bluuebunny/crossref_metadata_2025 huggingface dataset:
High water roost selection by waders: maximizing feeding opportunities or avoiding predation?
Authors: ROSA SUSANA , ENCARNAÇÃO ANA L. , GRANADEIRO JOSÉ P. , PALMEIRIM JORGE M.
Published: January 2006

During the highest spring tides the intertidal sediment flats of estuaries are fully inundated at high water, and waders have no choice but to move to supratidal roosts, e.g. on open farmland, saltpans or beaches. However, in many estuaries during the lowest neap or intermediate tides there are sectors of upper intertidal sediment flats that remain exposed even at the peak of high water, and so waders have the choice of roosting either there or in supratidal sites. In the Tagus Estuary, Portugal, as elsewhere, waders use both types of roosts during high water. Our main objective was to understand what makes waders opt for one of these two types of available roosts. We monitored wader use of saltpans and intertidal roosts from spring to neap tides, and measured foraging and alarm behaviour, prey availability and disturbance by predators. Most of the wader species studied chose intertidal (mudflat) roosts whenever these were available, and only roosted in saltpans during the peak of spring tides. We hypothesized that this preference was explained either by an attempt (i) to continue feeding into the high water period, or (ii) to minimize predation risk. Extending feeding time into the high water period did not seem to be very relevant for roost choice because both prey availability and foraging activity were low in both types of roosts. However, predator disturbance was several times higher in the saltpans than in the intertidal roosts, suggesting that this factor may be the determinant in the choice of roost type.
Declining winter survival and fitness implications associated with latitudinal distribution in Norwegian Greylag GeeseAnser anser
Authors: PISTORIUS PIERRE A. , FOLLESTAD ARNE , TAYLOR FRANCES E.
Published: January 2006

The Norwegian Greylag GooseAnser anserpopulation has been increasing steadily over the past few decades, causing increasing nuisance in terms of agricultural crop damage. This, in combination with the importance of Greylags as a hunting target, has called for demographic estimates for the population to assist in management decisions. To this end, we analysed long‐term mark–recapture data using Cormack–Jolly‐Seber models embedded in program MARK to obtain survival estimates for the population. No sex‐specific difference, or age effect on survival after juveniles had completed their first migration (3 months of age), was evident. Mean first‐year survival was reported as 0.485 and annual survival of older birds as 0.700. On a monthly basis, survival in Greylags during summer and winter was very similar over the study period. A significant linear decline in winter survival from 0.909 to 0.807 was, however, apparent during the study period. Over the second half of the study (1994–2002), summer survival was about 3% lower than in the first half (1986–94) but no linear relationship was evident. We found a significant inverse relationship between Greylag survival during summer and latitudinal distribution in Norway. A similar relationship was evident between survival and annual bag numbers. The changes in adult survival observed in this study are likely to have had a substantial impact on the growth rate of the Norwegian Greylag population.
ONTOGENY AND HETEROCHRONY IN THE EARLY CAMBRIAN ORYCTOCEPHALID TRILOBITES CHANGASPIS, DUYUNASPIS AND BALANGIA FROM CHINA
Authors: McNAMARA KENNETH J. , YU FENG , ZHIYI ZHOU
Published: January 2006

Abstract:  Ontogenies are described for the first time for three species of Early Cambrian oryctocephalid trilobites: the oryctocephaline Changaspis elongata Lee, in Chien and the oryctocarines Duyunaspis duyunensis Chang and Chien, in Zhou et al. and Balangia balangensis Chien from the Balang Formation in eastern Ghuizhou Province, south‐west China. The complete protaspid to holaspid ontogeny for Duyunaspis duyunensis and incomplete meraspid to holaspid ontogenies for Changaspis elongata and Balangia balangensis are described. The relative degree of ontogenetic variation within the lineage Duyunaspis duyunensis–Balangia balangensis is analysed and indicates that Balangia may have evolved from Duyunaspis by paedomorphosis. Decrease in thoracic segment number and concomitant increase in pygidial segment number in the later genus mirrors the pattern seen in the evolution of another oryctocephalid genus, Arthricocephalus. In both cases, selection was probably targeting an increase in cephalic convexity. This resulted in the evolution of a larger pygidium due to increased elevation of the axis above the substrate. The ontogenetic development of Changaspis provides evidence supporting the view that the Oryctocarinae may be considered as paedomorphic descendants of the Oryctocephalinae.
DEVONIAN TRILOBITES FROM THE FALKLAND ISLANDS
Authors: DE CARVALHO MARIA DA GLORIA PIRES
Published: January 2006

Abstract:  New trilobite material is described from the Fox Bay Formation (Lower Devonian; Pragian) of the Falkland Islands (South Atlantic). The fossils were collected from many localities in both East and West Falkland and represent the first significant collection of trilobites from East Falkland. The trilobites belong to three higher taxa: Proetida (the first proetid record in these islands); Homalonotidae, Burmeisteria Salter, 1865; and Calmoniidae, including Bainella Rennie, 1930 and Metacryphaeus Reed, 1907. All of the forms except proetids have now been found in both East and West Falkland.
THE EARLIEST ENCRINURID TRILOBITES FROM THE EAST BALTIC AND THEIR TAXONOMIC INTEREST
Authors: PÄRNASTE HELJE
Published: January 2006

