bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of diets and nutrients/drugs on early epigenetic programming
Authors: Junien Claudine 
Published: June 2006

SummarySpecific, often unbalanced diets are used to circumvent the metabolic defects of patients with monogenic inborn errors of metabolism. Human epidemiological studies and appropriately designed dietary interventions in animal models have provided considerable evidence to suggest that nutritional imbalance and metabolic disturbances, during critical time windows of developmental programming, may have a persistent effect on the health of the child and later in adulthood. Thus patients with monogenic inborn errors of metabolism may also suffer additional types of alterations due to the lack or excess of key nutrients. Interactions of nutrients with the epigenetic machinery lead to epigenetic changes associated with chromatin remodelling and regulation of gene expression that underlie the developmental programming of pathological consequences in adulthood. Today, with the explosion of new technologies, we can explore on a large scale the effects of nutrients on the level of expression of thousands of expressed genes (nutritional genomics and epigenomics), the corresponding protein products and their posttranslationally modified derivatives (proteomics), and the host of metabolites (metabolomics) generated from endogenous metabolic processes or exogenous dietary nutrients and can establish the relationship between these biological entities and diet, health or disease. The combination of these various lines of research on epigenetic programming processes should highlight new strategies for the prevention and treatment of inborn errors of metabolism.
Protein misfolding disorders: Pathogenesis and intervention
Authors: Gregersen N. 
Published: June 2006

SummaryNewly synthesized proteins in the living cell must go through a folding process to attain their functional structure. To achieve this in an efficient fashion, all organisms, including humans, have evolved a large set of molecular chaperones that assist the folding as well as the maintenance of the functional structure of cellular proteins. Aberrant proteins, the result of production errors, inherited or acquired amino acid substitutions or damage, especially oxidative modifications, can in many cases not fold correctly and will be trapped in misfolded conformations. To rid the cell of misfolded proteins, the living cell contains a large number of intracellular proteases, e.g. the proteasome, which together with the chaperones comprise the cellular protein quality control systems. Many inherited disorders due to amino acid substitutions exhibit loss‐of‐function pathogenesis because the aberrant protein is eliminated by one of the protein quality control systems. Examples are cystic fibrosis and phenylketonuria. However, not all aberrant proteins can be eliminated and the misfolded protein may accumulate and form toxic oligomeric and/or aggregated inclusions. In this case the loss of function may be accompanied by a gain‐of‐function pathogenesis, which in many cases determines the pathological and clinical features. Examples are Parkinson and Huntington diseases. Although a number of strategies have been tried to decrease the amounts of accumulated and aggregated proteins, a likely future strategy seems to be the use of chemical or pharmacological chaperones with specific effects on the misfolded protein in question. Positive examples are enzyme enhancement in a number of lysosomal disorders.
Breast feeding in IMD
Authors: MacDonald A. , Depondt E. , Evans S. , Daly A. , Hendriksz C. , Chakrapani A A. , Saudubray J.‐M. 
Published: June 2006

SummaryBreast feeding has proven benefits for many infants with inherited metabolic disorders (IMDs) but, with the exception of phenylketonuria, there are few reports in other conditions. A questionnaire, completed by dietitians and clinicians from 27 IMD centres from 15 countries (caring for a total of over 8000 patients with IMDs on diet) identified breast feeding experience in IMD. Successful, demand breast feeding (in combination with an infant amino acid formula free of precursor amino acids) was reported in 17 infants with MSUD, 14 with tyrosinaemia type I, and 5 with homocystinuria. Eighty‐nine per cent were still breast fed at 16 weeks. Fewer infants with organic acidaemias were demand breast fed (7 with propionic acidaemia; 6 with methylmalonic acidaemia and 13 with isovaleric acidaemia) (usually preceded by complementary feeds of a protein‐free infant formula or infant amino acid formula free of precursor amino acids). Only 12 infants with urea cycle disorders were given demand breast feeds, but this was unsuccessful beyond 8 days in CPS deficiency. Further work is needed in developing guidelines for feeding and for clinical and biochemical monitoring for breast‐fed infants with IMDs.
Sensorineural hearing loss with BrainStem Auditory Evoked Responses changes in homozygote and heterozygote sickle cell patients in Guadeloupe (France)
Authors: Jovanovic-Bateman L , Hedreville R 
Published: June 2006

