray Dionne , Collignon Jérôme , Zernicka-Goetz Magdalena
Published: August 2007

Background

Reciprocal interactions between two extra-embryonic tissues, the extra-embryonic ectoderm and the visceral endoderm, and the pluripotent epiblast, are required for the establishment of anterior-posterior polarity in the mouse. After implantation, two visceral endoderm cell types can be distinguished, in the embryonic and extra-embryonic regions of the egg cylinder. In the embryonic region, the specification of the anterior visceral endoderm (AVE) is central to the process of anterior-posterior patterning. Despite recent advances in our understanding of the molecular interactions underlying the differentiation of the visceral endoderm, little is known about how cells colonise the three regions of the tissue.

Results

As a first step, we performed morphological observations to understand how the extra-embryonic region of the egg cylinder forms from the blastocyst. Our analysis suggests a new model for the formation of this region involving cell rearrangements such as folding of the extra-embryonic ectoderm at the early egg cylinder stage. To trace visceral endoderm cells, we microinjected mRNAs encoding fluorescent proteins into single surface cells of the inner cell mass of the blastocyst and analysed the distribution of labelled cells at E5.0, E5.5 and E6.5. We found that at E5.0 the embryonic and extra-embryonic regions of the visceral endoderm do not correspond to distinct cellular compartments. Clusters of labelled cells may span the junction between the two regions even after the appearance of histological and molecular differences at E5.5. We show that in the embryonic region cell dispersion increases after the migration of the AVE. At this time, visceral endoderm cell clusters tend to become oriented parallel to the junction between the embryonic and extra-embryonic regions. Finally we investigated the origin of the AVE and demonstrated that this anterior signalling centre arises from more than a single precursor between E3.5 and E5.5.

Conclusion

We propose a new model for the formation of the extra-embryonic region of the egg cylinder involving a folding of the extra-embryonic ectoderm. Our analyses of the pattern of labelled visceral endoderm cells indicate that distinct cell behaviour in the embryonic and extra-embryonic regions is most apparent upon AVE migration. We also demonstrate the polyclonal origin of the AVE. Taken together, these studies lead to further insights into the formation of the extra-embryonic tissues as they first develop after implantation.
Modeling HIV quasispecies evolutionary dynamics
Authors: Sguanci Luca , Bagnoli Franco , Liò Pietro
Published: August 2007

Background

During the HIV infection several quasispecies of the virus arise, which are able to use different coreceptors, in particular the CCR5 and CXCR4 coreceptors (R5 and X4 phenotypes, respectively). The switch in coreceptor usage has been correlated with a faster progression of the disease to the AIDS phase. As several pharmaceutical companies are starting large phase III trials for R5 and X4 drugs, models are needed to predict the co-evolutionary and competitive dynamics of virus strains.

Results

We present a model of HIV early infection which describes the dynamics of R5 quasispecies and a model of HIV late infection which describes the R5 to X4 switch. We report the following findings: after superinfection (multiple infections at different times) or coinfection (simultaneous infection by different strains), quasispecies dynamics has time scales of several months and becomes even slower at low number of CD4+ T cells. Phylogenetic inference of chemokine receptors suggests that viral mutational pathway may generate a large variety of R5 variants able to interact with chemokine receptors different from CXCR4. The decrease of CD4+ T cells, during AIDS late stage, can be described taking into account the X4-related Tumor Necrosis Factor dynamics.

