bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractBackgroundThe 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.ResultsTwo 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.ConclusionThe 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

Abstract

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

AbstractBackgroundPolymorphisms 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.MethodsA 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.ResultsBorderline 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).ConclusionIn 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

Abstract

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

Abstract

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

AbstractBackgroundPrepubescent 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.MethodsThis 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.ResultsDuring 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.ConclusionThese 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.
Extensive parallelism in protein evolution
Authors: Bazykin Georgii A , Kondrashov Fyodor A , Brudno Michael , Poliakov Alexander , Dubchak Inna , Kondrashov Alexey S 
Published: August 2007

Abstract

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.
XCL1 (lymphotactin) chemokine produced by activated CD8 T cells during the chronic stage of infection withMycobacterium tuberculosisnegatively affects production of IFN-γ by CD4 T cells and participates in granuloma stability
Authors: Ordway Diane , Higgins David M , Sanchez-Campillo Joaquin , Spencer John S , Henao-Tamayo Marcela , Harton Marisa , Orme Ian M , Gonzalez Juarrero Mercedes 
Published: August 2007

AbstractCD8 T cell immune responses are known not to be essential during the initial stages of infection with Mycobacterium tuberculosis (Mtb), but their presence becomes important as the chronic infection ensues. The basis of this is still not clear. In previous studies, we showed that CD8 T cells have a distinctive positioning in the architecture of the granuloma lesion, with further changes throughout the course of the chronic infection. We have also hypothesized that further movement of lymphocytes once they are within the lung lesions could be associated with the levels of expression of the chemokine XCL1 (lymphotactin). XCL1 is produced mainly by activated CD8 T cells, and its chemotactic activity seems primarily controlling movement of CD4 and CD8 T cells. In this study, using a murine low-dose aerosol infection model coupled with antibody depletion of T cell subsets, we investigated the role of CD8 T cells in the control of the bacterial growth and in the pathogenesis of the disease in mice at early, mid, or late stages of the chronic disease state. Additionally, we also describe for the first time that during Mtb infection, activated CD8 T cells in the lungs produce XCL1 and that this chemokine is capable of controlling IFN-γ production by CD4 T cells.
Methanol-Associated Matrix Effects in Electrospray Ionization Tandem Mass Spectrometry
Authors: Annesley Thomas M 
Published: August 2007

Abstract
Background: Matrix effects can profoundly reduce the performance of electrospray ionization mass spectrometry. Preliminary observations indicated that the methanol used in the mobile phase could be a source of differential ionization or ion suppression.
Methods: Drug stability studies, analysis of biological extracts, mixing experiments, and postcolumn infusions were used to test 9 commercial methanols for ionization differences in liquid chromatography-tandem mass spectrometry assays for immunosuppressants. Area responses for the drugs and internal standards were compared for mobile phases prepared with each selected methanol. Postcolumn infusion experiments were performed to confirm the degree of ionization differences occurring at the ion source, and to evaluate the proportions of ammonium, sodium, and potassium adducts.
Results: The decrease in signal for the immunosuppressant drugs was shown to result from differential ionization associated with the selected methanols. Product ion intensity varied by 10-fold among the methanols tested. For sirolimus, tacrolimus, and mycophenolic acid, the percentage change in ionization was the same for the drug and its corresponding internal standard. Postcolumn sirolimus infusion evaluation revealed that a 1000-fold analyte concentration difference did not affect ionization. The proportions of ammonium, sodium, and potassium adducts of sirolimus precursor ions differed in relation to the source of methanol.
Conclusions: Organic solvents used in mobile phases and extract preparation of biological samples may be associated with ion suppression, affecting adduct formation and assay sensitivity.
Lernobjekt-Metadatenerstellung in Zeiten des Web 2.0 (Learning Object Metadata Generation in the Web 2.0 Era)
Authors: Dahl Daniel , Vossen Gottfried 
Published: August 2007

Abstract
Die Ziele, die mit der Einführung des Metadatenstandards LOM verfolgt wurden (z. B. die Auffindbarkeit und die Wiederverwendbarkeit von Lernobjekten) werden aktuell trotz einer weit reichenden Verbreitung und Akzeptanz nur in geringem Maße erreicht: Aufgrund der großen Komplexität des Standards steht dem in der Theorie immensen Potential eine deutliche Zurückhaltung in der Praxis gegenüber. Dies lässt sich u. a. darauf zurückführen, dass der Prozess der Metadatenerstellung (wer erstellt wann wie welche Attribute) bislang nicht im Detail definiert ist. Dieses Papier zeigt einen Weg auf, der gleichzeitig eine hohe Quantität wie Qualität bei der Erstellung von Lernobjekt-Metadaten sicherstellt. Dafür werden bekannte Ansätze der Metadatenerstellung kombiniert und erstmals die Potentiale des im Kontext der Web 2.0-Entwicklungen vorbildlich umgesetzten User-zentrierten Paradigmas zur Communitygetriebenen Metadatenerstellung von Lernobjekten genutzt. Am konkreten Beispiel des Einsatzes einer Lernplattform wird definiert, wer wann welche Metadatenattribute des Standards auf welche Art und Weise füllt.
Design, Entwicklung und Evaluation von Benutzerschnittstellen für Wearable Computer (Design, Development and Evaluation of User Interfaces for Wearable Computers)
Authors: Witt Hendrik 
Published: August 2007

Abstract
Benutzerschnittstellen für das Wearable Computing Paradigma unterscheiden sich signifikant von ihrem Pendant aus der Desktop Computing Welt. Dieser Artikel schlägt die Entwicklung eines systematischen Entwicklungsprozesses für die Erstellung von Benutzerschnittstellen für Wearable Computer und dessen Integrationsmöglichkeit in existierende und zukünftige Software-Entwicklungsmodelle vor. Zur Unterstützung der vorgeschlagenen Prozesse werden zwei spezielle Werkzeuge, das „WUI-Toolkit” und der „HotWire Primäraufgaben Simulator” verwendet, die speziell auf die Anforderungen des Wearable Computings im Bereich der Implementierungs- und anschließenden Evaluationsphase von Schnittstellen abgestimmt wurden.
Implications of Coupling Fractional Flow and Geochemistry for CO2 Injection in Aquifers
Authors: Noh M. , Lake L. W. , Bryant S. L. , Araque-Martinez A. 
Published: August 2007

Summary
The geochemical changes caused by carbon dioxide (CO2) injection into aquifers include acidification and carbonation of the native brine. There are also potential mineral-dissolution and mineral-precipitation reactions caused by the aqueous-composition changes. The latter are important for evaluating the potential CO2-storage capacity in the form of minerals. Reactions also may influence the performance of the injection well.
The theories of geochemical flows and of fractional flow provide useful insight into several aspects of CO2 sequestration. This paper gives the mathematical formalism of combined geochemical reactions and multiphase flow. If the local-equilibrium assumption applies, the theory leads to a graphical solution, from which it is easy to see when and under what conditions mineralization will occur. The theory also illustrates the modes of CO2 trapping (hydrodynamic, solubility, mineral, residual saturation). Trapping mechanisms are identified analytically. We also show that the natural groundwater flow alters the modes of trapping significantly.