bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of elevation and forest cover on winter birds in mature forest ecosystems of southern British Columbia
Authors: Herbers Jim R , Serrouya Robert , Maxcy Katherine A
Published: February 2005

Winter diversity, distribution, and density of nonmigratory birds were examined in six mature forest ecosystems from two study areas in southern British Columbia. Forest age ranged from 91 to 150 years and the ecosystems ranged from 500 to 2100 m above sea level. Sampled forest stands had no previous history of logging and were a minimum 30 ha in size. The main objectives of this study were to measure nonmigratory birds in relation to elevation and to percentage of stand-level lodgepole pine composition. Twenty-one nonmigratory bird species totaling 2747 observations were detected at 775 point-count stations in 107 stands using 10-min unlimited-distance point counts. Pine siskins (Carduelis pinus (Wilson, 1810)), red-breasted nuthatches (Sitta canadensis L., 1766), and red crossbills (Loxia curvirostra L., 1758) were the three most commonly detected species. Mature forests at low elevation had between 1.7 and 3.5 times more species and between 2.0 and 4.7 times more birds than forests at high elevation. In addition, species richness and bird density declined with increasing stand-level composition of lodgepole pine. We suggest that low-elevation ecosystems be given high priority in coarse-filter management of winter bird habitat.
Territory size and overlap in male Ovenbirds: contrasting a fragmented and contiguous boreal forest
Authors: Mazerolle Daniel F , Hobson Keith A
Published: February 2005

We evaluated if male age and body size, density of conspecifics, and arthropod biomass contributed to variation in territory size and overlap of Ovenbirds, Seiurus aurocapillus (L., 1766), in a fragmented and contiguous boreal forest. Territory size and overlap were determined by radio-tracking territorial male Ovenbirds in fragmented (n = 22) and contiguous forest (n = 13) from late May to the end of June 1999 and 2000. Variation in male territory size was most strongly associated with individual characteristics, specifically body size and age. Furthermore, we found strong support for an effect of density of conspecifics on territory overlap, suggesting that the exclusivity of territories and perhaps levels of territoriality were greater for males in contiguous forest than for those in fragments. Our findings (i.e., mean territory size was similar between landscapes and territory overlap was greater in fragments than in contiguous forest) suggest that fragments either have larger areas of unsuitable habitat or are less saturated with Ovenbirds. Furthermore, because resources were not distributed equally among individuals, our results were consistent with the ideal dominance model of habitat selection. Finally, previous studies based on acoustical surveys have likely underestimated space-use requirements in forest passerines.
The effect of depth on the diving behaviour of common eiders
Authors: Guillemette Magella , Woakes Anthony J , Henaux Viviane , Grandbois Jean-Marc , Butler Patrick J
Published: February 2005

Diving in endotherms is largely constrained by the depth of the foraging area, as they withstand long periods without breathing. Foraging theory predicts that all phases of a dive cycle, including travel, bottom, and surface durations, are positively correlated with depth. With continued increase in depth, bottom duration should level off and then decline. We tested these qualitative predictions with common eiders (Somateria mollissima (L., 1758)), a sea duck foraging routinely on the bottom. Using data loggers implanted in the body cavity of four females for 1 year, we showed that average diving depth over the summer and winter was distinct for each female. When averaged for each female, the data were qualitatively similar to theoretical predictions since travel, bottom, and surface durations all increased with depth. However, within individual females, the data only supported the theory partially because some relationships between depth and phases of a dive cycle were not significant. In particular, bottom duration failed to increase with depth for two individual females during the summer. In addition, significant relationships differed substantially among individual females and even within individual females when summer and winter seasons were compared. We suggest that the large variation observed in the diving behaviour of female eiders reflects individual female diving capability, which is probably related to their physiological states.
Aromatase Inhibitors: Rationale and Use in Breast Cancer
Authors: Osborne Cynthia , Tripathy Debu
Published: February 2005

Considerable data implicate estrogens in breast cancer carcinogenesis and progression. In the postmenopausal woman, estrogens are produced in breast tissues and many other sites throughout the body when androgen precursors are converted into estrogens via the enzyme aromatase. Inhibition of this enzyme with aromatase inhibitors (AIs) has demonstrated reductions in systemic as well as intratumoral estrogens. These drugs have now been utilized in large phase 3 randomized trials and have led to greater improved clinical benefit than the “gold standard,” tamoxifen. Questions remain about the long-term side effects and safety profile of AIs. They are associated with increasing incidence of osteoporosis and bone fractures. Nevertheless, AIs add to our armamentarium for therapy and possible prevention of breast cancer.
Genetics of Longevity and Aging
Authors: Vijg Jan , Suh Yousin
Published: February 2005

Longevity, i.e., the property of being long-lived, has its natural limitation in the aging process. Longevity has a strong genetic component, as has become apparent from studies with a variety of organisms, from yeast to humans. Genetic screening efforts with invertebrates have unraveled multiple genetic pathways that suggest longevity is promoted through the manipulation of metabolism and the resistance to oxidative stress. To some extent, these same mechanisms appear to act in mammals also, despite considerable divergence during evolution. Thus far, evidence from population-based studies with humans suggests the importance of genes involved in cardiovascular disease as important determinants of longevity. The challenge is to test if the candidate longevity genes that have emerged from studies with model organisms exhibit genetic variation for life span in human populations. Future investigations are likely to involve large-scale case-control studies, in which large numbers of genes, corresponding to entire gene functional modules, will be assessed for all possible sequence variation and associated with detailed phenotypic information on each individual over extended periods of time. This should eventually unravel the genetic factors that contribute to each particular aging phenotype.
Administered mesenchymal stem cells protect against ischemic acute renal failure through differentiation-independent mechanisms
Authors: Tögel Florian , Hu Zhuma , Weiss Kathleen , Isaac Jorge , Lange Claudia , Westenfelder Christof
Published: February 2005