Conclusion

The results of this study bridge the gap between the within-patient and the inter-patients (i.e. world-wide) evolutionary processes during HIV infection and may represent a framework relevant for modeling vaccination and therapy.
Phylogenetic analysis of mitochondrial protein coding genes confirms the reciprocal paraphyly of Hexapoda and Crustacea
Authors: Carapelli Antonio , Liò Pietro , Nardi Francesco , van der Wath Elizabeth , Frati Francesco
Published: August 2007

Background

The phylogeny of Arthropoda is still a matter of harsh debate among systematists, and significant disagreement exists between morphological and molecular studies. In particular, while the taxon joining hexapods and crustaceans (the Pancrustacea) is now widely accepted among zoologists, the relationships among its basal lineages, and particularly the supposed reciprocal paraphyly of Crustacea and Hexapoda, continues to represent a challenge. Several genes, as well as different molecular markers, have been used to tackle this problem in molecular phylogenetic studies, with the mitochondrial DNA being one of the molecules of choice. In this study, we have assembled the largest data set available so far for Pancrustacea, consisting of 100 complete (or almost complete) sequences of mitochondrial genomes. After removal of unalignable sequence regions and highly rearranged genomes, we used nucleotide and inferred amino acid sequences of the 13 protein coding genes to reconstruct the phylogenetic relationships among major lineages of Pancrustacea. The analysis was performed with Bayesian inference, and for the amino acid sequences a new, Pancrustacea-specific, matrix of amino acid replacement was developed and used in this study.

Results

Two largely congruent trees were obtained from the analysis of nucleotide and amino acid datasets. In particular, the best tree obtained based on the new matrix of amino acid replacement (MtPan) was preferred over those obtained using previously available matrices (MtArt and MtRev) because of its higher likelihood score. The most remarkable result is the reciprocal paraphyly of Hexapoda and Crustacea, with some lineages of crustaceans (namely the Malacostraca, Cephalocarida and, possibly, the Branchiopoda) being more closely related to the Insectas.s. (Ectognatha) than two orders of basal hexapods, Collembola and Diplura. Our results confirm that the mitochondrial genome, unlike analyses based on morphological data or nuclear genes, consistently supports the non monophyly of Hexapoda.

Conclusion

The finding of the reciprocal paraphyly of Hexapoda and Crustacea suggests an evolutionary scenario in which the acquisition of the hexapod condition may have occurred several times independently in lineages descending from different crustacean-like ancestors, possibly as a consequence of the process of terrestrialization. If this hypothesis was confirmed, we should therefore re-think our interpretation of the evolution of the Arthropoda, where terrestrialization may have led to the acquisition of similar anatomical features by convergence. At the same time, the disagreement between reconstructions based on morphological, nuclear and mitochondrial data sets seems to remain, despite the use of larger data sets and more powerful analytical methods.
Identification of QTL with effects on intramuscular fat content and fatty acid composition in a Duroc × Large White cross
Authors: Sanchez Marie-Pierre , Iannuccelli Nathalie , Basso Benjamin , Bidanel Jean-Pierre , Billon Yvon , Gandemer Gilles , Gilbert Hélène , Larzul Catherine , Legault Christian , Riquet Juliette , Milan Denis , Le Roy Pascale
Published: August 2007

Background

Improving pork quality can be done by increasing intramuscular fat (IMF) content. This trait is influenced by quantitative trait loci (QTL) sought out in different pig populations. Considering the high IMF content observed in the Duroc pig, it was appealing to determine whether favourable alleles at a major gene or QTL could be found. The detection was performed in an experimental F2 Duroc × Large White population first by segregation analysis, then by QTL mapping using additional molecular information.

Results

Segregation analysis provided evidence for a major gene, with a recessive Duroc allele increasing IMF by 1.8% in Duroc homozygous pigs. However, results depended on whether data were normalised or not. After Box-Cox transformation, likelihood ratio was indeed 12 times lower and no longer significant. The QTL detection results were partly consistent with the segregation analysis. Three QTL significant at the chromosome wide level were evidenced. Two QTL, located on chromosomes 13 and 15, showed a high IMF Duroc recessive allele with an overall effect slightly lower than that expected from segregation analysis (+0.4 g/100 g muscle). The third QTL was located on chromosome 1, with a dominant Large White allele inducing high IMF content (+0.5 g/100 g muscle). Additional QTL were detected for muscular fatty acid composition.