Abstract:  The earliest known representative of the subfamily Encrinurinae, Encrinuroides regularis sp. nov., is described from the glauconitic sandstone of the Mäeküla Member, Billingen Stage (Arenig), from localities in the Baltic‐Ladoga Clint area. Cybele (subfamily Cybelinae) has its earliest appearance at about the same level, but at different localities, probably indicating their facies dependence. The predominant developing area of the pygidial axis and the general array of spines on the exoskeleton serve to distinguish the Encrinurinae and Cybelinae, but resolve the Staurocephalidae and Dindymeninae within the Encrinuridae. A reassessment of Encrinuroides and the genera recently excluded from it (Frencrinuroides, Physemataspis and Walencrinuroides) sustains the utility of an Encrinuroides sensu lato grouping and endorses Strusz's evolutionary lineages. Encrinuroides uncatus Evitt and Tripp, E. neuter Evitt and Tripp and probably Encrinuroides lapworthi Tripp belong in Erratencrinurus Krueger.
Taxing work
Authors: CUSACK THOMAS R. , BERAMENDI PABLO
Published: January 2006

Abstract. This article examines the development of tax regimes across OECD countries in the latter part of the twentieth century. It gives particular emphasis to taxes on labour income. Taxes on labour income represent a major drain on private households. They have become the mainstay of many of these countries’ public sector finances. Taxes on labour income rather than on capital appear to be the preferred instrument of finance for those economic and political interests that advocate and support a strong (and thereby expensive) welfare state. There is little ‘free lunch’ to be had in these welfare states; if anything, ‘socialism in one class’ seems to be the rule. Coordinated market economies tend to impose higher tax rates on labour because they have higher levels of wage coordination, their governments are more likely to be oriented to the left and their executives are relatively weak in relation to their legislatures.
The East European ‘ethnic nation’– Myth or reality?
Authors: BJÖRKLUND FREDRIKA
Published: January 2006

Abstract. This article challenges the assumption that there is an essential difference between a West European ‘civic’ and an East European ‘ethnic’ conceptualisation of the nation. If there were such a distinction, one should be able to trace a distinctive ‘ethnic’ concept of the nation among the populations of East European countries. The article analyses public opinion in three East European countries – Latvia, Poland and Lithuania – using a survey of more than 1,100 respondents in each country. This data suggests, first, that we must question the model of a general East European definition of the nation as an ethnic unit. Second, it is evident that the respondents of each country define the nation differently. For example, Latvian respondents presented a specific concept of the nation – one with clear ethnic undertones. A certain number of the Latvian respondents defined members of the nation according to a single criterion: having Latvian as one's mother tongue. The article also shows how we can deconstruct the concepts of the ethnic versus the civic nation, and thus analyse their separate components. This makes the distinction less rigid, and encourages the discovery of different combinations of ethnic and civic arguments. The result should be more nuanced studies of concepts of the nation and of national belonging.
Pairwise Fitting of Mixed Models for the Joint Modeling of Multivariate Longitudinal Profiles
Authors: Fieuws Steffen , Verbeke Geert
Published: January 2006

Summary A mixed model is a flexible tool for joint modeling purposes, especially when the gathered data are unbalanced. However, computational problems due to the dimension of the joint covariance matrix of the random effects arise as soon as the number of outcomes and/or the number of used random effects per outcome increases. We propose a pairwise approach in which all possible bivariate models are fitted, and where inference follows from pseudo‐likelihood arguments. The approach is applicable for linear, generalized linear, and nonlinear mixed models, or for combinations of these. The methodology will be illustrated for linear mixed models in the analysis of 22‐dimensional, highly unbalanced, longitudinal profiles of hearing thresholds.
Delineation of diversified desmoglein distribution in stratified squamous epithelia: implications in diseases
Authors: Mahoney Mỹ G. , Hu Ying , Brennan Donna , Bazzi Hisham , Christiano Angela M. , Wahl James K.
Published: January 2006

Abstract:  Desmogleins play critical roles in cell adhesion and skin blistering diseases, as they are the target antigens of autoimmune antibodies and bacterial toxins. We recently cloned several novel members of the desmoglein gene family, bringing the number of desmogleins to four in the rat and human genomes and six in the mouse. Here, we have produced a monoclonal antibody to a cytoplasmic epitope of Dsg4, assessed its specificity and compared it to several existing Dsg1–3 antibodies. We also demonstrated cross‐reactivity of commercially available and often used Dsg1 antibodies. Using these tools, we delineated the unique expression patterns of each desmoglein isoform in various human and mouse stratified squamous epithelia, including skin, hair, palm, and oral mucosa. Interestingly, in the epidermis, the expression of each desmoglein correlates with their gene arrangement in the cadherin locus. In human, Dsg4 was detected primarily in the granular and cornified cell layers of the epidermis, while present throughout all differentiated layers of the oral mucosa and palm, and in the matrix cells of anagen hair bulb. Similar pattern of expression for Dsg4 was observed in mouse, with the exception that it was expressed at significantly lower levels in the mouse epidermis. These results demonstrate the complexity of desmoglein gene expression and provide additional insights into the correlation between tissue expression patterns and disease phenotypes.
Low systemic exposure in infants with atopic dermatitis in a 1‐year pharmacokinetic study with pimecrolimus cream 1%*
Authors: Lakhanpaul M. , Davies T. , Allen B. R. , Schneider D.
Published: January 2006