Severe acute renal failure (ARF) remains a common, largely treatment-resistant clinical problem with disturbingly high mortality rates. Therefore, we tested whether administration of multipotent mesenchymal stem cells (MSC) to anesthetized rats with ischemia-reperfusion-induced ARF (40-min bilateral renal pedicle clamping) could improve the outcome through amelioration of inflammatory, vascular, and apoptotic/necrotic manifestations of ischemic kidney injury. Accordingly, intracarotid administration of MSC (∼ 106/animal) either immediately or 24 h after renal ischemia resulted in significantly improved renal function, higher proliferative and lower apoptotic indexes, as well as lower renal injury and unchanged leukocyte infiltration scores. Such renoprotection was not obtained with syngeneic fibroblasts. Using in vivo two-photon laser confocal microscopy, fluorescence-labeled MSC were detected early after injection in glomeruli, and low numbers attached at microvasculature sites. However, within 3 days of administration, none of the administered MSC had differentiated into a tubular or endothelial cell phenotype. At 24 h after injury, expression of proinflammatory cytokines IL-1β, TNF-α, IFN-γ, and inducible nitric oxide synthase was significantly reduced and that of anti-inflammatory IL-10 and bFGF, TGF-α, and Bcl-2 was highly upregulated in treated kidneys. We conclude that the early, highly significant renoprotection obtained with MSC is of considerable therapeutic promise for the cell-based management of clinical ARF. The beneficial effects of MSC are primarily mediated via complex paracrine actions and not by their differentiation into target cells, which, as such, appears to be a more protracted response that may become important in late-stage organ repair.
Altered expression profile of transporters in the inner medullary collecting duct of aquaporin-1 knockout mice
Authors: Morris Ryan G. , Uchida Shinichi , Brooks Heddwen , Knepper Mark A. , Chou Chung-Lin
Published: February 2005

Aquaporin-1 is the major protein responsible for transport of water across the epithelia of the proximal tubule and thin descending limbs. Rapid water efflux across the thin descending limb is required for the normal function of the countercurrent multiplier mechanism. Therefore, urinary concentrating capacity is severely impaired in aquaporin-1 knockout (AQP1 −/−) mice. Here, we have investigated the long-term consequences of deletion of the AQP1 gene product by profiling abundance changes in transporters expressed in the inner medullas of AQP1 (−/−) mice vs. heterozygotes [AQP1 (+/−)], which have a normal concentrating capacity. Semiquantitative immunoblotting demonstrated marked suppression of two proteins strongly expressed in the inner medullary collecting duct (IMCD): UT-A1 (a urea transporter) and AQP4 (a basolateral water channel). Furthermore, the urea permeability of the IMCD was significantly reduced in AQP1 (−/−) mice. In contrast, there was increased expression of three proteins normally expressed at higher levels in the cortical collecting duct (CCD) than in IMCD: AQP3 (another basolateral water channel) and the epithelial sodium channel subunits β-ENaC and γ-ENaC. Changes in expression of these proteins were confirmed by immunocytochemistry. Messenger RNA profiling (real-time RT-PCR) revealed changes in UT-A1, β-ENaC, γ-ENaC, and AQP3 transcript abundance that paralleled the changes in protein abundance. Thus, from the perspective of transport proteins, the IMCDs of AQP1 (−/−) mice have a significantly altered phenotype. To address whether these changes are specific to AQP1 (−/−) mice, we profiled IMCD transporter expression in a second knockout model manifesting a concentrating defect, that of ClC-nK1, a chloride channel in the ascending thin limb important for urinary concentration. As in the AQP1 knockout mice, ClC-nK1 (−/−) mice showed decreased expression of UT-A1 and increased expression of β-ENaC and γ-ENaC vs. WT controls. In conclusion, the expression profile of IMCD transporters is markedly altered in AQP1 −/− mice and this manifestation is related to the associated concentrating defect.
CD40/CD154 ligation induces mononuclear cell adhesion to human renal proximal tubule cells via increased ICAM-1 expression
Authors: Li Hongye , Nord Edward P.
Published: February 2005

