bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accurate mass filtering of ion chromatograms for metabolite identification using a unit mass resolution liquid chromatography/mass spectrometry system
Authors: Gu Ming , Wang Yongdong , Zhao Xian‐guo , Gu Zhe‐ming 
Published: February 2006

AbstractAcceleration of liquid chromatography/mass spectrometric (LC/MS) analysis for metabolite identification critically relies on effective data processing since the rate of data acquisition is much faster than the rate of data mining. The rapid and accurate identification of metabolite peaks from complex LC/MS data is a key component to speeding up the process. Current approaches routinely use selected ion chromatograms that can suffer severely from matrix effects. This paper describes a new method to automatically extract and filter metabolite‐related information from LC/MS data obtained at unit mass resolution in the presence of complex biological matrices. This approach is illustrated by LC/MS analysis of the metabolites of verapamil from a rat microsome incubation spiked with biological matrix (bile). MS data were acquired in profile mode on a unit mass resolution triple‐quadrupole instrument, externally calibrated using a unique procedure that corrects for both mass axis and mass spectral peak shape to facilitate metabolite identification with high mass accuracy. Through the double‐filtering effects of accurate mass and isotope profile, conventional extracted ion chromatograms corresponding to the parent drug (verapamil at m/z 455), demethylated verapamil (m/z 441), and dealkylated verapamil (m/z 291), that contained substantial false‐positive peaks, were simplified into chromatograms that are substantially free from matrix interferences. These filtered chromatograms approach what would have been obtained by using a radioactivity detector to detect radio‐labeled metabolites of interest. Copyright © 2006 John Wiley & Sons, Ltd.
Inference for case–control studies when exposure status is both informatively missing and misclassified
Authors: Lyles Robert H. , Allen Andrew S. , Dana Flanders W. , Kupper Lawrence L. , Christensen Deborah L. 
Published: February 2006

AbstractIn case–control studies, it is common for a categorical exposure variable to be misclassified. It is also common for exposure status to be informatively missing for some individuals, in that the probability of missingness may be related to exposure. Procedures for addressing the bias due to misclassification via validation data have been extensively studied, and related methods have been proposed for dealing with informative missingness based on supplemental sampling of some of those with missing data. In this paper, we introduce study designs and analytic procedures for dealing with both problems simultaneously in a 2×2 analysis. Results based on convergence in probability illustrate that the combined effects of missingness and misclassification, even when the latter is non‐differential, can lead to naïve exposure odds ratio estimates that are inflated or on the wrong side of the null. The motivating example comes from a case–control study of the association between low birth weight and the diagnosis of breast cancer later in life, where self‐reported birth weight for some women is supplemented by accurate information from birth certificates. Copyright © 2006 John Wiley & Sons, Ltd.
Confidence intervals for the amount of heterogeneity in meta‐analysis
Authors: Viechtbauer Wolfgang 
Published: February 2006

AbstractEffect size estimates to be combined in a systematic review are often found to be more variable than one would expect based on sampling differences alone. This is usually interpreted as evidence that the effect sizes are heterogeneous. A random‐effects model is then often used to account for the heterogeneity in the effect sizes. A novel method for constructing confidence intervals for the amount of heterogeneity in the effect sizes is proposed that guarantees nominal coverage probabilities even in small samples when model assumptions are satisfied. A variety of existing approaches for constructing such confidence intervals are summarized and the various methods are applied to an example to illustrate their use. A simulation study reveals that the newly proposed method yields the most accurate coverage probabilities under conditions more analogous to practice, where assumptions about normally distributed effect size estimates and known sampling variances only hold asymptotically. Copyright © 2006 John Wiley & Sons, Ltd.
Characterization of chito-oligosaccharides prepared by chitosanolysis with the aid of papain and Pronase, and their bactericidal action against Bacillus cereus and Escherichia coli
Authors: Vishu Kumar Acharya B. , Varadaraj Mandyam C. , Gowda Lalitha R. , Tharanathan Rudrapatnam N. 
Published: February 2006

Papain (from papaya latex; EC 3.4.22.2) and Pronase (from Streptomyces griseus; EC 3.4.24.31) caused optimum depolymerization of chitosan at pH 3.5 and 37 °C, resulting in LMMC (low molecular mass chitosan) and chito-oligomeric–monomeric mixture. The yield of the latter was 14–16% and 14–19% respectively for papain- and Pronase-catalysed reactions, depending on the reaction time (1–5 h). HPLC revealed the presence of monomer(s) and oligomers of DP (degree of polymerization) 2–6, which was also confirmed by matrix-assisted laser-desorption ionization–time-of-flight MS. Along with the chito-oligomers, the appearance of only GlcNAc (N-acetylglucosamine) in Pronase-catalysed chitosanolysis was indicative of its different action pattern compared with papain. Fourier-transform infrared, liquid-state 13C-NMR spectra and CD analyses of chito-oligomeric–monomeric mixture indicated the release of GlcNAc/GlcNAc-rich oligomers. The monomeric sequence at the non-reducing ends of chito-oligomers was elucidated using N-acetylglucosaminidase. The chito-oligomeric–monomeric mixture showed better growth inhibitory activity towards Bacillus cereus and Escherichia coli compared with native chitosan. Optimum growth inhibition was observed with chito-oligomers of higher DP having low degree of acetylation. The latter caused pore formation and permeabilization of the cell wall of B. cereus, whereas blockage of nutrient flow due to the aggregation of chito-oligomers–monomers was responsible for the growth inhibition and lysis of E. coli, which were evidenced by scanning electron microscopy analysis. The spillage of cytoplasmic enzymes and native PAGE of the cell-free supernatant of B. cereus treated with chito-oligomeric–monomeric mixture further confirmed bactericidal activity of the latter. Use of papain and Pronase, which are inexpensive and easily available, for chitosanolysis, is of commercial importance, as the products released are of considerable biomedical value.
Modulation of differential transcription of tRNA genes through chromatin organization
Authors: Parthasarthy Akhila , Gopinathan Karumathil P. 
Published: February 2006