This prospective study involved 79 homozygote and heterozygote sickle cell anaemia patients (16 to 50 years old) and a control group of 40 people.All patients underwent ENT, audiological and brainstem auditory evoked responses (BSER) examinations in order to evaluate the incidence of sensorineural hearing loss (SNHL), to identify the changes at the level of the cochlear nerve and the central pathways, and to determine the most vulnerable group, in order to intervene with early prevention and rehabilitation for this condition.A hearing loss of greater than 20 dB at two or more frequencies was found in 36 (45.57 per cent) sickle cell patients (19 (47.22 per cent) HbSC patients and 17 (43.59 per cent) HbSS patients) and three (7.5 per cent) members of the control group. Homozygote and heterozygote patients, as well as both sexes, were equally affected.Bilateral hearing loss occurred in 19 (52.78 per cent) patients, unilateral right-sided hearing loss in five (13.89 per cent) patients and unilateral left-sided hearing loss in 12 (33.33 per cent) patients.Brainstem auditory evoked potential demonstrated a prolonged I–V (III–V) interpeak latency in 13 (25.35 per cent) sickle cell patients (11 men (eight with HbSS) and two women).The hearing loss in HbSS patients was neural in nature and of earlier onset; the hearing loss in HbSC patients was usually cochlear in nature and of later onset.Despite high medical standards and 100 per cent social security cover, the high incidence of SNHL in our sickle cell affected patients (the majority with the Benin haplotype) was probably due to their specific haematological profile and to the original geographical distribution of the disease in the tropics.Our results highlight the necessity for early and regular hearing assessment of sickle cell patients, including BSER examination, especially in male patients with SNHL.
ESTIMATES OF BEST CONSTANTS FOR WEIGHTED POINCARÉ INEQUALITIES ON CONVEX DOMAINS
Authors: CHUA SENG-KEE , WHEEDEN RICHARD L. 
Published: June 2006

Let $1 \le q \le p <\infty$ and let $\mathcal{C}$ be the class of all bounded convex domains $\Omega$ in $\mathbb{R}^n$. Following the approach in `An optimal Poincaré inequality in $L^1$ for convex domains', by G. Acosta and R. G. Durán (Proc. Amer. Math. Soc. 132 (2003) 195–202), we show that the best constant $C$ in the weighted Poincaré inequality$$ \| f - f_{av} \|_{L^q_w (\Omega)} \le C w(\Omega)^{\frac{1}{q} - \frac{1}{p}} \mbox{diam}(\Omega) \| \nabla f \|_{L^p_w(\Omega)} $$for all $\Omega \in \mathcal{C}$, all Lipschitz continuous functions $f$ on $\Omega$, and all weights $w$ which are any positive power of a non-negative concave function on $\Omega$ is the same as the best constant for the corresponding one-dimensional situation, where $\mathcal{C}$ reduces to the class of bounded intervals. Using facts from `Sharp conditions for weighted 1-dimensional Poincaré inequalities', by S.-K. Chua and R. L. Wheeden (Indiana Math. J. 49 (2000) 143–175), we estimate the best constant. In the case $q = 1$ and $1 <\infty$, our estimate is between the best constant and twice the best constant. Furthermore, when $p = q = 1$ or $p = q = 2$, the estimate is sharp. Finally, in the case where the domains in $\mathbb{R}^n$ are further restricted to be parallelepipeds, we obtain a slightly different form of Poincaré's inequality which is better adapted to directional derivatives and the sidelengths of the parallelepipeds. We also show that this estimate is sharp for a fixed rectangle.
Effects of Deer Browsing, Fabric Mats, and Tree Shelters on Quercus rubra Seedlings
Authors: Ret;Kathleen L. Shea Erik E. Stange 
Published: June 2006