Abstract:  Systemic drug exposure following the application of topical agents is a very important safety consideration, particularly in infants, who have a significantly higher ratio of body surface area to body mass than older children and adults. Here, we report on drug exposure in five infants aged 5.7–11.9 months at baseline, with extensive, moderate‐to‐severe atopic dermatitis (AD). Patients were treated bid for 1 year, as needed, with pimecrolimus cream 1% in an open‐label, non‐controlled study. No indication of drug accumulation was found; pimecrolimus blood concentrations were consistently low, ranging from below the limit of quantitation (0.1 ng/ml) to 1.94 ng/ml. Treatment over this prolonged period was well tolerated, with no evidence of any treatment‐related adverse events. The results of this 1‐year study indicate that long‐term management of AD with pimecrolimus cream 1% is associated with consistently very low systemic absorption, even in the youngest patients with extensive disease.
Killer Immunoglobulin‐like Receptor and Human Leukocyte Antigen Expression as Immunodiagnostic Parameters for Pelvic Endometriosis
Authors: Zhang Chunbin , Maeda Nagamasa , Izumiya Chiaki , Yamamoto Yorito , Kusume Tomoaki , Oguri Hiroyoshi , Yamashita Chika , Nishimori Yoshiko , Hayashi Kazutoshi , Luo Jiabin , Fukaya Takao
Published: January 2006

Problem  We investigated host immunologic responses to endometriosis by comparing immune cell surface antigens in peripheral blood (PB) and peritoneal fluid (PF) from women with endometriosis with those in PB and PF from other patients.

Method of study  Japanese women with endometriosis (n = 56) were compared with controls with other laparoscopic diagnoses (n = 68). PB and PF were collected at the time of laparoscopy for flow cytometry.

Results  No significant difference in phenotypic parameters of T cells (CD3, CD4, and CD8), B cells (CD19), natural killer (NK) cells (CD56), or monocytes/macrophages (CD14) was seen between women with and without endometriosis. However, increased killer immunoglobulin‐like receptor (CD158a) expression by NK cells and decreased human leukocyte antigen (HLA)‐ABC and ‐DR expression by macrophages, all suggesting decreased functional activation were found in endometriosis. These markers showed significant association with endometriosis by odds ratio, logistic regression, and decision tree analyses.

Conclusions  Increased CD158a+ NK cells in PB and PF indicated decreased NK cell cytotoxicity in endometriosis, while decreased HLA expression on PF macrophages suggested impaired antigen presentation. Thus, aberrant immune responses by NK cells and macrophages may represent risk factors for endometriosis.
The Progesterone‐Induced Blocking Factor Modulates the Balance of PKC and Intracellular Ca++
Authors: Kozma Noemi , Halasz Melinda , Palkovics Tamas , Szekeres‐Bartho Julia
Published: January 2006

Problem  Progesterone‐induced blocking factor (PIBF) induces Th2 biased cytokine production; therefore, this study investigates the effects of PIBF on the protein kinase C (PKC)/Ca++ system – which plays a key role in Th1/Th2 differentiation.

Method of study  Proteins from PIBF‐treated cells were reacted on Western blots with phospho‐specific antibodies recognizing different PKC izoforms. Intracellular free calcium was measured by flow cytometry.

Results  Both interleukin (IL)‐4 and PIBF induced PKC phosphorylation, which was abrogated by anti‐IL‐4Rα or anti‐PIBF immunoglobulin G pre‐treatment. PIBF treatment did not alter intracellular Ca++ levels. Inhibition of PKCζ or PKCθ phosphorylation, but not that of PKCα/β resulted in the loss of STAT6 and Jak1 phosphorylation by PIBF.

Conclusions  Our data show that PIBF phosphorylates PKC via binding to the IL‐4R, without affecting intracellular Ca++. Phosphorylation of PKCζ and PKCθ is required for Jak1 and STAT6 activation, whereas PKCα/β is not involved. These findings explain the mechanism by which PIBF supports a Th2 dominant cytokine pattern.
Does Seed Priming Induce Changes in the Levels of Some Endogenous Plant Hormones in Hexaploid Wheat Plants Under Salt Stress?
Authors: Iqbal Muhammad , Ashraf Muhammad , Jamil Amer , Ur‐Rehman Shafiq
Published: January 2006

In order to assess whether salt tolerance could be improved in spring wheat (Triticum aestivum L.), the present study was performed by soaking the seeds of two cultivars, namely MH‐97 (salt sensitive) and Inqlab‐91 (salt tolerant), for 12 h in distilled water or 100 mol/m3 CaCl2, KCl, or NaCl. Primed seeds from each treatment group and non‐primed seeds were sown in a field in which NaCl salinity of 15 dS/m was developed. Priming of seeds with CaCl2, followed by priming with KCl and NaCl, was found to be effective in alleviating the adverse effects of salt stress on both wheat cultivars in terms of shoot fresh and dry weights and grain yield. Priming with CaCl2 alleviated the adverse effects of salt stress on hormonal balance in plants of both cultivars. In MH‐97 plants, CaCl2 pretreatment considerably reduced leaf abscisic acid (ABA) concentrations and increased leaf free salicylic acid (SA) concentrations under both saline and non‐saline conditions. In contrast, in the Inqlab‐91 plant, CaCl2 increased free indoleacetic acid (IAA) and indolebutyric acid (IBA) content. However, priming of seeds with CaCl2 did not alter free polyamine levels in either cultivar, although spermidine levels were considerably lower in plants raised from seeds treated with CaCl2 for both cultivars under saline conditions. Priming with KCl increased growth in Inqlab‐91 plants, but not in MH‐97 plants, under saline conditions. The salinity induced reduction in auxins (IAA and IBA) was alleviated by NaCl priming in both cultivars under saline conditions. However, NaCl increased leaf free ABA content and lowered leaf SA and putrescine levels in Inqlab‐91 plants under saline conditions. In conclusion, although all three priming agents (i.e. CaCl2, KCl, and NaCl) were effective in alleviating the adverse effects of salt stress on wheat plants, their effects on altering the levels of different plant hormones were different in the two cultivars.