The role of CD40/CD154 ligation in the upregulation of genes of the proinflammatory nuclear factor-κB (NF-κB) signal transduction pathway was explored in primary cultures of human renal proximal tubule epithelial cells. Using a cDNA gene array specific for human NF-κB signal pathway genes, 38 genes were upregulated at 1 h, and 7 of these genes remained upregulated at 3 h. Of these genes, intercellular adhesion molecule-1 (ICAM-1) was explored in further detail. Quantitative real-time PCR for ICAM-1 mRNA expression confirmed the gene array findings. Western blot analysis and quantitative sandwich-enzyme ELISA confirmed this observation at the protein level. A cell-surface ELISA assay showed that ICAM-1 expression doubled by 48 h of CD154 exposure, and fluorescence-activated cell sorter analysis suggested that both the number of cells expressing ICAM-1 and the expression of ICAM-1 on these cells had increased. A cell adhesion assay using fluorescein-labeled human peripheral mononuclear cells showed that ICAM-1 upregulation resulted in increased mononuclear cell adhesion to the monolayer, which was abrogated by pretreatment of the monolayer with a neutralizing ICAM-1 antibody. The p38 mitogen-activated protein kinase (MAPK) inhibitor SB-203580 but not the extracellular signal-regulated kinase 1/2 inhibitor (PD-98059) nor the protein kinase C inhibitor (calphostin) blunted ICAM-1 expression and mononuclear cell adhesion to the monolayer. We conclude that, in human renal proximal tubule epithelial cells, CD40 activation upregulates ICAM-1 (and other NF-κB pathway genes) expression with concomitant enhanced adhesion of mononuclear cells, which is mediated via the p38 MAPK signal transduction pathway.
Insulin treatment enhances AT1receptor function in OK cells
Authors: Banday Anees Ahmad , Siddiqui Athar H. , Menezes Michelle M. , Hussain Tahir
Published: February 2005

Increased renal sodium retention is considered a major risk factor contributing to hypertension associated with chronic hyperinsulinemia and obesity. However, the molecular mechanism involved is not understood. The present study investigates the effect of insulin treatment on AT1receptor expression and ANG II-induced stimulation of Na/H exchanger (NHE) and Na-K-ATPase (NKA) in opossum kidney (OK) cells, a proximal tubule cell line. The presence of the AT1receptors in OK cells was confirmed by the specific binding of125I-sar-ANG II and by detecting ∼43-kDa protein on Western blot analysis with AT1receptor antibody and blocking peptide as well as by expression of AT1receptor mRNA as determined by RT-PCR. Insulin treatment (100 nM for 24 h) caused an increase in125I-sar-ANG II binding, AT1receptor protein content, and mRNA levels. The whole cell lysate and membrane showed similar insulin-induced increase in the AT1receptor protein expression, which was blocked by genistein (100 nM), a tyrosine kinase inhibitor, and cycloheximide (1.5 μg/ml), a protein synthesis inhibitor. Determination of ethyl isopropyl amiloride-sensitive22Na+uptake, a measure of the NHE activity, revealed that ANG II (1–100 pM)-induced stimulation of NHE in insulin-treated cells was significantly greater than in the control cells. Similarly, ANG II (1–100 pM)-induced stimulation of ouabain-sensitive86Rb+uptake, a measure of NKA activity in insulin-treated cells, was significantly greater than in the control cells. ANG II stimulation of both the transporters was blocked by AT1receptor antagonist losartan, suggesting the involvement of AT1receptors. Thus chronic insulin treatment causes upregulation of AT1receptors, which evoked ANG II-induced stimulation of NHE and NKA. We propose that insulin-induced increase in the renal AT1receptor function serves as a mechanism responsible for the increased renal sodium reabsorption and thus may contribute to development of hypertension in conditions associated with hyperinsulinemia.
Evolution of vertebrate E protein transcription factors: comparative analysis of the E protein gene family in Takifugu rubripes and humans
Authors: Hikima Jun-ichi , Lennard Mara L. , Wilson Melanie R. , Miller Norman W. , Clem L. William , Warr Gregory W.
Published: February 2005

E proteins are essential for B lymphocyte development and function, including immunoglobulin (Ig) gene rearrangement and expression. Previous studies of B cells in the channel catfish ( Ictalurus punctatus) identified E protein homologs that are capable of binding the μE5 motif and driving a strong transcriptional response. There are three E protein genes in mammals, HEB (TCF12), E2A (TCF3), and E2-2 (TCF4). The major expressed E proteins found in catfish B cells are homologs of HEB and of E2A. Here we sought to define the complete family of E protein genes in a teleost fish, Takifugu rubripes, taking advantage of the completed genome sequence. The catfish CFEB (HEB homolog) sequence identified homologous E-protein-encoding sequences in five scaffolds in the Takifugu genome database. Detailed comparative analysis with the human genome revealed the presence of five E protein homologs in Takifugu. Single genes orthologous to HEB and to E2-2 were identified. In contrast, two members of the E2A gene family were identified in Takifugu; one of these shows the alternative processing of transcripts that identifies it as the ortholog of the E12/E47-encoding mammalian E2A gene, whereas the second Takifugu E2A gene has no predicted alternative splice products. A novel fifth E protein gene (EX) was identified in Takifugu. Phylogenetic analysis revealed four E protein branches among vertebrates: EX, E2A, HEB, and E2-2.
Periodic boundary value problems for nth‐order ordinary differential equations with p‐laplacian
Authors: Liu Yuji , Ge Weigao
Published: February 2005

We prove existence results for solutions of periodic boundary value problems concerning the nth‐order differential equation
with p‐Laplacian and the boundary value conditions x(i)(0) = x(i)(T), i = 0, …, n − 1. Our method is based upon the coincidence degree theory of Mawhin. It is interesting that f may be a polynomial and the degree of some variables among x0, x1, …, xn−1 in the function f(t, x0, x1, …, xn−1) is allowed to be greater than 1.
Global solutions of a strongly coupled reaction‐diffusion system with different diffusion coefficients
Authors: Somathilake L. W. , Peiris J. M. J. J.
Published: February 2005