AbstractWe examined the effects of deer browsing, fabric mats, and tree shelters on the growth and survival of Quercus rubra (northern red oak) seedlings planted as part of a reforestation project in southcentral Minnesota. Browsing by white‐tailed deer occurred on 68.6% of the seedlings growing without tree shelters, whereas only 3.6% of the trees were browsed by mice or voles and 2.5% were browsed by rabbits. Fabric mats, used to control competition from herbaceous plants for roughly half of the seedlings included in the study, had a detrimental effect overall. Seedlings grown with mats had a greater frequency of deer browsing and a greater chance of dying than seedlings grown without mats. Stem height for seedlings browsed by deer was less overall than for nonbrowsed seedlings, although this pattern varied with use of fabric mats and plot location. The use of plastic tree shelters effectively prevented deer browsing and reduced the mortality rate from 34.6% to 3.2%. Our results indicate that fabric mats should not be used in restoration projects with large deer populations. They also suggest that planting seedlings away from existing forest edges and using seedling protection measures such as tree shelters will increase seedling survival and growth in future restoration projects.
tuple_plot: Fast pairwise nucleotide sequence comparison with noise suppression
Authors: Szafranski Karol , Jahn Niels , Platzer Matthias 
Published: June 2006

Abstract
Summary: The program tuple_plot identifies and visualizes local similarities between two genomic sequences, typically 100 kb or longer, by applying the well-known dotplot principle. A dictionary of sequence words built from the input sequences serves to construct a task-specific expectancy model that is used to attribute significance values to pairwise word hits. The dictionary-based approach allows fast computation, the computation time scaling to O(N log N), depending on the size of the input sequences. The proposed scoring scheme appreciably increases the signal-to-noise ratio and may help to improve other word-based sequence comparison approaches.
Availability: tuple_plot is available at and may be used under GNU public license.
Contact: szafrans@fli-leibniz.de
Multiple doses of the antimuscarinic agent solifenacin do not affect the pharmacodynamics or pharmacokinetics of warfarin or the steady‐state pharmacokinetics of digoxin in healthy subjects
Authors: Smulders R. A. , Kuipers M. E. , Krauwinkel W. J. J. 
Published: June 2006

AimsSolifenacin succinate is used for the treatment of overactive bladder (OAB). The potential for pharmacokinetic and/or pharmacodynamic interactions between solifenacin and warfarin or digoxin was investigated.MethodsThe solifenacin–warfarin study was a two‐period crossover trial conducted in healthy males. Subjects received warfarin on the 10th day of 16 days of dosing with either solifenacin or placebo. The solifenacin–digoxin study was an one‐sequence crossover trial conducted in healthy males and females. Following a phase‐in period for digoxin, solifenacin was administered concomitantly with the drug on days 9–18.ResultsThe AUCPT; 0−168 h following a single dose of warfarin was unchanged in the presence of solifenacin [point estimate = 1.005; 90% confidence interval (CI) 0.98, 1.02)]. The AUC0–∞ values for both warfarin enantiomers were also unchanged. A small increase in the Cmax of digoxin was observed during treatment with solifenacin, but for AUCss,tau and Cmax the 90% CI fell within the prespecified interval of 0.80–1.25. Combined administration of solifenacin and warfarin or digoxin was well tolerated.ConclusionsSince the pharmacokinetics and pharmacodynamics of a single dose of warfarin and the steady‐state pharmacokinetics of digoxin were not affected by coadministration of solifenacin in healthy subjects, the need for dosing adjustments for digoxin and/or warfarin does not seem warranted.
An analysis of microband orientation in a commercial purity aluminium alloy subjected to forward and reverse torsion using Electron Backscatter Diffraction (EBSD)
Authors: LOPEZ‐PEDROSA M. , WYNNE B. P. , RAINFORTH W. M. 
Published: June 2006

