bluuebunny/crossref_metadata_2025_split huggingface dataset:
Positional distribution of decanoic acid: Effect on chylomicron and VLDL TAG structures and postprandial lipemia
Authors: Yli‐Jokipii Kaisa M. , Schwab Ursula S. , Tahvonen Raija L. , Xu Xuebing , Mu Huiling , Kallio Heikki P. T. 
Published: November 2006

AbstractAlthough medium‐chain FA (MCFA) are mainly absorbed via the portal venous system, they are also incorporated into chylomicron TAG; therefore, the positional distribution of MCFA in TAG is likely to affect their metabolic fate. We studied chylomicron and VLDL TAG structures, as well as the magnitude of postprandial lipemia, after two oral fat loads containing decanoic acid (10∶0) predominantly at the sn‐1(3),2 (MML) or at the sn‐1,3 positions (MLM) of TAG in a randomized, double‐blind, crossover clinical trial with 10 healthy, normal‐weight volunteers. An MS‐MS method was used to analyze TAG regioisomers. The position of decanoic acid in chylomicron TAG reflected its position in the TAG ingested, and TAG with none, one, two, or three decanoic acid residues were detected after ingestion of both fats. More (P<0.05) 30∶0 and 38∶1 TAG (acyl carbons:double bonds) and fewer 46∶5, 54∶5 and 54∶4 TAG were found in chylomicrons after ingestion of MML than after MLM. The VLDL TAG composition did not differ between the fat loads but did change (P<0.05) 2 to 6 h after ingestion of both fats. No statistical differences were seen between the fat loads in areas under the plasma, chylomicron, or VLDL TAG response curves or in FFA concentrations. Thus, the positional distribution of MCFA in TAG affects their metabolic, fate, but the magnitude of postprandial lipemia does not seem to be dependent on the positional distribution of MCFA in the ingested fat.
Cytoplasmic pH‐dependent spreading of polymorphonuclear leukocytes: Regulation by pH of PKC subcellular distribution and F‐actin assembly
Authors: Suzuki Kingo , Namiki Hideo 
Published: November 2006

AbstractCytoplasmic pH (pHi) plays an important role in the regulation of polymorphonuclear leukocyte (PMN) spreading, but the molecular mechanisms involved have long been obscure. In the present study, we investigated the pH‐dependence of phorbol myristate acetate (PMA)‐induced PMN spreading. A change in pHi alone did not induce spreading, but cytoplasmic alkalinization promoted the spreading induced by PMA, whereas acidification inhibited it. To further investigate the mechanism by which pHi affects cell spreading, we employed subcellular fractionation and immunoblot analyses to evaluate the effect of pH on the subcellular distribution of protein kinase C (PKC) and assembly of the actin cytoskeleton. We found that cytoplasmic alkalinization enhanced PKC membrane distribution and quantitatively up‐regulated the actin cytoskeleton. On the other hand, cytoplasmic acidification was found to have effects on these signaling molecules that were opposite to those of cytoplasmic alkalinization. These results may provide a potential explanation for the pH‐regulation of the PMA‐induced PMN spreading.
Syndrome stability and psychological predictors of symptom severity in idiopathic environmental intolerance and somatoform disorders
Authors: BAILER JOSEF , WITTHÖFT MICHAEL , BAYERL CHRISTIANE , RIST FRED 
Published: November 2006