(Managing editor: Ping He)
Disruption of Cortical Microtubules by Overexpression of Green Fluorescent Protein‐Tagged α‐Tubulin 6 Causes a Marked Reduction in Cell Wall Synthesis
Authors: Burk David H. , Zhong Ruiqin , Morrison W. Herbert , Ye Zheng‐Hua
Published: January 2006

It has been known that the transverse orientation of cortical microtubules (MTs) along the elongation axis is essential for normal cell morphogenesis, but whether cortical MTs are essential for normal cell wall synthesis is still not clear. In the present study, we have investigated whether cortical MTs affect cell wall synthesis by direct alteration of the cortical MT organization in Arabidopsis thaliana. Disruption of the cortical MT organization by expression of an excess amount of green fluorescent protein‐tagged α‐tubulin 6 (GFP‐TUA6) in transgenic Arabidopsis plants was found to cause a marked reduction in cell wall thickness and a decrease in the cell wall sugars glucose and xylose. Concomitantly, the stem strength of the GFP‐TUA6 overexpressors was markedly reduced compared with the wild type. In addition, expression of excess GFP‐TUA6 results in an alteration in cell morphogenesis and a severe effect on plant growth and development. Together, these results suggest that the proper organization of cortical MTs is essential for the normal synthesis of plant cell walls.

(Managing editor: Wei Wang)
Gene Discovery and Functional Analyses in the Model Plant Arabidopsis
Authors: Feng Cai‐Ping , Mundy John
Published: January 2006

The present mini‐review describes newer methods and strategies, including transposon and T‐DNA insertions, TILLING, Deleteagene, and RNA interference, to functionally analyze genes of interest in the model plant Arabidopsis. The relative advantages and disadvantages of the systems are also discussed.

(Managing editor: Ping He)
Analysis of Global Expression Profiles of Arabidopsis Genes Under Abscisic Acid and H2O2 Applications
Authors: Wang Peng‐Cheng , Du Yan‐Yan , An Guo‐Yong , Zhou Yun , Miao Chen , Song Chun‐Peng
Published: January 2006

To gain insight into the coordination of gene expression profiles under abscisic acid (ABA) and H2O2 applications, global changes in gene expression in response to ABA and H2O2 in Arabidopsis seedlings were investigated using GeneChip (Santa Clara, CA, USA) arrays. Among over 24 000 genes present in the arrays, 459 transcripts were found to be significantly increased, whereas another 221 decreased following H2O2 treatment compared with control. Similar to treatment with H2O2, ABA treatment elevated the transcription of 391 genes and repressed that of 322 genes. One hundred and forty‐three upregulated genes and 75 downregulated genes were shared between the two treatments and these genes were mainly involved in metabolism, signal transduction, transcription, defense, and resistance. Only two genes, which encode an APETALA2/dehydration‐responsive element binding protein (AP2/DREBP) family transcriptional factor and a late embryogenesis‐abundant protein, were downregulated by H2O2, but upregulated by ABA. These results suggest that, similar to ABA, H2O2 plays a global role in gene transcription of Arabidopsis seedlings. The transcriptional responses induced by the application of exogenous ABA and H2O2 overlapped substantially. These two treatments regulated most of the downstream genes in a coordinated manner.

(Managing editor: Li‐Hui Zhao)
Improving Reverse Supply Chain Operational Performance: A Transshipment Application Study for Not‐for‐Profit Organizations
Authors: Reyes Pedro M. , Meade Laura M.
Published: January 2006

This paper describes an approach for improving the operational performance in the reverse supply chain in a not‐for‐profit environment. The authors present a model based on risk pooling through preventive lateral transshipment as a method for improving the responsiveness of not‐for‐profit core business practice of redistributing donated products in order to increase revenues. The model considers a three‐echelon structure consisting of three collection centers, one sorting and disposition center, and three retail stocking locations. The ensuing simulation indicates a favorable response of the model. Results indicated that while the daily average inventories slightly increased, the frequency of lost sales significantly decreased, thus offering the potential increased revenues.
Effect of spontaneous exercise on antioxidant capacity in rat muscles determined by electron spin resonance
Authors: Tanabe K. , Masuda K. , Hirayama A. , Nagase S. , Kono I. , Kuno S.
Published: January 2006

Aims:  The effect of physical activity on antioxidant capacity in muscle remains unknown. This study investigated the effect of spontaneous exercise on antioxidant capacity in rat muscles determined by electron spin resonance (ESR), which is a technique for the direct detection of free radicals.

Methods:  Ten‐week‐old male Wistar rats were housed individually in cages with a running wheel. Rats were classified as high activity (HA), middle activity (MA) or low activity group (LA), based on an assessment of running distance covered over a 23‐week period. After 23 weeks of housing, soleus (Sol), plantaris (Pl), gastrocnemius [deep/surface portions (GasD/GasS)] and heart (Hrt) muscles were isolated, and scavenging activity against superoxide anions () and hydroxyl radicals (HO·) was determined by ESR using a spin‐trap chemical. The citrate synthase (CS) activity was used as a marker of mitochondrial oxidative phosphorylation capacity.

Results:  Among the parameters measured, only scavenging activity in GasD significantly correlated with the running distance. The highest scavenging activity was observed in Hrt of HA rats. The scavenging activity in Pl of MA rats was significantly higher than that of LA rats. The scavenging activity of Sol and GasS was not significantly different between the three groups. Furthermore, the HO· scavenging activity of any muscle specimens was similar among the three groups and did not correlate with running distance at all. CS activity did not significantly differ between the three groups.