SummaryHigh‐resolution electron backscatter diffraction has been used to study the effects of strain reversal on the evolution of microbands in commercial purity aluminium alloy AA1200. Deformation was carried out using two equal steps of forward/forward or forward/reverse torsion at a temperature of 300 °C and strain rate of 1 s−1 to a total equivalent tensile strain of 0.5. In both cases, microbands were found in the majority of grains examined with many having microband walls with more than one orientation. For the forward/forward condition, the microband clusters were centred around −20° and +45° to the equivalent tensile stress axis, whereas for material subjected to a strain reversal, the clusters were at −65° and −45°. There was no evidence of microbands that were formed in the forward deformation step in the reversed material, which would suggest that a strain of 0.25 is sufficient to dissolve any microstructure history generated by the first step. Furthermore, the microbands within the strain‐reversed material had a reduction in misorientation compared with the lineally strained material, suggesting that these microbands only formed at the onset of the second deformation step. This confirms that microband formation is complex and sensitive to strain path; however, it is still unclear to what extent microband formation is dependent on strain path history compared with the instantaneous deformation mode.
EBSD investigation of the microstructure and texture characteristics of hot deformed duplex stainless steel
Authors: CIZEK P. , WYNNE B. P. , RAINFORTH W. M. 
Published: June 2006

SummaryThe microstructure and crystallographic texture characteristics were studied in a 22Cr‐6Ni‐3Mo duplex stainless steel subjected to plastic deformation in torsion at a temperature of 1000 °C using a strain rate of 1 s−1. High‐resolution EBSD was successfully used for precise phase and substructural characterization of this steel. The austenite/ferrite ratio and phase morphology as well as the crystallographic texture, subgrain size, misorientation angles and misorientation gradients corresponding to each phase were determined over large sample areas. The deformation mechanisms in each phase and the interrelationship between the two are discussed.
A physical phantom for the calibration of three‐dimensional X‐ray microtomography examination
Authors: PERILLI E. , BARUFFALDI F. , BISI M. C. , CRISTOFOLINI L. , CAPPELLO A. 
Published: June 2006

SummaryX‐ray microtomography is rapidly gaining importance as a non‐destructive investigation technique, especially in the three‐dimensional examination of trabecular bone. Appropriate quantitative three‐dimensional parameters describing the investigated structure were introduced, such as the model‐independent thickness and the structure model index. The first parameter calculates a volume‐based thickness of the structure in three dimensions independent of an assumed structure type. The second parameter estimates the characteristic form of which the structure is composed, i.e. whether it is more plate‐like, rod‐like or even sphere‐like. These parameters are now experiencing a great diffusion and are rapidly growing in importance. To measure the accuracy of these three‐dimensional parameters, a physical three‐dimensional phantom containing different known geometries and thicknesses, resembling those of the examined structures, is needed. Unfortunately, such particular phantoms are not commonly available and neither does a consolidated standard exist. This work describes the realization of a calibration phantom for three‐dimensional X‐ray microtomography examination and reports an application example using an X‐ray microtomography system. The calibration phantom (external size 13 mm diameter, 23 mm height) was based on various aluminium inserts embedded in a cylinder of polymethylmethacrylate. The inserts had known geometries (wires, foils, meshes and spheres) and thicknesses (ranging from 20 µm to 1 mm). The phantom was successfully applied to an X‐ray microtomography device, providing imaging of the inserted structures and calculation of three‐dimensional parameters such as the model‐independent thickness and the structure model index. With the indications given in the present work it is possible to design a similar phantom in a histology laboratory and to adapt it to the requested applications.
Filter cubes with built‐in ultrabright light‐emitting diodes as exchangeable excitation light sources in fluorescence microscopy
Authors: MOSER C. , MAYR T. , KLIMANT I. 
Published: June 2006

SummaryThe use of ultrabright light‐emitting diodes as a potential substitute for conventional excitation light sources in fluorescence microscopy is demonstrated. We integrated ultrabright light‐emitting diodes in the filter block of a conventional fluorescence microscope together with a collimating Fresnel lens, a holographic diffuser and emission filters. This setup enabled convenient changes between different excitation light sources and resulted in high excitation efficiencies. Quantitative comparison of image intensities of test samples revealed that light‐emitting diodes yielded intensities in the range of a mercury arc lamp depending on the wavelength. The use of ultrabright light‐emitting diodes also enabled luminescence lifetime imaging without the need for image intensification.
Microsatellites provide insight into contrasting mating patterns in arribada vs. non‐arribada olive ridley sea turtle rookeries
Authors: JENSEN M. P. , ABREU‐GROBOIS F. A. , FRYDENBERG J. , LOESCHCKE V. 
Published: June 2006