Background. Previous studies suggest that idiopathic environmental intolerance (IEI) is a variant of somatoform disorders (SFDs) or the so-called functional somatic syndromes. Little is known, however, about the stability and the psychological predictors of IEI.Method. This prospective study examined the 1-year stability of somatic symptoms and IEI features in three diagnostic groups: 49 subjects with IEI, 43 subjects with SFD but without IEI, and 54 subjects (control group, CG) with neither IEI nor SFD. The predictive value of typical psychological predictors for somatization was tested using zero-order correlations and multiple linear regression analyses.Results. Somatic symptoms and IEI features proved to be temporally stable over the 1-year follow-up period. The SFD and IEI groups scored significantly higher than CG on all measures of somatic symptoms and on questionnaires assessing psychological predictors for somatization. Measures of trait negative affectivity (NA), somatic symptom attribution and somatosensory amplification predicted somatic symptom severity within the IEI and SFD groups, both at baseline and 1 year later. The strongest predictors of IEI complaints in the IEI group were somatic attributions, followed by prominent cognitions of environmental threat and a tendency to focus on unpleasant bodily sensations and to consider them as pathological.Conclusions. IEI and SFD are highly stable conditions. In both SFD and IEI, NA and the processes of symptom perception, interpretation and attribution contribute substantially to the persistence of typically somatoform symptoms and IEI complaints. Treatment of IEI and SFD should address these psychological factors and mechanisms.
Review and critical discussion of assumptions and modelling options to study the spread of the bovine viral diarrhoea virus (BVDV) within a cattle herd
Authors: VIET A.-F. , FOURICHON C. , SEEGERS H. 
Published: November 2006

SUMMARYRelevance of epidemiological models depends on assumptions on the population structure and dynamics, on the biology of the host–parasite interaction, and on mathematical modelling. In this paper we reviewed published models of the bovine viral diarrhoea virus (BVDV) spread within a herd. Modelling options and assumptions on herd dynamics and BVDV transmission were discussed. A cattle herd is a population with a controlled size. Animals are separated into subgroups according to their age or their physiological status inducing heterogeneity of horizontal transmission. Complexity of models results from: (1) horizontal and vertical virus transmission, (2) birth of persistently infected animals, (3) excretion by transiently and persistently infected animals. Areas where there was a lack of knowledge were identified. Assumptions on the force of infection used to model the horizontal virus transmission were presented and discussed. We proposed possible ways of improving models (e.g. force of infection, validation) and essential model features for further BVDV models.
Specific detection ofCampylobacter jejunifrom faeces using single nucleotide polymorphisms
Authors: Best E. L. , Fox A. J. , Owen R. J. , Cheesbrough J. , Bolton F. J. 
Published: November 2006

SUMMARYSpecimens of human faeces were tested by a rapid strategy for detection ofCampylobacter jejunilineages by the presence of specific single nucleotide polymorphisms (SNPs) based on theC. jejunimulti locus sequence typing (MLST) scheme. This strategy was derived from analysis of the MLST databases to identify clonal complex specific SNPs followed by the design of real-time PCR assays to enable identification of six majorC. jejuniclonal complexes associated with cases of human infection. The objective was to use the MLST SNP-based assays for the direct detection ofC. jejuniby clonal complex from specimens of human faeces, and then confirm the accuracy of the clonal complex designation from the SNP-based assays by performing MLST on the cultured faecal material, this targeted at determining the validity of direct molecular specimen identification. Results showed it was possible to identify 38% of the isolates to one of the six major MLST clonal complexes using a rapid DNA extraction method directly from faeces in under 3 h. This method provides a novel strategy for the use of real-time PCR for detection and characterization beyond species level, supplying real-time epidemiological data, which is comparable with MLST results.
Monitoring seasonal and long‐term changes in test performance in elite swimmers
Authors: Anderson Megan E. , Hopkins William G. , Roberts Alan D. , Pyne David B. 
Published: November 2006

AbstractThe purpose of this study was to characterize changes and variability in test performance of swimmers within and between seasons over their elite competitive career. Forty elite swimmers (24 male, 16 female) performed a 7×200‐m incremental swimming step test several times each 6‐month season (10±5 tests, spanning 0.5–6.0 y). Mixed linear modeling provided estimates of percent change in the mean and individual responses (within‐athlete variation as a coefficient of variation) for measures based on submaximal performance (fixed 4‐mM lactate), maximal performance (the seventh step) and lean mass (from skinfolds and body mass). Submaximal and maximal swim speed increased within each season from pre to taper phase by ∼2.2% for females and ∼1.5% for males (95% confidence limits ±1.0%), with variable contributions from stroke rate and stroke length. Most of the gains in speed were lost in the off‐season, leaving a net average annual improvement of ∼1.0% for females and ∼0.6% for males (±1.0%). For submaximal and maximal speed, individual variation between phases was ±2.2% and the typical measurement error was ±0.80%. Step test and anthropometric measures can be used to confidently monitor progressions in swimmers in an elite training program within and between seasons.
Truth makers for judgement calls
Authors: Mumford Stephen 
Published: November 2006