We deal with a mathematical model for a four‐component chemical reaction‐diffusion process. The model is described by a system of strongly coupled reaction‐diffusion equations with different diffusion rates. The existence of the global solution of this reaction‐diffusion system in unbounded domain is proved by using semigroup theory and estimates on the growth of solutions.
Generalized resolvents and spectrum for a certain class of perturbed symmetric operators
Authors: Hebbeche A.
Published: February 2005

The generalized resolvents for a certain class of perturbed symmetric operators with equal and finite deficiency indices are investigated. Using the Weinstein‐Aronszajn formula, we give a classification of the spectrum.
"Consider that it is a Raid on the Path of God": The Spiritual Manual of the Attackers of 9/11
Authors: Kippenberg Hans
Published: February 2005

The document found with three of the four cells responsible for the crimes of 9/11 is unique in providing specific information about how the Muslim suicide terrorists conceived of their action. The document shows that they found justification for violence by emulating the moment in early Islamic history when Muhammad cancelled contracts with non-Muslims and organized raids (ghazwa) against the Meccans in order to establish Islam as a political order. No statement in the Manual explicitly identifies the United States as the financial, military, and political center of today's paganism; rather, such identification is tacitly assumed, as was shown by the action itself. Instead, the Manual prescribes recitations, prayers and rituals by which each member of the four cells should prepare for the ghazwa, purify his intention and anticipate in his mind the successive stages of the struggle to come. Not the objective aim but the subjective intention is at the center of the Manual. The article places this type of justification of violence in the history of Islamic activism since the 1980s.
Shared and distinct roles mediated through C-terminal subdomains of acute myeloid leukemia/Runt-related transcription factor molecules in murine development
Authors: Fukushima-Nakase Yoko , Naoe Yoshinori , Taniuchi Ichiro , Hosoi Hajime , Sugimoto Tohru , Okuda Tsukasa
Published: February 2005

AML1/Runx1 is a frequent target of human leukemia–associated gene aberration and encodes a transcription factor with nonredundant biologic functions in initial development of definitive hematopoiesis, T-cell development, and steady-state platelet production. AML1/Runx1 and 2 closely related family genes, AML2/Runx3 and AML3/Runx2/Cbfa1, present in mammals, comprise the Runt-domain transcription factor family. Although they have similar structural and biochemical properties, gene-targeting experiments have identified distinct biologic roles. To directly determine the presence of functional overlap among runt-related transcription factor (Runx) family molecules, we replaced the C-terminal portion of acute myeloid leukemia 1 (AML1) with that derived from its family members, which are variable in contrast to conserved Runt domain, using the gene knock-in method. We found that C-terminal portions of either AML2 or AML3 could functionally replace that of AML1 for myeloid development in culture and within the entire mouse. However, while AML2 substituted for AML1 could effectively rescue lymphoid lineages, AML3 could not, resulting in a smaller thymus and lymphoid deficiency in peripheral blood. Substitution by the C-terminal portion of AML3 also led to high infantile mortality and growth retardation, suggesting that AML1 has as yet unidentified effects on these phenotypes. Thus, the C-terminal portions of Runx family members have both similar and distinct biologic functions.
CD25+CD4+ regulatory T cells generated by exposure to a model protein antigen prevent allograft rejection: antigen-specific reactivation in vivo is critical for bystander regulation
Authors: Karim Mahzuz , Feng Gang , Wood Kathryn J. , Bushell Andrew R.
Published: February 2005

The importance of CD25+CD4+ regulatory T (Treg) cells in the control of immune responses is established, but their antigen specificity in vivo remains unclear. Understanding Treg-cell specificity requirements will be important if their potential is to be developed for immunotherapy. Pretreatment of recipient mice with donor alloantigen plus anti-CD4 antibody generates CD25+CD4+ Treg cells with the capacity to prevent skin allograft rejection in adoptive transfer recipients. Here we demonstrate that, although this regulation can be antigen-specific, reactivation with the original tolerizing alloantigen allows the Treg cells to suppress rejection of third-party allografts. Aware of the limitations of alloantigen pretreatment, we asked whether graft-protective Treg cells could be generated against unrelated, nongraft antigens. We demonstrate that bystander regulation also extends to CD25+CD4+ Treg cells generated in vivo by exposure to nominal antigens under anti-CD4 antibody cover. Providing these Treg cells are reexposed to the tolerizing antigens before adoptive transfer, they prevent the rejection of fully allogeneic skin grafts. That this might form the basis of a clinically relevant tolerance induction strategy is demonstrated by the fact that, when combined with subtherapeutic anti-CD8 antibody, Treg cells generated in response to nongraft antigens facilitate the acceptance of cardiac allografts in primary recipients. (Blood. 2005;105:4871-4877)
Pharmacogenetics of outcome in children with acute lymphoblastic leukemia
Authors: Rocha Jose Claudio C. , Cheng Cheng , Liu Wei , Kishi Shinji , Das Soma , Cook Edwin H. , Sandlund John T. , Rubnitz Jeffrey , Ribeiro Raul , Campana Dario , Pui Ching-Hon , Evans William E. , Relling Mary V.
Published: February 2005