Conclusion

The study presented results from two complementary approaches, a segregation analysis and a QTL detection, to seek out genes involved in the higher IMF content observed in the Duroc population. Discrepancies between both methods might be partially explained by the existence of at least two QTL with similar characteristics located on two different chromosomes for which different boars were heterozygous. The favourable and dominant allele detected in the Large White population was unexpected. Obviously, in both populations, the favourable alleles inducing high IMF content were not fixed and improving IMF by fixing favourable alleles using markers can then be applied both in Duroc and LW populations. With QTL affecting fatty acid composition, combining an increase of IMF content enhancing monounsaturated fatty acid percentage would be of great interest.
Polymorphisms in XPC, XPD, XRCC1, and XRCC3 DNA repair genes and lung cancer risk in a population of Northern Spain
Authors: Felicitas López-Cima M , González-Arriaga Patricia , García-Castro Laura , Pascual Teresa , Marrón Manuel G , Puente Xose S , Tardón Adonina
Published: August 2007

Background

Polymorphisms in DNA repair genes have been associated to repair DNA lesions, and might contribute to the individual susceptibility to develop different types of cancer. Nucleotide excision repair (NER), base excision repair (BER), and double-strand break repair (DSBR) are the main DNA repair pathways. We investigated the relationship between polymorphisms in two NER genes,XPC(poly (AT) insertion/deletion: PAT-/+) andXPD(Asp312Asn and Lys751Gln), the BER geneXRCC1(Arg399Gln), and the DSBR geneXRCC3(Thr241Met) and the risk of developing lung cancer.

Methods

A hospital-based case-control study was designed with 516 lung cancer patients and 533 control subjects, matched on ethnicity, age, and gender. Genotypes were determined by PCR-RFLP and the results were analysed using multivariate unconditional logistic regression, adjusting for age, gender and pack-years.

Results

Borderline association was found forXPCandXPDNER genes polymorphisms, while no association was observed for polymorphisms in BER and DSBR genes.XPC PAT+/+genotype was associated with no statistically significant increased risk among ever smokers (OR = 1.40; 95%CI = 0.94–2.08), squamous cell carcinoma (OR = 1.44; 95%CI = 0.85–2.44), and adenocarcinoma (OR = 1.72; 95%CI = 0.97–3.04).XPDvariant genotypes (312Asn/Asnand751Gln/Gln) presented a not statistically significant risk of developing lung cancer (OR = 1.52; 95%CI = 0.91–2.51; OR = 1.38; 95%CI = 0.85–2.25, respectively), especially among ever smokers (OR = 1.58; 95%CI = 0.96–2.60), heavy smokers (OR = 2.07; 95%CI = 0.74–5.75), and adenocarcinoma (OR = 1.88; 95%CI = 0.97–3.63). On the other hand, individuals homozygous for the XRCC1399Glnallele presented no risk of developing lung cancer (OR = 0.87; 95%CI = 0.57–1.31) except for individuals carriers of399Gln/Glngenotype and without family history of cancer (OR = 0.57; 95%CI = 0.33–0.98) and no association was found betweenXRCC3Thr241Met polymorphism and lung cancer risk (OR = 0.92; 95%CI = 0.56–1.50), except for the241Met/Metgenotype and squamous cell carcinoma risk (OR = 0.47; 95%CI = 0.23–1.00).

Conclusion

In conclusion, we analysed the association betweenXPC,XPD,XRCC1, andXRCC3polymorphisms and the individual susceptibility to develop lung cancer in the Spanish population, specifically with a highly tobacco exposed population. We attempt to contribute to the discovery of which biomarkers of DNA repair capacity are useful for screening this high-risk population for primary preventing and early detection of lung cancer.
Causes of stigma and discrimination associated with tuberculosis in Nepal: a qualitative study
Authors: Baral Sushil C , Karki Deepak K , Newell James N
Published: August 2007

Background

Tuberculosis (TB) is a major cause of death. The condition is highly stigmatised, with considerable discrimination towards sufferers. Although there have been several studies assessing the extent of such discrimination, there is little published research explicitly investigating the causes of the stigma and discrimination associated with TB. The objectives of our research were therefore to take the first steps towards determining the causes of discrimination associated with TB.