Conclusion:  These data suggest that scavenging activity in specific types of muscle tissues would increase especially in spontaneously active animals. However, HO· scavenging activity would not.
Metabolic cost, mechanical work, and efficiency during walking in young and older men
Authors: Mian O. S. , Thom J. M. , Ardigò L. P. , Narici M. V. , Minetti A. E.
Published: January 2006

Aim:  To investigate mechanical work, efficiency, and antagonist muscle co‐activation with a view to better understand the cause of the elevated metabolic cost of walking (CW) in older adults.

Methods:  Metabolic, mechanical and electromyographic measurements were made as healthy young (YOU; n = 12, age = 27 ± 3 years) and older (OLD; n = 20, age = 74 ± 3 years) men of equivalent body mass and leg length walked on a treadmill at four speeds (ranging from 0.83 to 1.67 m s−1).

Results:  Net (above resting) CW, determined by indirect calorimetry was 31% higher (average across speeds) in OLD (P < 0.05). The integrity of the passive pendulum like interchange of mechanical energies of the centre of mass (COMB), an energy‐saving mechanism, was maintained in OLD. Furthermore, total mechanical work, determined from fluctuations in mechanical energy of COMB and of body segments relative to COMB, was not significantly elevated in OLD. This resulted in a lower efficiency in OLD (−17%, P < 0.05). Co‐activation, temporally quantified from electromyography recordings, was 31% higher in OLD for antagonist muscles of the thigh (P < 0.05). Thigh co‐activation was moderately correlated with CW at three speeds (r = 0.38–0.52, P < 0.05).

Conclusion:  Healthy septuagenarians with no gait impairment have an elevated CW which is not explained by an elevation in whole body mechanical work. Increased antagonist muscle co‐activation (possibly an adaptation to ensure adequate joint stability) may offer partial explanation of the elevated CW.
Ground Effect Aerodynamics of Race Cars
Authors: Zhang Xin , Toet Willem , Zerihan Jonathan
Published: January 2006

We review the progress made during the last 30years on ground effect aerodynamics associated with race cars, in particular open wheel race cars. Ground effect aerodynamics of race cars is concerned with generating downforce, principally via low pressure on the surfaces nearest to the ground. The “ground effect” parts of an open wheeled car’s aerodynamics are the most aerodynamically efficient and contribute less drag than that associated with, for example, an upper rear wing. While drag reduction is an important part of the research, downforce generation plays a greater role in lap time reduction. Aerodynamics plays a vital role in determining speed and acceleration (including longitudinal acceleration but principally cornering acceleration), and thus performance. Attention is paid to wings and diffusers in ground effect and wheel aerodynamics. For the wings and diffusers in ground effect, major physical features are identified and force regimes classified, including the phenomena of downforce enhancement, maximum downforce, and downforce reduction. In particular the role played by force enhancement edge vortices is demonstrated. Apart from model tests, advances and problems in numerical modeling of ground effect aerodynamics are also reviewed and discussed. This review article cites 89 references.
Methylation of tRNA
Asp
by the DNA Methyltransferase Homolog Dnmt2
Authors: Goll Mary Grace , Kirpekar Finn , Maggert Keith A. , Yoder Jeffrey A. , Hsieh Chih-Lin , Zhang Xiaoyu , Golic Kent G. , Jacobsen Steven E. , Bestor Timothy H.
Published: January 2006

The sequence and the structure of DNA methyltransferase-2 (Dnmt2) bear close affinities to authentic DNA cytosine methyltransferases. A combined genetic and biochemical approach revealed that human DNMT2 did not methylate DNA but instead methylated a small RNA; mass spectrometry showed that this RNA is aspartic acid transfer RNA (tRNA
Asp
) and that DNMT2 specifically methylated cytosine 38 in the anticodon loop. The function of DNMT2 is highly conserved, and human DNMT2 protein restored methylation in vitro to tRNA
Asp
from Dnmt2-deficient strains of mouse, Arabidopsis thaliana, and Drosophila melanogaster in a manner that was dependent on preexisting patterns of modified nucleosides. Indirect sequence recognition is also a feature of eukaryotic DNA methyltransferases, which may have arisen from a Dnmt2-like RNA methyltransferase.
Core Knowledge of Geometry in an Amazonian Indigene Group
Authors: Dehaene Stanislas , Izard Véronique , Pica Pierre , Spelke Elizabeth
Published: January 2006

Does geometry constitute a core set of intuitions present in all humans, regardless of their language or schooling? We used two nonverbal tests to probe the conceptual primitives of geometry in the Mundurukú, an isolated Amazonian indigene group. Mundurukú children and adults spontaneously made use of basic geometric concepts such as points, lines, parallelism, or right angles to detect intruders in simple pictures, and they used distance, angle, and sense relationships in geometrical maps to locate hidden objects. Our results provide evidence for geometrical intuitions in the absence of schooling, experience with graphic symbols or maps, or a rich language of geometrical terms.
Linking Neurons and Ethics
Authors: Bosch Xavier
Published: January 2006

The Ethical Brain
.
By Michael S. Gazzaniga
. Dana Press, Washington, DC, 2005. 221 pp. $25, £17.50. ISBN 1-932594-01-9.