Acquired genetic characteristics of acute lymphoblastic leukemia (ALL) cells are used to individualize therapy, whereas germ line genetic characteristics generally are not. We determined whether ALL outcome was related to 16 genetic polymorphisms affecting the pharmacodynamics of antileukemic agents. Of 246 children, 116 were treated on the lower-risk (LR) and 130 on the higher-risk (HR) arms of a St Jude protocol. Patients in the HR group with the glutathione S-transferase (GSTM1) nonnull genotype had greater risk of hematologic relapse (P = .03), which was further increased by the thymidylate synthetase (TYMS) 3/3 genotype (P = .03). These genotypes remained predictive in multivariate analyses (P < .001 and .003, respectively). No genotypes were predictive in the LR arm. Expression of these 2 genes in ALL blasts was lower in those with low-activity genotypes. For central nervous system relapse, among the HR group, the vitamin D receptor start site (P = .02) and intron 8 genotypes (P = .04) predisposed, whereas for LR patients the TYMS 3/3 genotype predisposed (P = .04). The GSTM1 non-null and TYMS 3/3 genotypes are plausibly linked to drug resistance. Polymorphisms interact to influence antileukemic outcome and represent determinants of response that can be used to optimize therapy. (Blood. 2005;105:4752-4758)
Rate variation in parasitic plants: correlated and uncorrelated patterns among plastid genes of different function
Authors: Young Nelson D , dePamphilis Claude W
Published: February 2005

Background

The analysis of synonymous and nonsynonymous rates of DNA change can help in the choice among competing explanations for rate variation, such as differences in constraint, mutation rate, or the strength of genetic drift. Nonphotosynthetic plants of the Orobanchaceae have increased rates of DNA change. In this study 38 taxa of Orobanchaceae and relatives were used and 3 plastid genes were sequenced for each taxon.

Results

Phylogenetic reconstructions of relative rates of sequence evolution for three plastid genes (rbcL, matK and rps2) show significant rate heterogeneity among lineages and among genes. Many of the non-photosynthetic plants have increases in both synonymous and nonsynonymous rates, indicating that both (1) selection is relaxed, and (2) there has been a change in the rate at which mutations are entering the population in these species. However, rate increases are not always immediate upon loss of photosynthesis. Overall there is a poor correlation of synonymous and nonsynonymous rates. There is, however, a strong correlation of synonymous rates across the 3 genes studied and the lineage-speccific pattern for each gene is strikingly similar. This indicates that the causes of synonymous rate variation are affecting the whole plastid genome in a similar way. There is a weaker correlation across genes for nonsynonymous rates. Here the picture is more complex, as could be expected if there are many causes of variation, differing from taxon to taxon and gene to gene.

Conclusions

The distinctive pattern of rate increases in Orobanchaceae has at least two causes. It is clear that there is a relaxation of constraint in many (though not all) non-photosynthetic lineages. However, there is also some force affecting synonymous sites as well. At this point, it is not possible to tell whether it is generation time, speciation rate, mutation rate, DNA repair efficiency or some combination of these factors.
Comparative linkage analysis and visualization of high-density oligonucleotide SNP array data
Authors: Leykin Igor , Hao Ke , Cheng Junsheng , Meyer Nicole , Pollak Martin R , Smith Richard JH , Wong Wing Hung , Rosenow Carsten , Li Cheng
Published: February 2005

Background

The identification of disease-associated genes using single nucleotide polymorphisms (SNPs) has been increasingly reported. In particular, the Affymetrix Mapping 10 K SNP microarray platform uses one PCR primer to amplify the DNA samples and determine the genotype of more than 10,000 SNPs in the human genome. This provides the opportunity for large scale, rapid and cost-effective genotyping assays for linkage analysis. However, the analysis of such datasets is nontrivial because of the large number of markers, and visualizing the linkage scores in the context of genome maps remains less automated using the current linkage analysis software packages. For example, the haplotyping results are commonly represented in the text format.

Results

Here we report the development of a novel software tool called CompareLinkage for automated formatting of the Affymetrix Mapping 10 K genotype data into the "Linkage" format and the subsequent analysis with multi-point linkage software programs such as Merlin and Allegro. The new software has the ability to visualize the results for all these programs in dChip in the context of genome annotations and cytoband information. In addition we implemented a variant of the Lander-Green algorithm in the dChipLinkage module of dChip software (V1.3) to perform parametric linkage analysis and haplotyping of SNP array data. These functions are integrated with the existing modules of dChip to visualize SNP genotype data together with LOD score curves. We have analyzed three families with recessive and dominant diseases using the new software programs and the comparison results are presented and discussed.

Conclusions

The CompareLinkage and dChipLinkage software packages are freely available. They provide the visualization tools for high-density oligonucleotide SNP array data, as well as the automated functions for formatting SNP array data for the linkage analysis programs Merlin and Allegro and calling these programs for linkage analysis. The results can be visualized in dChip in the context of genes and cytobands. In addition, a variant of the Lander-Green algorithm is provided that allows parametric linkage analysis and haplotyping.
An in vitro evaluation of standard rotational thromboelastography in monitoring of effects of recombinant factor VIIa on coagulopathy induced by hydroxy ethyl starch
Authors: Engström Martin , Reinstrup Peter , Schött Ulf
Published: February 2005

Background

Rotational thromboelastography (ROTEG) has been proposed as a monitoring tool that can be used to monitor treatment of hemophilia with recombinant factor VIIa (rFVIIa). In these studies special non-standard reagents were used as activators of the coagulation. The aim of this study was to evaluate if standard ROTEG analysis could be used for monitoring of effects of recombinant factor VIIa (rFVIIa) on Hydroxy Ethyl Starch-induced dilutional coagulopathy.