Methods

Data collection was performed in Kathmandu, Nepal. Thirty four in-depth interviews were performed with TB patients, family members of patients, and members of the community.

Results

Causes of self-discrimination identified included fear of transmitting TB, and avoiding gossip and potential discrimination. Causes of discrimination by members of the general public included: fear of a perceived risk of infection; perceived links between TB and other causes of discrimination, particularly poverty and low caste; perceived links between TB and disreputable behaviour; and perceptions that TB was a divine punishment. Furthermore, some patients felt they were discriminated against by health workers

Conclusion

A comprehensive package of interventions, tailored to the local context, will be needed to address the multiple causes of discrimination identified: basic population-wide health education is unlikely to be effective.
Body fat measurement by bioelectrical impedance and air displacement plethysmography: a cross-validation study to design bioelectrical impedance equations in Mexican adults
Authors: Macias Nayeli , Alemán-Mateo Heliodoro , Esparza-Romero Julián , Valencia Mauro E
Published: August 2007

Background

The study of body composition in specific populations by techniques such as bio-impedance analysis (BIA) requires validation based on standard reference methods. The aim of this study was to develop and cross-validate a predictive equation for bioelectrical impedance using air displacement plethysmography (ADP) as standard method to measure body composition in Mexican adult men and women.

Methods

This study included 155 male and female subjects from northern Mexico, 20–50 years of age, from low, middle, and upper income levels. Body composition was measured by ADP. Body weight (BW, kg) and height (Ht, cm) were obtained by standard anthropometric techniques. Resistance, R (ohms) and reactance, Xc (ohms) were also measured. A random-split method was used to obtain two samples: one was used to derive the equation by the "all possible regressions" procedure and was cross-validated in the other sample to test predicted versus measured values of fat-free mass (FFM).

Results and Discussion

The final model was: FFM (kg) = 0.7374 * (Ht2 /R) + 0.1763 * (BW) - 0.1773 * (Age) + 0.1198 * (Xc) - 2.4658. R2 was 0.97; the square root of the mean square error (SRMSE) was 1.99 kg, and the pure error (PE) was 2.96. There was no difference between FFM predicted by the new equation (48.57 ± 10.9 kg) and that measured by ADP (48.43 ± 11.3 kg). The new equation did not differ from the line of identity, had a high R2 and a low SRMSE, and showed no significant bias (0.87 ± 2.84 kg).

Conclusion

The new bioelectrical impedance equation based on the two-compartment model (2C) was accurate, precise, and free of bias. This equation can be used to assess body composition and nutritional status in populations similar in anthropometric and physical characteristics to this sample.
Relative fat oxidation is higher in children than adults
Authors: Kostyak John C , Kris-Etherton Penny , Bagshaw Deborah , DeLany James P , Farrell Peter A
Published: August 2007

Background

Prepubescent children may oxidize fatty acids more readily than adults. Therefore, dietary fat needs would be higher for children compared with adults. The dietary fat recommendations are higher for children 4 to 18 yrs (i.e., 25 to 35% of energy) compared with adults (i.e., 20 to 35% of energy). Despite this, many parents and children restrict dietary fat for health reasons.

Methods

This study assessed whether rates of fat oxidation are similar between prepubescent children and adults. Ten children (8.7 ± 1.4 yr, 33 ± 13 kg mean ± SD) in Tanner stage 1 and 10 adults (41.6 ± 8 yr, 74 ± 13 kg) were fed a weight maintenance diet for three days to maintain body weight and to establish a consistent background for metabolic rate measurements (all foods provided). Metabolic rate was measured on three separate occasions before and immediately after breakfast and for 9 hrs using a hood system (twice) or a room calorimeter (once) where continuous metabolic measurements were taken.

