bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractThe 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

Abstract
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 &lt; .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

Abstract
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

Abstract
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

Abstract
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

AbstractWe 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

AbstractToddlers 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

AbstractRetaining 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.
Effects of Back Pressure and Strain Rate Used in Triaxial Testing of Stabilized Organic Soils and Clays
Authors: Åhnberg H 
Published: February 2005

AbstractIn 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

Abstract
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

Abstract
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

Abstract
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.
Methanol and Ethanol Decomposition in Supercritical Water
Authors: Hack Walter , Masten David A. , Buelow Steven J. 
Published: February 2005

Abstract
The decomposition of CH3OH and C2H5OH in supercritical water was studied in a flow reactor tube (Ni/Mo/Cr/Fe alloy) in the temperature range 597 ≤ T/K ≤ 797 at a pressure of p = 315 bar for technical application of scH2O for hazardous chemical waste destruction. The CH3OH and C2H5OH concentrations in the liquid as a function of the residence times were determined by a Raman spectrometer.
The [CH3OH] and [C2H5OH] resp. decay followed first order kinetics and a rate constant k
1(653 K) = 1.3 × 10−2 s−1 for CH3OH and k
2(653 K) = 5.5 × 10−2 s−1 for C2H5OH was determined. The rate constant k
1 was found to be independent of the initial CH3OH concentration in the mass fraction range 0.002 ≤ x
m ≤ 0.04. The rate depended on the history of the reactor. Treatment with NH4OH, C2H5OH or with H2O2 at T = 653 K, did not change the rate. Treatment with HNO3/H2O2, however, at T = 838 K reduced the rate by about a factor of 1000.
The Arrhenius-activation energy over the above temperature range was determined to be E
A = 164 kJ/mol for methanol and E
A = 145 kJ/mol for ethanol.
The major products from methanol decomposition were CH4, H2, and CO2 as observed by gas chromatography and CH4 and CO2 by FTIR-spectrometry. No other products were found. The products were not effected by the pretreatment of the reactor wall. A non-radical mechanism, which explains the formation of only these products, will be discussed.
The Totally Symmetric Vibrations of NH3···HF and NH3···HCN: a CCSD(T) Study Including Anharmonicity Effects
Authors: Botschwina Peter , Oswald Rainer 
Published: February 2005

Abstract
The coupled cluster variant CCSD(T) has been employed to calculate potential energy and dipole moment surfaces for the hydrogen-bonded complexes NH3···HF and NH3···HCN, restricting the treatment to the totally symmetric coordinates. Both complexes have C
3ν symmetry, with equilibrium dissociation energies (D
e) predicted to be 52.1 and 27.1 kJ mol−1, respectively. Vibrational term energies and wavefunctions as well as absolute IR intensities are calculated under inclusion of anharmonicity effects. In contrast to previous theoretical work for NH3···HF, the umbrella bending vibration of this complex as well as for NH3···HCN is found to be rather anharmonic. The familiar double harmonic approximation fails to yield reliable values for the IR intensities of the NH3 (ND3) symmetric stretching vibrations of either NH3···HF or ND3···DF. The wavenumbers of the intermolecular stretching vibrations are predicted as ν4 = 277 cm−1 (NH3···HF) and ν5 = 154 cm−1 (NH3···HCN). Owing to a large quadratic coupling term in the electric dipole moment function, the band ν4(NH3···HF) has virtually zero intensity. The effects of deuterium substitution on wavenumbers and IR intensities have been studied for both complexes.
Pediatric Fabry Disease
Authors: Ries Markus , Gupta Surya , Moore David F. , Sachdev Vandana , Quirk Jane M. , Murray Gary J. , Rosing Douglas R. , Robinson Chevalia , Schaefer Ellen , Gal Andreas , Dambrosia James M. , Garman Scott C. , Brady Roscoe O. , Schiffmann Raphael 
Published: February 2005

Background. Fabry disease is an underdiagnosed, treatable, X-linked, multisystem disorder.Objectives. To test the hypothesis that quality of life and sweating are decreased among pediatric patients with Fabry disease, compared with control subjects, and to provide quantitative natural history data and novel clinical end points for therapeutic trials.Design. Prospective, cross-sectional, observational study.Setting. Referral to the National Institutes of Health.Participants. Twenty-five male children with Fabry disease (mean age: 12.3 ± 3.5 years) and 21 age-matched control subjects.Main Outcome Measures. Quality of life (measured with the Child Health Questionnaire) and sweating (assessed with the quantitative sudomotor axon reflex test).Results. Quality of life scores for pediatric patients &lt;10 years of age with Fabry disease, compared with published normative values, were 55 ± 17 vs 83 ± 19 for bodily pain and 62 ± 19 vs 80 ± 13 for mental health. Bodily pain scores for patients ≥10 years of age were 54 ± 22 vs 74 ± 23. Sweat volume in the Fabry disease group was 0.41 ± 0.46 μL/mm2, compared with 0.65 ± 0.44 μL/mm2 in the control group. Renal function, urinary protein excretion, and cardiac function and structure were normal for the majority of patients. The 3 patients with residual α-galactosidase A activity ≥1.5% of normal values were free of cornea verticillata and had normal serum and urinary globotriaosylceramide levels. All other children had glycolipid levels comparable to those of adult patients with Fabry disease. Acroparesthesia and cardiac abnormalities were generally present before anhidrosis and proteinuria. Mapping of the missense mutations on the crystallographic structure of α-galactosidase A revealed that the mutations were partially surface-exposed and distal to the active site among individuals with residual enzyme activity. Mutations associated with left ventricular hypertrophy (defined as left ventricular mass index of &gt;51 g/m2.7) were localized near the catalytic site of the enzyme.Conclusions. Despite the absence of major organ dysfunction, Fabry disease demonstrates significant morbidity already in childhood. We have identified important, potentially correctable or preventable, outcome measures for future therapeutic trials. Prevention of complications involving major organs should be the goal for long-term specific therapy.