Methods

The study was performed in vitro on healthy volunteers. Prothrombin time (PT) and ROTEG analysis were performed after dilution with 33% hydroxy ethyl starch and also after addition of rFVIIa to the diluted blood.

Results

PT was impaired with INR changing from 0.9 before dilution to 1.2 after dilution while addition of rFVIIa to diluted blood lead to an overcorrection of the PT to an International Normalized Ratio (INR) value of 0.6 (p = 0.01). ROTEG activated with the contact activator ellagic acid was impaired by hemodilution (p = 0.01) while addition of rFVIIa had no further effects. ROTEG activated with tissue factor (TF) was also impaired by hemodilution (p = 0.01) while addition of rFVIIa lead to further impairment of the coagulation (p = 0.01).

Conclusions

The parameters affected in the ROTEG analysis were Clot Formation Time and Amplitude after 15 minutes while the Clotting Time was unaffected. We believe these effects to be due to methodological problems when using standard activators of the coagulation in the ROTEG analysis in combination with rFVIIa.
The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data
Authors: Hayamizu Terry F , Mangan Mary , Corradi John P , Kadin James A , Ringwald Martin
Published: February 2005

We have developed an ontology to provide standardized nomenclature for anatomical terms in the postnatal mouse. The Adult Mouse Anatomical Dictionary is structured as a directed acyclic graph, and is organized hierarchically both spatially and functionally. The ontology will be used to annotate and integrate different types of data pertinent to anatomy, such as gene expression patterns and phenotype information, which will contribute to an integrated description of biological phenomena in the mouse.
An Exploration of Toddlers' Problems in a Search Task
Authors: Kloos Heidi , Keen Rachel
Published: February 2005

Toddlers show a surprising lack of knowledge about solidity when they are asked to search for a ball that rolled behind a screen and stopped at a barrier whose top was visible above the screen. They search incorrectly, failing to take into account the position of the barrier. This study examined details of this failure by simplifying the task in 2 ways: by using a search task that did not require children to understand solidity, and by using a prediction task that did not require children to conduct a search. For the prediction task, children had to predict where a ball was going to stop when a barrier intersected its trajectory. Children 2.0 and 2.5 years old were able to conduct a simple search and could predict, to some extent, where the ball was going to stop when the barrier was fully visible. Children did not show this predictive knowledge when the barrier was partially occluded by the screen.
English‐Learning Infants' Representations of Word Forms With Iambic Stress
Authors: Johnson Elizabeth K.
Published: February 2005

Retaining detailed representations of unstressed syllables is a logical prerequisite for infants' use of probabilistic phonotactics to segment iambic words from fluent speech. The head‐turn preference study was used to investigate the nature of English‐learners' representations of iambic word onsets. Fifty‐four 10.5‐month‐olds were familiarized to passages containing the nonsense iambic word forms ginome and tupong. Following familiarization, infants were either tested on familiar (ginome and tupong) or near‐familiar (pinome and bupong) versus unfamiliar (kidar and mafoos) words. Infants in the familiar test group (familiar vs. unfamiliar) oriented significantly longer to familiar than unfamiliar test items, whereas infants in the near‐familiar test group (near‐familiar vs. unfamiliar) oriented equally long to near‐familiar and unfamiliar test items. Our results provide evidence that infants retain fairly detailed representations of unstressed syllables and therefore support the hypothesis that infants use phonotactic cues to find words in fluent speech.
Ask the Pharmacist: An Analysis of Online Drug Information Services
Authors: Holmes Erin R , Desselle Shane P , Nath Danielle M , Markuss Jason J
Published: February 2005

BACKGROUND:

The Internet plays a large role in the provision of drug information. Given the growing number of patients seeking consultation on the Internet and the difficulty in regulating online pharmacy providers, an analysis of drug information provided by Internet pharmacies is warranted.

OBJECTIVE:

To assess the response rates and quality of responses to drug information questions submitted to “ask the pharmacist” services on Internet pharmacy sites and determine whether differences exist between National Association of Boards of Pharmacy—approved and nonapproved sites and among free-standing, chain, and independent pharmacy sites in the quality of information provided.

METHODS:

A content analysis was conducted on responses to 5 drug information questions electronically mailed to each of 64 Internet pharmacies identified through a meta-engine search. Three judges rated the quality of response components using a scoring system developed by an expert panel, with inter-rater reliabilities subsequently calculated. Both t-test and ANOVA procedures tested for differences in response quality.

RESULTS:

Responses were received for 51% of all questions submitted to the sites. Few differences in quality were found between approved/unapproved sites and among types of pharmacies. The percentage of correct responses provided for each of 22 response components ranged from 7% to 96%.