In this thought-provoking exploration of ethical issues raised by the findings and techniques of brain science, the author devotes considerable attention to how we reach our moral judgments.
Solvent-Induced Association of Polymers: Clustering and Network Formation
Authors: Pouchlý Julius , Živný Antonín , Sikora Antonín
Published: January 2006

A thermodynamic treatment of a random, solvent-assisted association of polyfunctional macromolecules is developed. In the model proposed, a multiple association junction connecting m primary chains consists of m polymer functional groups with bm solvent molecules incorporated. Using Veytsman's procedure, basic thermodynamic functions and association equilibrium relations are derived. Different association characteristics are examined. When passing from a system with solvent-free junctions (b = 0) to our model with b > 0, the shape of the calculated curves changes strikingly, e.g. the relative association degree α vanishes both in the neat solvent and neat polymer points, showing a maximum near the middle of the composition range. This results in the existence of two critical points of network formation (gel points), delimitating the compositional range of the coexistence of a network with finite clusters (gel region). Using extinction probability, the quantitative parameters characterizing the cluster-network relationships are calculated and analyzed. All of them display an extreme near the middle of the gel region, and various kinds of singularities appear in the two gel points. The effect of the stoichiometric ratio b on characteristic system parameters is discussed.
Synthesis of N4-Substituted Derivatives of 1-[2-(Phosphonomethoxy)ethyl]cytosine and Its Diisopropyl Ester as a Model Reaction for the Synthesis of N4-Substituted Derivatives of Cidofovir
Authors: Chalupová Šárka , Holý Antonín , Masojídková Milena
Published: January 2006

We have studied the reaction of 1-[2-(phosphonomethoxy)ethyl]cytosine (1) and its diisopropyl ester (2) with triethylammonium hydrogensulfite in 60% aqueous methanol. In the presence of some primary or secondary amine salts, at 25-70 °C, this reaction affords transaminated derivatives 4a-4e and 5a, 5b as main products accompanied by uracil compounds. However, with certain amines the reaction failed.
A DYNAMICAL MECHANISM TO EXPLAIN THE TOP-BOTTOM QUARK MASS HIERARCHY
Authors: DOFF A. , NATALE A. A.
Published: January 2006

We discuss the mass splitting between the the top and bottom quarks in a technicolor scenario. The model proposed here contains a left–right electroweak gauge group. An extended technicolor group and mirror fermions are introduced. The top-bottom quark mass splitting turns out to be intimately connected to the breaking of the left–right gauge symmetry. Weak isospin violation occurs within the experimental limits.
APPLICATION OF ARTIFICIAL NEURAL NETWORK TO THE IDENTIFICATION OF QUARK AND GLUON JETS
Authors: YU MEILING , ZHANG KUNSHI , LIU LIANSHOU
Published: January 2006

The Back-Propagation neural network method is used to identify quark and gluon jets generated by Monte Carlo method. The effects of some factors, such as the architecture of neural network, the input parameters, the training precision and the acceptance cut, on the performance of the neural network are studied in detail. The efficiency and purity of identified quark and gluon jets are calculated for different network architectures. It is found that in order to keep the role of all the input parameters balance, they have to be scaled to the same order of magnitude. Through the study on how the efficiency and purity of the identified quark- and gluon-jets vary with the training precision and acceptance cut, a guidance for how to choose these two parameters is given.
THE DEVELOPMENT OF THE GRAVITATIONAL AND YANG–MILLS FIELDS, AND THE TREATMENT OF ACCELERATED FRAMES
Authors: HSU JONG-PING , FINE DANA
Published: January 2006

We discuss ideas and problems regarding classical and quantum gravity, gauge theory of gravity, and space–time transformations between accelerated frames. Both Einstein's theory of gravity and Yang–Mills theory are gauge invariant. The invariance principles are at the very heart of our understanding of the physical world. This paper attempts to survey the development and to reveal problems and limitations of various formulations to gravitational and Yang–Mills fields, and to space–time transformations of accelerated frames. Gravitational force and accelerated frames are two ingredients in Einstein's thought in the period around 1907. Accelerated frames are difficult to define and are not well developed. However, one cannot claim to have a complete understanding of the physical world, if one understands flat space–time physics only from the viewpoint of the special class of inertial frames and ignores the vast class of noninertial frames. The paper highlights three aspects: (1) ideas of gravity as a Yang–Mills field, first discussed by Utiyama; (2) problems of quantum gravity, discussed by Feynman, Dyson and others; (3) space–time properties and the physics of fields and particles in accelerated frames of reference. These unfulfilled aspects of Einstein and Yang–Mills' profound thoughts present a challenge to physicists and mathematicians in the 21st century.
PULSATING NEUTRON STAR AS A SOURCE OF QUASISTATIC WAVES OF GRAVITY IN INTERSTELLAR MEDIUM
Authors: BASTRUKOV S. , MOLODTSOVA I. , YANG J. , PAPOYAN V.
Published: January 2006

The hydrodynamic waves of gravity in the galactic interstellar medium generated by a pulsating neutron star are discussed in this paper. It is shown that the frequency of oscillations of interstellar gas–dust matter in this wave is proportional to that for the g-mode in the neutron star bulk. The corresponding periods are of the millisecond duration. The collective oscillations of charged species in the interstellar wave of gravity can produce electromagnetic radiation, and that the only radio waves of this radiation can freely travel through the galactic gas–dust clouds, suggests that this kind of interstellar waves can manifest itself in the radio range of spectra of a neutron star undergoing pulsations triggered by starquake. This inference is in line with the statement that quasiperiodic micropulses with a time scale of a few milliseconds located in the windows of the main pulse train of the radio pulsar spectra owe their origin to pulsations of neutron stars.
BLOCH–NORDSIECK ESTIMATES OF A HIGH-TEMPERATURE SCALAR FIELD THEORY
Authors: CANDELPERGHER B. , FRIED H. M. , GRANDOU T.
Published: January 2006