AbstractTruths of sport seem to admit a certainty that is not to be found in other domains. I offer a diagnosis of this phenomenon. Awards in sport have a performative force: the making of an award thereby deems that it so. There are other elements, however, that have equal importance. There is an epistemic element in that umpire or referee must make a judgement about the award. This must be based on the metaphysical element, which is some fact or state of affairs in the world. Such a tripartite account allows that referees can make mistakes or that they can deliberately make an unjustified award. Because such awards are performatives, however, such facts about sport will not typically admit rational doubt.
SAGA: a subgraph matching tool for biological graphs
Authors: Tian Yuanyuan , McEachin Richard C. , Santos Carlos , States David J. , Patel Jignesh M. 
Published: November 2006

AbstractMotivation: With the rapid increase in the availability of biological graph datasets, there is a growing need for effective and efficient graph querying methods. Due to the noisy and incomplete characteristics of these datasets, exact graph matching methods have limited use and approximate graph matching methods are required. Unfortunately, existing graph matching methods are too restrictive as they only allow exact or near exact graph matching. This paper presents a novel approximate graph matching technique called SAGA. This technique employs a flexible model for computing graph similarity, which allows for node gaps, node mismatches and graph structural differences. SAGA employs an indexing technique that allows it to efficiently evaluate queries even against large graph datasets.Results: SAGA has been used to query biological pathways and literature datasets, which has revealed interesting similarities between distinct pathways that cannot be found by existing methods. These matches associate seemingly unrelated biological processes, connect studies in different sub-areas of biomedical research and thus pose hypotheses for new discoveries. SAGA is also orders of magnitude faster than existing methods.Availability: SAGA can be accessed freely via the web at . Binaries are also freely available at this website.Contact: jignesh@eecs.umich.eduSupplementary material: Supplementary material is available at .
Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment
Authors: Kim Jaebum , Sinha Saurabh 
Published: November 2006

AbstractMotivation: A quantitative study of molecular evolutionary events such as substitutions, insertions and deletions from closely related genomes requires (1) an accurate multiple sequence alignment program and (2) a method to annotate the insertions and deletions that explain the ‘gaps’ in the alignment. Although the former requirement has been extensively addressed, the latter problem has received little attention, especially in a comprehensive probabilistic framework.Results: Here, we present Indelign, a program that uses a probabilistic evolutionary model to compute the most likely scenario of insertions and deletions consistent with an input multiple alignment. It is also capable of modifying the given alignment so as to obtain a better agreement with the evolutionary model. We find close to optimal performance and substantial improvement over alternative methods, in tests of Indelign on synthetic data. We use Indelign to analyze regulatory sequences in Drosophila, and find an excess of insertions over deletions, which is different from what has been reported for neutral sequences.Availability: The Indelign program may be downloaded from the websiteSupplementary information: Supplementary material is available at Bioinformatics online.Contact: sinhas@uiuc.edu
Network neighborhood analysis with the multi-node topological overlap measure
Authors: Li Ai , Horvath Steve 
Published: November 2006

AbstractMotivation: The goal of neighborhood analysis is to find a set of genes (the neighborhood) that is similar to an initial ‘seed’ set of genes. Neighborhood analysis methods for network data are important in systems biology. If individual network connections are susceptible to noise, it can be advantageous to define neighborhoods on the basis of a robust interconnectedness measure, e.g. the topological overlap measure. Since the use of multiple nodes in the seed set may lead to more informative neighborhoods, it can be advantageous to define multi-node similarity measures.Results: The pairwise topological overlap measure is generalized to multiple network nodes and subsequently used in a recursive neighborhood construction method. A local permutation scheme is used to determine the neighborhood size. Using four network applications and a simulated example, we provide empirical evidence that the resulting neighborhoods are biologically meaningful, e.g. we use neighborhood analysis to identify brain cancer related genes.Availability: An executable Windows program and tutorial for multi-node topological overlap measure (MTOM) based analysis can be downloaded from the webpage ().Contact: shorvath@mednet.ucla.eduSupplementary information: Supplementary material is available at Bioinformatics online.
Spreading of antibody reactivity to non-thyroid antigens during experimental immunization with human thyroglobulin
Authors: Thrasyvoulides A , Liakata E , Lymberi P 
Published: November 2006