CONCLUSIONS:

While few differences were found among sites based on their approval status or type, low response rates and incomplete counseling information among many of the responses are cause for concern.
Photon Moment Analysis in Cells in the Presence of Photo-Bleaching
Authors: Caccia Michele , Camozzi Elisa , Collini Maddalena , Zaccolo Manuela , Chirico Giuseppe
Published: February 2005

The photon counting histogram (PCH) analysis of the fluorescence fluctuations provides the molecular brightness (ε) and the average number of fluorophores (〈Nn〉) in an open observation volume. PCH, which is based on the analysis of the whole of the photon counting histogram, has been recently improved by taking into account the detector dead time effect, which is relevant at high fluorescence rates. We investigate here the possibility of quantitatively applying the PCH analysis in the simplified form of photon moment analysis, in which only the first two moments of the photon counting histogram are computed. We have applied this analysis to low fluorescence signals from living cells in the presence of cell micro-movements and molecular photo-bleaching and describe a simple algorithm for its routine application. The algorithm has been tested on Saccharomyces Cerevisiæ (yeast) cells labeled with Dimethyl-pepep and Rhodamine 6G, and Chinese Hamster Ovary (CHO) cells stably expressing the regulatory subunit (RII) of protein kinase A fused to the cyan-emitting variant of GFP (CFP). Our statistical analysis allows us to estimate the local concentrations and the brightness of the fluorophores in different cellular compartments (nucleus, membrane, and cytoplasm) despite the occurrence of microscopic cell movements and significant photo-bleaching.
Blind Source Separation of Photoacoustic Depth Profiles into Independent Components
Authors: Pichler Arthur , Sowa Michael G.
Published: February 2005

Step-scan photoacoustic spectroscopy is a powerful tool to nondestructively retrieve depth related information from a sample. Through digital signal processing a series of spectra with effectively different modulation frequencies, probing different thermal diffusion lengths within a sample, can be collected simultaneously. For layered samples spectra of the constituent layers can then be obtained by calculating spectra at specific phase angles from the in-phase and quadrature data through phase projection. However, without prior knowledge of the spectra of the constituent layers, this approach can be difficult. In this report we present an alternate possibility for evaluating step scan photoacoustic data, namely independent component analysis (ICA), which allows for “blind separation” of the mixed photoacoustic spectra without prior knowledge of the constituent spectra. Phase projection and ICA are applied to photoacoustic data acquired from a multilayer sample in an attempt to isolate the spectra of the constituent layers. The results for the two methods are comparable, with ICA offering the advantage that no prior information about the pure spectra of the sample layers is needed.
Speciation of Chromium via Laser-Induced Breakdown Spectroscopy of Ion Exchange Polymer Membranes
Authors: Dockery Christopher R. , Pender Jack E. , Goode Scott R.
Published: February 2005

A new method for the speciation of ng/mL concentrations of Cr(III) and Cr(VI) solutions with analysis by laser-induced breakdown spectroscopy (LIBS) is reported. Speciation is achieved by pre-concentration of the chromium onto commercially available cation exchange polymer membranes. Chromium(III) is removed directly by cation exchange; chromium(VI) in the filtrate is reduced to Cr(III) and concentrated onto a second cation exchange membrane, affording independent measurement of both species. Large volumes of waters containing Cr(III) and Cr(VI) can be concentrated onto the membranes and directly analyzed by laser-induced breakdown spectroscopy. The estimated limit of detection corresponds to 500 ng of Cr on the membrane: if a solution volume of 1 L is used, then the detection limit corresponds to a solution concentration of 0.5 ng/mL. Excellent separation of the chromium species is attained. Results show that overall method efficiencies range from 94–116% and are independent of the matrix. The influence of pH has been measured, and although Cr(VI) converts to Cr(III) in acidic solutions, the total Cr recoveries are not appreciably influenced by pH over the range of natural waters (4 to 9). In addition, speciation was performed in the presence of a number of different cations and showed that the method is robust in many different and complex matrices.
Fourier Transform Infrared Imaging of Human Hair with a High Spatial Resolution without the Use of a Synchrotron
Authors: Chan K. L. A. , Kazarian S. G. , Mavraki A. , Williams D. R.
Published: February 2005

The cross-section of a human hair has been imaged for the first time using the micro attenuated total reflection (ATR) Fourier transformed infrared (FT-IR) method in combination with a focal plane array (FPA) detector. A rigorous approach was applied to determine the spatial resolution, namely, measuring the distance over which the band absorbance changes from 95 to 5% of the maximum absorbance when passing through a sharp interface. The measured value for IR transmission was ∼16 μm, while the value obtained using ATR imaging was ∼5 μm. The enhanced spatial resolution achieved by this method allows the medulla of the hair (∼8 μm in diameter) to be imaged clearly without the need for a synchrotron source. The spatial resolution of transmission and ATR imaging is compared, and advantages of ATR imaging are discussed.
Integration of studio and theory in the teaching of graphic design
Authors: Raein Maziar
Published: February 2005

Traditionally, art and design education in many higher education institutions has been characterized by a split between the teaching of theory and practice. This article argues that this split ignores the possible common ground between the two, largely to the detriment of students.
In particular, it will illustrate how and why many art and design students feel alienated by the methods employed in the primarily classroom-based teaching of theory. The article further argues that there exists common ground between theory and practice in the form of research and that this
common ground provides opportunities to integrate the two. Students will therefore be able to learn about theory through practice, which corresponds much more closely to students’ needs and abilities. The Context programme of the BA Graphic Design at Central Saint Martins College of
Art and Design provides an example where such an integration has taken place successfully.
Effects of Back Pressure and Strain Rate Used in Triaxial Testing of Stabilized Organic Soils and Clays
Authors: Åhnberg H
Published: February 2005