AbstractMolecular studies of sea turtles have shown that the frequency of multiple paternity (MP) varies between species, and between rookeries of the same species. This study uses nuclear microsatellite markers to compare the incidence of MP in two neighbouring olive ridley rookeries on the Pacific coast of Costa Rica, with contrasting nesting behaviours — the ‘arribada’ population nesting at Ostional and the solitary nesters of Playa Hermosa. Using two highly polymorphic microsatellite markers, we tested 13 nests from each location and found a significant difference (P < 0.001) between the level of MP of the arribada rookery (92%— the highest found for marine turtles) and that of the solitary nesting rookery (30%). Additional analyses based on six microsatellite loci revealed no genetic differentiation between nesting females from the two locations, or between nesting females and attendant males from the Ostional breeding area. Sixty‐nine per cent of the nests with MP were fathered by a minimum of three different males, and three nests showed evidence of at least four fathers. The results suggest that the differences observed in levels of MP between arribada and solitary rookeries are due to an effect of abundance of individuals on the mating system. This is supported by a regression analysis combining other paternity studies on sea turtles which shows that levels of MP increase with increasing abundance of nesting females.
Allosensitized humans are at no greater risk of humoral rejection of GT‐KO pig organs than other humans
Authors: Hara Hidetaka , Ezzelarab Mohamed , Rood Pleunie P. M. , Lin Yih Jyh , Busch Jamie , Ibrahim Zuhaib , Zhu Xiaocheng , Ball Suyapa , Ayares David , Zeevi Adriana , Awwad Michel , Cooper David K. C. 
Published: June 2006

Abstract:  Background:  The availability of pigs homozygous for α1,3‐galactosyltransferase gene‐knockout (GT‐KO) has enabled study of the incidence and cytotoxicity of primate antibodies directed to antigens other than Galα1,3Gal (Gal), termed non‐Gal antigens.Methods:  Sera from 27 healthy humans and 31 patients awaiting renal allotransplantation, who were either unsensitized [panel reactive antibodies (PRA) < 10%] or allosensitized (PRA > 70%), were tested by flow cytometry for binding of immunoglobulin M (IgM) and IgG to peripheral blood mononuclear cells (PBMC) from both wild‐type (WT) and GT‐KO pigs. Complement‐dependent cytotoxicity to WT and GT‐KO PBMC was also measured.Results:  IgM and IgG from all 27 (100%) healthy human sera bound to WT PBMC, while 78% and 63% of these sera had IgM and IgG that bound to GT‐KO PBMC, respectively. Mean binding to WT PBMC was significantly greater than GT‐KO PBMC. Whereas 100% of sera were cytotoxic to WT PBMC, only 61% were cytotoxic to GT‐KO PBMC, and the extent of lysis was significantly less. Neither mean binding of IgM and IgG nor cytotoxicity of unsensitized and allosensitized sera to WT and GT‐KO PBMC was significantly different to that of healthy sera.Conclusions:  More than half of the healthy humans tested had cytotoxic antibodies to GT‐KO PBMC, but allosensitized patients will be at no greater risk of rejecting a pig xenograft by a humoral mechanism.
Cope's rule in cryptodiran turtles: do the body sizes of extant species reflect a trend of phyletic size increase?
Authors: Moen D. S. 
Published: June 2006

Abstract
Cope's rule of phyletic size increase is questioned as a general pattern of body size evolution. Most studies of Cope's rule have examined trends in the paleontological record. However, neontological approaches are now possible due to the development of model-based comparative methods, as well as the availability of an abundance of phylogenetic data. I examined whether the phylogenetic distribution of body sizes in extant cryptodiran turtles is consistent with Cope's rule. To do this, I examined body size evolution in each of six major clades of cryptodiran turtles and also across the whole tree of cryptodirans (n = 201 taxa). Extant cryptodiran turtles do not appear to follow Cope's rule, as no clade showed a significant phyletic body size trend. Previous analyses in other extant vertebrates have also found no evidence for phyletic size increase, which is in contrast to the paleontological data that support the rule in a number of extinct vertebrate taxa.