SummaryIntermolecular spreading of antibody reactivity has been implicated in the evolution of autoimmune disease. In this study, spreading of antibody reactivity to non-thyroid autoantigens after experimental immunization with thyroglobulin (Tg) was investigated. For this purpose, two rabbits were injected with human Tg six times (stages 1–6) every 3 weeks. Animals were also bled before priming. Antisera were tested by enzyme-linked immunosorbent assay (ELISA) for reactivity to several non-thyroid antigens: bovine serum albumin (BSA), native DNA (nDNA), human myosin, human globular (G) and filamentous (F) actin and porcine tubulin. Tg-immunized animals developed the following serological reactivity pattern: (a) high reactivity to myosin from stage 2 onward, (b) significant reactivity to F-actin, remaining high up to stage 6, (c) reactivity to BSA with a peak at stage 3, (d) a small increase of reactivity to G-actin at stage 3 and (e) no increase of reactivity to nDNA and tubulin. The study of affinity-purified anti-Tg antibodies and the use of competitive assays revealed that reactivity to F-actin was not due to cross-reaction with Tg. On the contrary, reactivity to myosin during the first stages of immunization was due to cross-reaction with Tg, while at stage 6 it became myosin-specific. Reactivity to BSA at stage 3 was also due to cross-reaction with Tg. We conclude that at least part of the induced anti-Tg antibodies may result from the expansion of B cell clones producing polyreactive natural autoantibodies, and polyreactivity of anti-Tg antibodies during the first stages of Tg-immunization may be responsible for the intermolecular spreading of antibody response.
Innate immunity mediated by epidermal keratinocytes promotes acquired immunity involving Langerhans cells and T cells in the skin
Authors: Sugita K , Kabashima K , Atarashi K , Shimauchi T , Kobayashi M , Tokura Y 
Published: November 2006

SummarySkin is an immunological organ consisting of epidermal cells, i.e. keratinocytes and Langerhans cells (LCs, antigen-presenting dendritic cells), and both innate and acquired immune systems operate upon exposure of the skin to various external microbes or their elements. To explore the relationship between innate and acquired immunities in the skin, we investigated whether Toll-like receptor (TLR) ligation of epidermal cells enhances the ability of LCs to present a specific antigen to T cells in mice. LC-containing epidermal cells were incubated with CpG oligonucleotide (TLR9 ligand) modified with trinitrophenyl hapten, and cultured with hapten-primed CD4+ T cells. TLR9 ligand was capable of enhancing the hapten-presenting ability of LCs when LC-enriched epidermal cells, but not purified LCs, were used as the LC source, suggesting that bystander keratinocytes play a role in the enhancement of LC function. Cultivation of freshly isolated epidermal cells with CpG promoted the expression of major histocompatibility complex (MHC) class II and CD86 molecules on LCs. CpG enhanced the production of interleukin (IL)-1α, granulocyte–macrophage colony-stimulating factor (GM-CSF) and tumour necrosis factor (TNF)-α by primarily cultured keratinocytes. The addition of a cocktail of neutralizing antibodies against these cytokines abrogated the CpG-promoted, antigen-presenting ability of LC-enriched epidermal cells. Moreover, the addition of culture supernatants from CpG-stimulated keratinocytes restored the ability of purified LCs. Our study demonstrated that although the direct effect of CpG on LCs is minimal, LC function can be up-regulated indirectly by cytokines released by CpG-stimulated keratinocytes. This also implies that innate immunity evoked by TLR ligation of keratinocytes enhances acquired immunity comprising LCs and T cells.
Effects of ultraviolet (UV) exclusion on the seasonal concentration of photosynthetic and UV‐screening pigments in Scots pine needles
Authors: MARTZ FRANÇOISE , SUTINEN MARJA‐LIISA , DEROME KIRSTI , WINGSLE GUNNAR , JULKUNEN‐TIITTO RIITTA , TURUNEN MINNA 
Published: November 2006