Results

During all three sessions whole body fat oxidation was higher in children (lower RQ) compared to adults (mean RQ= 0.84 ± .016 for children and 0.87 ± .02, for adults, p < 0.02). Although, total grams of fat oxidized was similar in children (62.7 ± 20 g/24 hrs) compared to adults (51.4 ± 19 g/24 hrs), the grams of fat oxidized relative to calorie expenditure was higher in children (0.047 ± .01 g/kcal, compared to adults (0.032 ± .01 p < 0.02). Females oxidized more fat relative to calorie expenditure than males of a similar age. A two way ANOVA showed no interaction between gender and age in terms of fax oxidation.

Conclusion

These data suggest that fat oxidation relative to total calorie expenditure is higher in prepubescent children than in adults. Consistent with current dietary guidelines, a moderate fat diet is appropriate for children within the context of a diet that meets their energy and nutrient needs.
Barriers to adoption of recent technology in cervical screening
Authors: Jhala Darshana , Eltoum Isam
Published: August 2007

The Pap smear is one of the modern success stories in the field of preventive medicine. Since its introduction as a screening test, there has been a dramatic reduction in the incidence of cervical cancer. However, the search for a better screening test continues. The new technologies, including liquid-based cytology (LBC), Human Papilloma Virus (HPV) testing and automated or machine-assisted screening have been introduced. However, there is continuous debate about whether society's limited resources are better spent on reaching the underserved rather than on these technologies. Another question is whether these technologies create yet another kind of disparity in delivering preventive care. For example, despite the wide use of LBC (99% of tests submitted to our laboratory are LBC), conventional Pap smears are still used to screen/follow up some women. It is not clear why some providers continue to prefer conventional smear over LBC and what are the barriers for adopting LBC in cervical cancer screening. We hypothesize the lower cost of conventional compared to LBC Pap testing, patient's lower socio-economic indices, a patient's medical history and provider's subspecialty/training all appear to play a role in the choice of using conventional Pap testing rather than LBC. Unintentionally, this choice results in repeat testing, delayed treatment and potentially higher costs than intended. The ultimate goal of this review article is to understand and explore possible barriers and disparities to adopting new technology in cancer screening.
Extensive parallelism in protein evolution
Authors: Bazykin Georgii A , Kondrashov Fyodor A , Brudno Michael , Poliakov Alexander , Dubchak Inna , Kondrashov Alexey S
Published: August 2007

Background

Independently evolving lineages mostly accumulate different changes, which leads to their gradual divergence. However, parallel accumulation of identical changes is also common, especially in traits with only a small number of possible states.

Results

We characterize parallelism in evolution of coding sequences in three four-species sets of genomes of mammals, Drosophila, and yeasts. Each such set contains two independent evolutionary paths, which we call paths I and II. An amino acid replacement which occurred along path I also occurs along path II with the probability 50–80% of that expected under selective neutrality. Thus, the per site rate of parallel evolution of proteins is several times higher than their average rate of evolution, but still lower than the rate of evolution of neutral sequences. This deficit may be caused by changes in the fitness landscape, leading to a replacement being possible along path I but not along path II. However, constant, weak selection assumed by the nearly neutral model of evolution appears to be a more likely explanation. Then, the average coefficient of selection associated with an amino acid replacement, in the units of the effective population size, must exceed ~0.4, and the fraction of effectively neutral replacements must be below ~30%. At a majority of evolvable amino acid sites, only a relatively small number of different amino acids is permitted.

Conclusion

High, but below-neutral, rates of parallel amino acid replacements suggest that a majority of amino acid replacements that occur in evolution are subject to weak, but non-trivial, selection, as predicted by Ohta's nearly-neutral theory.

Reviewers

This article was reviewed by John McDonald (nominated by Laura Landweber), Sarah Teichmann and Subhajyoti De, and Chris Adami.