In anticipation of subsequent application to QED and QCD, we consider the case of a model, high temperature, relativistic, scalar field theory. We introduce into the exact, nonperturbative, functional expressions of this "quenched" model, a new Fradkin representation, and extract the infrared/Bloch–Nordsieck/(IR/BN) contributions of every perturbative graph, in order to circumvent the lack of a clear-cut separation of energy scales of previous semiperturbative treatments. Our results are applicable to the absorption of a fast particle which enters a heat bath, as well as to the propagation of a symmetric pulse within the thermal medium due to the appearance of an instantaneous, shockwave-like source acting in the medium. In momentum space, the former case displays a propagator which decays exponentially with increasing time, in addition to a new damping factor independent of time. The latter case displays an exponential growth with time of the symmetric pulse, generating effective and increasing plasmon waves, in competition with damping independent of time. When extended to QCD, qualitative applications could be made to RHIC scattering, in which a fireball appears, expands and is damped away.
B-MESON DISTRIBUTION AMPLITUDES
Authors: GROZIN ANDREY
Published: January 2006

B-meson light-cone distribution amplitudes are discussed in these lectures in the framework of HQET. The evolution equation for the leading-twist distribution amplitude is derived in one-loop approximation. QCD sum rules for distribution amplitudes are discussed.
SEMICLASSICAL INITIAL VALUE TREATMENTS OF ATOMS AND MOLECULES
Authors: Kay Kenneth G.
Published: January 2006

▪ Abstract  This review describes some developments in the theory and application of the semiclassical initial representation for the treatment of the dynamical and static properties of atoms and molecules. The theoretical basis of initial value treatments for the propagator is discussed. A variety of useful alternative initial value expressions for the propagator and other quantities are presented as generalizations of the well-known Herman-Kluk approximation. Special emphasis is given to treatments that involve integration over only half the phase space variables. The recent development of semiclassical initial value expressions that are exact for specific, desired systems is reviewed and some of the implications are described.
Relation between muscle fiber conduction velocity and fiber size in neuromuscular disorders
Authors: Blijham P. J. , ter Laak H. J. , Schelhaas H. J. , van Engelen B. G. M. , Stegeman D. F. , Zwarts M. J.
Published: January 2006

To determine the relation between muscle fiber conduction velocity (MFCV) and muscle fiber diameter (MFD) in pathological conditions, we correlated invasively measured MFCV values with MFD data obtained from muscle needle biopsies in 96 patients with various neuromuscular disorders. MFCV was significantly correlated with MFD and independent of the underlying disorder. Pathological diameter changes were fiber-type dependent, with corresponding MFCVs. A linear equation expresses the relation well: MFCV (m/s) = 0.043·MFD (μm) + 0.83. We conclude that fiber diameter determines MFCV largely independent of the underlying neuromuscular disorders studied.
Specificity of Cone Inputs to Macaque Retinal Ganglion Cells
Authors: Sun Hao , Smithson Hannah E. , Zaidi Qasim , Lee Barry B.
Published: January 2006

The specificity of cone inputs to ganglion cells has implications for the development of retinal connections and the nature of information transmitted to higher areas of the brain. We introduce a rapid and precise method for measuring signs and magnitudes of cone inputs to visual neurons. Colors of stimuli are modulated around circumferences of three color planes in clockwise and counterclockwise directions. For each neuron, the projection of the preferred vector in each plane was estimated by averaging the response phases to clockwise and counterclockwise modulation. The signs and weights of cone inputs were derived directly from the preferred vectors. The efficiency of the method enables us to measure cone inputs at different temporal frequencies and short-wavelength-sensitive (S) cone adaptation levels. The results show that S-cone inputs to the parvocellular and magnocellular ganglion cells are negligible, which implies underlying connectional specificity in the retinal circuitry.
Effects of a Chronic Compression of the Dorsal Root Ganglion on Voltage-Gated Na+ and K+ Currents in Cutaneous Afferent Neurons
Authors: Tan Z. Y. , Donnelly D. F. , LaMotte R. H.
Published: January 2006

A chronic compression of the dorsal root ganglion (CCD) produces ipsilateral cutaneous hyperalgesia that is associated with an increased excitability of neuronal somata in the compressed ganglion, as evidenced by spontaneous activity and a lower rheobase. We searched for differences in the properties of voltage-gated Na+ and K+ currents between somata of CCD- and control (unoperated) rats. CCD was produced in adult rats by inserting two rods through the intervertebral foramina, one compressing the L4, and the other, the ipsilateral, L5 dorsal root ganglion (DRG). After 5–9 days, DRG somata were dissociated and placed in culture for 16–26 h. Cutaneous neurons of medium size (35–45 μm), Fluorogold-labeled from the hindpaw, were selected for whole cell patch-clamp recording of action potentials and ion currents. In comparison with control neurons, CCD neurons had steady-state activation curves for TTX-sensitive (TTX-S) Na+ currents that were shifted in the hyperpolarizing direction, and CCD neurons had enhanced TTX-resistant (TTX-R) current. CCD neurons also had smaller, fast-inactivating K+ currents (Ka) at voltages from −30 to 50 mV. The reduction in Ka, the hyperpolarizing shift in TTX-S Na+ current activation, and the enhanced TTX-R Na+ current may all contribute to the enhanced neuronal excitability and thus to the pain and hyperalgesia associated with CCD.
Diagnostic Markers of Ovarian Cancer by High-Throughput Antigen Cloning and Detection on Arrays
Authors: Chatterjee Madhumita , Mohapatra Saroj , Ionan Alexei , Bawa Gagandeep , Ali-Fehmi Rouba , Wang Xiaoju , Nowak James , Ye Bin , Nahhas Fatimah A. , Lu Karen , Witkin Steven S. , Fishman David , Munkarah Adnan , Morris Robert , Levin Nancy K. , Shirley Natalie N. , Tromp Gerard , Abrams Judith , Draghici Sorin , Tainsky Michael A.
Published: January 2006