AbstractThe effects of ultraviolet (UV) radiation on the photosynthetic and UV‐screening pigments in needles of Scots pine (Pinus sylvestris L.) saplings were studied in a UV‐exclusion field chamber experiment in northern Finland (67°N) during 2001–2002. The chambers held filters that excluded both UVB and UVA, only UVB, transmitted all UV, or lacked filters. Analyses of control needles (no filter and polyethene filter) showed that the first changes to occur in spring (end of April) was an abrupt increase in the epoxidation state (EPS) of the xanthophyll cycle pigments, likely in relation with the beginning of the photosynthetic activity. The concentration of chlorophyll, lutein, neoxanthin, α‐carotene, β‐carotene, and the size of the xanthophyll cycle pool (violaxanthin+antheraxanthin+zeaxanthin=VAZ) changed only later when needles reached their summer photosynthesis state. Exclusion of UV radiation significantly affected the xanthophyll cycle but not the other photosynthetic pigments analysed. Interestingly, the effects on xanthophylls were dependent on the sampling date. Under UVA/B‐exclusion, the EPS was increased and VAZ pool size was unchanged in April, whereas EPS remained unchanged and the VAZ pool size was reduced in May and June. The existence of two sustained and active antenna modes during winter and summer could be an explanation for the specific UV‐exclusion effect in the different season. A high‐performance liquid chromatography analysis of soluble phenolics showed that the exclusion of UVA/B radiation caused a significant effect on five compounds out of 46 studied, without affecting the concentration of the total soluble phenolics. Under UVA/B‐exclusion, the concentration of three of them (secoisolariciresinol‐glucopyranoside, two unknown) was reduced while the concentration of dicoumaroyl‐astragalin and pinosylvin monomethylether was increased compared with both controls separately. In general, the exclusion of UVA/B caused a stronger effect than the exclusion of UVB on both photosynthetic and UV screening pigments. The effects of UV radiation on xanthophyll cycle pigments were season‐specific and detectable only under stressful spring conditions (freezing temperatures and high irradiance due to snow reflection). The effect on the xanthophyll cycle could be a direct consequence of UV treatments, or an indirect consequence of the changed flavonoid composition, or a combination of both.
Soils, a sink for N2O? A review
Authors: CHAPUIS‐LARDY LYDIE , WRAGE NICOLE , METAY AURÉLIE , CHOTTE JEAN‐LUC , BERNOUX MARTIAL 
Published: November 2006

AbstractSoils are the main sources of the greenhouse gas nitrous oxide (N2O). The N2O emission at the soil surface is the result of production and consumption processes. So far, research has concentrated on net N2O production. However, in the literature, there are numerous reports of net negative fluxes of N2O, (i.e. fluxes from the atmosphere to the soil). Such fluxes are frequent and substantial and cannot simply be dismissed as experimental noise.Net N2O consumption has been measured under various conditions from the tropics to temperate areas, in natural and agricultural systems. Low mineral N and large moisture contents have sometimes been found to favour N2O consumption. This fits in with denitrification as the responsible process, reducing N2O to N2. However, it has also been reported that nitrifiers consume N2O in nitrifier denitrification. A contribution of various processes could explain the wide range of conditions found to allow N2O consumption, ranging from low to high temperatures, wet to dry soils, and fertilized to unfertilized plots. Generally, conditions interfering with N2O diffusion in the soil seem to enhance N2O consumption. However, the factors regulating N2O consumption are not yet well understood and merit further study.Frequent literature reports of net N2O consumption suggest that a soil sink could help account for the current imbalance in estimated global budgets of N2O. Therefore, a systematic investigation into N2O consumption is necessary. This should concentrate on the organisms, reactions, and environmental factors involved.