In deep stabilization of soft soils in Sweden, dry binders such as cement and quicklime are normally used. Mixing dry binders into the soils will lead to a lower degree of saturation than that of the unstabilized soils, which normally are fully saturated before stabilization. In triaxial testing of stabilized soils, the applied back pressure chosen for the tests may affect the degree of saturation and in turn also the results obtained. A number of triaxial tests have been performed using different back pressures in order to study the effect on measured shear strengths of stabilized organic soils and clays. The effect of rate of strain on the strength of stabilized organic soils was also studied in a series of tests. The results show that in particular the chosen back pressure can greatly affect the strength of stabilize soils, although the rate of strain can also exert an influence on the measured strength.
Model Pile Pull-Out Tests Using Polyethylene Sheets to Reduce Downdrag on Cast In Situ Piles
Authors: Chow SH , Wong KS
Published: February 2005

Low-density polyethylene sheets (LDPE) were used in this study to investigate its effectiveness in reducing downdrag on cast in situ piles. Eight model pile pull-out tests were conducted using three reinforced concrete circular model piles with different surface conditions (smooth, smooth with necking and bulging, and rough) in combination with three different LDPE sheet arrangements (one-sheet, two-sheet, and three-sheet). The pile was embedded partially in Ottawa sand with a surcharge of 19.3 kPa on sand surface. The test results showed that an arrangement with 3 pieces of 0.25-mm thick LDPE sheet was most effective in reducing side friction up to an average of 89 %. It was also found that the effectiveness of LDPE sheets is independent of the concrete surface roughness. However, the presence of necking and bulging was found to increase the side resistance up to 40 % for the plain pile without LDPE sheets.
Some Problems in the Measurement of Dynamic Modulus of Viscoelastic Model Materials
Authors: Zhou L , Chen J
Published: February 2005

Commonly used model materials in structural model testing are gypsum, added-weight emulsion, added-weight rubber, PlexiglasTM, epoxy resin, and polyvinyl chloride PVC. These materials are viscoelastic and their mechanical properties are unstable, especially the elastic dynamic modulus. To discuss the principle of variation on the elastic dynamic modulus, the materials PlexiglasTM, PVC plastic, and added-weight rubber were chosen for dynamic testing; the factors of temperature effect, size effect, and the effect of loading modes are also discussed.
Water Testing Natural Rubber Latex Condoms: A Comparison of Surveillance Test Methods
Authors: Thomas LC , Kerr LN , Andersen PC , Carter EJ , McIlvain LD
Published: February 2005

Manufacturers, consumers, and regulators use various water test methods to test the integrity of the barrier offered by natural rubber latex condoms. The purpose of this study is to analyze three alternative water test methods and determine which is the best method for detecting holes in condoms. Three types of holes (laser, acupuncture, and 28 gage insulin needles), approximating defects that occur in condoms, were placed in condoms and then into equal size test sets for testing by six laboratories for the purpose of evaluating the three alternative methods: the ASTM method, the ISO/FDA method, and the CSI/FHI method. Each method shares a hang portion for 1 min, and then uses a different form of manipulation; either elevate (ASTM), roll (ISO/FDA), or squeeze (CSI/FHI). The interlaboratory study data indicate the CSI/FHI is the most sensitive method for locating holes in condoms, becoming more sensitive as the defect approaches the closed end.
Hippocampal Synaptic Modulation by the Phosphotyrosine Adapter Protein ShcC/N-Shc via Interaction with the NMDA Receptor
Authors: Miyamoto Yoshiaki , Chen Ling , Sato Masahiro , Sokabe Masahiro , Nabeshima Toshitaka , Pawson Tony , Sakai Ryuichi , Mori Nozomu
Published: February 2005

N-Shc (neural Shc) (also ShcC), an adapter protein possessing two phosphotyrosine binding motifs [PTB (phosphotyrosine binding) and SH2 (Src homology 2) domains], is predominantly expressed in mature neurons of the CNS and transmits neurotrophin signals from the TrkB receptor to the Ras/mitogen-activated protein kinase (MAPK) pathway, leading to cellular growth, differentiation, or survival. Here, we demonstrate a novel role of ShcC, the modulation of NMDA receptor function in the hippocampus, usingShcCgene-deficient mice. In behavioral analyses such as the Morris water maze, contextual fear conditioning, and novel object recognition tasks, ShcC mutant mice exhibited superior ability in hippocampus-dependent spatial and nonspatial learning and memory. Consistent with this finding, electrophysiological analyses revealed that hippocampal long-term potentiation in ShcC mutant mice was significantly enhanced, with no alteration of presynaptic function, and the effect of an NMDA receptor antagonist on its expression in the mutant mice was notably attenuated. The tyrosine phosphorylation of NMDA receptor subunits NR2A and NR2B was also increased, suggesting that ShcC mutant mice have enhanced NMDA receptor function in the hippocampus. These results indicate that ShcC not only mediates TrkB-Ras/MAPK signaling but also is involved in the regulation of NMDA receptor function in the hippocampus via interaction with phosphotyrosine residues on the receptor subunits and serves as a modulator of hippocampal synaptic plasticity underlying learning and memory.