A noninvasive screening test would significantly facilitate early detection of epithelial ovarian cancer. This study used a combination of high-throughput selection and array-based serologic detection of many antigens indicative of the presence of cancer, thereby using the immune system as a biosensor. This high-throughput selection involved biopanning of an ovarian cancer phage display library using serum immunoglobulins from an ovarian cancer patient as bait. Protein macroarrays containing 480 of these selected antigen clones revealed 65 clones that interacted with immunoglobulins in sera from 32 ovarian cancer patients but not with sera from 25 healthy women or 14 patients having other benign or malignant gynecologic diseases. Sequence analysis data of these 65 clones revealed 62 different antigens. Among the markers, we identified some known antigens, including RCAS1, signal recognition protein-19, AHNAK-related sequence, nuclear autoantogenic sperm protein, Nijmegen breakage syndrome 1 (Nibrin), ribosomal protein L4, Homo sapiens KIAA0419 gene product, eukaryotic initiation factor 5A, and casein kinase II, as well as many previously uncharacterized antigenic gene products. Using these 65 antigens on protein microarrays, we trained neural networks on two-color fluorescent detection of serum IgG binding and found an average sensitivity and specificity of 55% and 98%, respectively. In addition, the top 6 of the most specific clones resulted in an average sensitivity and specificity of 32% and 94%, respectively. This global approach to antigenic profiling, epitomics, has applications to cancer and autoimmune diseases for diagnostic and therapeutic studies. Further work with larger panels of antigens should provide a comprehensive set of markers with sufficient sensitivity and specificity suitable for clinical testing in high-risk populations. (Cancer Res 2006; 66(2): 1181-90)
c-Myc Overexpression Causes Anaplasia in Medulloblastoma
Authors: Stearns Duncan , Chaudhry Aneeka , Abel Ty W. , Burger Peter C. , Dang Chi V. , Eberhart Charles G.
Published: January 2006

Both anaplasia and increased c-myc gene expression have been shown to be negative prognostic indicators for survival in medulloblastoma patients. myc gene amplification has been identified in many large cell/anaplastic medulloblastoma, but no causative link between c-myc and anaplastic changes has been established. To address this, we stably overexpressed c-myc in two medulloblastoma cell lines, DAOY and UW228, and examined the changes in growth characteristics. When analyzed in vitro, cell lines with increased levels of c-myc had higher rates of growth and apoptosis as well as significantly improved ability to form colonies in soft agar compared with control. When injected s.c. into nu/nu mice, flank xenograft tumors with high levels of c-myc in DAOY cell line background were 75% larger than those derived from control. Overexpression of c-myc was required for tumor formation by UW228 cells. Most remarkably, the histopathology of the Myc tumors was severely anaplastic, with large areas of necrosis/apoptosis, increased nuclear size, and macronucleoli. Indices of proliferation and apoptosis were also significantly higher in Myc xenografts. Thus, c-myc seems to play a causal role in inducing anaplasia in medulloblastoma. Because anaplastic changes are often observed in recurrent medulloblastoma, we propose that c-myc dysregulation is involved in the progression of these malignant embryonal neoplasms. (Cancer Res 2006; 66(2): 673-81)
Profiling Genetic Variation along the Androgen Biosynthesis and Metabolism Pathways Implicates Several Single Nucleotide Polymorphisms and Their Combinations as Prostate Cancer Risk Factors
Authors: Mononen Nina , Seppälä Eija H. , Duggal Priya , Autio Ville , Ikonen Tarja , Ellonen Pekka , Saharinen Juha , Saarela Janna , Vihinen Mauno , Tammela Teuvo L.J. , Kallioniemi Olli , Bailey-Wilson Joan E. , Schleutker Johanna
Published: January 2006

Several candidate genes along androgen pathway have been suggested to affect prostate cancer risk but no single gene seems to be overwhelmingly important for a large fraction of the patients. In this study, we first screened for variants in candidate genes and then chose to explore the association between 18 variants and prostate cancer risk by genotyping DNA samples from unselected (n = 847) and familial (n = 121) prostate cancer patients and population controls (n = 923). We identified a novel single nucleotide polymorphism (SNP) in the CYP19A1 gene, T201M, with a mild significant association with prostate cancer [odds ratio (OR), 2.04; 95% confidence interval (95% CI), 1.03-4.03; P = 0.04]. Stratified analysis revealed that this risk was most apparent in patients with organ-confined (T1-T2) and low-grade (WHO grade 1) tumors (OR, 5.42; 95% CI, 2.33-12.6; P < 0.0001). In contrast, CYP17A1 −34T>C alteration was associated with moderate to poorly differentiated (WHO grade 2-3) organ-confined disease (OR, 1.42; 95% CI, 1.09-1.83; P = 0.007). We also tested a multigenic model of prostate cancer risk by calculating the joint effect of CYP19A1 T201M with five other common SNPs. Individuals carrying both the CYP19A1 and KLK3 −252A>G variant alleles had a significantly increased risk for prostate cancer (OR, 2.87; 95% CI, 1.10-7.49; P = 0.03). In conclusion, our results suggest that several SNPs along the androgen pathway, especially in CYP19A1 and CYP17A1, may influence prostate cancer development and progression. These genes may have different contributions to distinct clinical subsets as well as combinatorial effects in others illustrating that profiling and joint analysis of several genes along each pathway may be needed to understand genetic contributions to prostate cancer etiology. (Cancer Res 2006; 66(2): 743-7)