In higher eukaryotes, tRNA multigene families comprise several copies encoding the same tRNA isoacceptor species. Of the 11 copies of a tRNA1Gly family from the mulberry silkworm Bombyx mori, individual members are differentially transcribed in vivo in the B. mori-derived BmN cell lines and in vitro in silk gland nuclear extracts. These genes have identical coding regions and hence harbour identical internal control sequences (the A and B boxes), but differ significantly in their 5′ and 3′ flanking regions. In the present study, we demonstrate the role of chromatin structure in the down-regulation of the poorly expressed copy, tRNA1Gly-6,7. Distinct footprints in the 5′-upstream region of the poorly transcribed gene in vitro as well as in vivo suggested the presence of nucleosomes. A theoretical analysis of the immediate upstream sequence of this gene copy also revealed a high propensity of nucleosome formation. The low transcription of tRNA1Gly-6,7 DNA was further impaired on assembly into chromatin and this inhibition was relieved by externally supplemented TFIIIC with an associated histone acetyltransferase activity. The inhibition due to nucleosome assembly was absent when the 5′-upstream region beyond −53 nt was deleted or entirely swapped with the 5′-upstream region of the highly transcribed gene copy, which does not position a nucleosome. Footprinting of the in vitro assembled tRNA1Gly-6,7 chromatin confirmed the presence of a nucleosome in the immediate upstream region potentially masking TFIIIB binding. Addition of TFIIIC unmasked the footprints present on account of the nucleosome. Our studies provide the first evidence for nucleosomal repression leading to differential expression of individual members from within a tRNA multigene family.
The development of harmful social behaviour in pigs with intact tails and different enrichment backgrounds in two housing systems
Authors: Van de Weerd H. A. , Docking C. M. , Day J. E. L. , Edwards S. A. 
Published: February 2006

AbstractThe present study compared the performance and development of adverse behaviours of pigs with intact tails, when housed in a straw-bedded system or a part-slatted system enriched with a commercial device. The pigs had previously received different enrichment treatments (rooting box, liquid dispenser, straw bedding or none), either in the farrowing crate or with their lactating dam or post weaning. The pigs were mixed in groups at 10 weeks of age and from then on, every 2 weeks, behavioural observations were performed, focusing mainly on harmful social behaviour and enrichment use. The study showed that pigs with undocked tails can be at high risk of tail biting in part-slatted systems, whereas the straw bedding prevented the development of tail biting. The immediate effects of the environment seemed to exert a greater influence on the development of adverse behaviour than early life enrichment and adding a simple enrichment device could not compensate for the deficiencies in the barren environment of the part-slatted system. In order to prevent vice, functional design of environmental enrichment is required.
Effects of sow nutrition on maternal and foetal serum growth factors and on foetal myogenesis
Authors: Nissen P. M. , Sørensen I. L. , Vestergaard M. , Oksbjerg N. 
Published: February 2006

AbstractThe objective of this study was to examine the effect of increased maternal nutrition in early to mid gestation on changes in serum growth factors of the sow and foetuses. Furthermore, the effect of the foetal sera on in vitro proliferation and differentiation of porcine primary myoblasts was examined. Pregnant sows were either given food either in accordance to requirements (2 kg/day; C) until day 50 or 70 of gestation or given food in accordance to requirements until day 25 and then ad libitum (A) until day 50 or 70. Sows were slaughtered at the Institute's veterinary controlled slaughterhouse at day 50 or 70, respectively. Serum from sows and pools of cord-blood serum from each litter were analysed for glucose, lactate, insulin, insulin-like growth factor (IGF; IGF-1 and -2) and IGF binding proteins (IGFBPs). IGF-1 (P < 0·001) was higher in A compared with C sows, and a 28-kDa IGFBP (P < 0·05) and a 24-kDa IGFBP (P < 0·05) was higher in serum from day 70 compared with day 50 sows. There was no significant effect of food intake on growth factor concentrations in foetal serum or on serum-induced proliferation and differentiation of myoblasts. A 28 kDa IGFBP, IGFBP-2 and -3 were all higher (P < 0·06) and serum-induced proliferation (P < 0·001) and differentiation (P < 0·1) lower at day 70 than day 50. Maternal food intake did not influence the DNA and RNA concentrations and the CPK activity in the foetal longissimus dorsi muscle. The glucose concentration in the liver was higher in C than A foetuses at day 70 of gestation, but not at day 50.In conclusion, no significant effects of maternal nutrition were found on serum growth factor concentrations in the foetuses or on serum-induced proliferation and differentiation of primary myoblasts.
Performance of weanling pigs offered low or high lactose diets supplemented with avilamycin or inulin
Authors: Pierce K. M. , Callan J. J. , McCarthy P. , O'Doherty J. V. 
Published: February 2006

AbstractOne hundred and eighty piglets (24 days old, 6·0 kg live weight) were used to investigate interactions between lactose, avilamycin and inulin on growth performance and nutrient digestibility in weaned piglets. The piglets were blocked on the basis of live weight and within each block assigned to one of six dietary treatments (six replicates (pens) per treatment). The piglets were offered diets containing either a low (175 g/kg) or high (295 g/kg) lactose levels with one of the following food additives (1) 0 supplementation (2) avilamycin (60 mg/kg) or (3) inulin (15 g/kg) in a 2 × 3 factorial arrangement. The starter diets were offered for 21 days and all diets contained chromium III oxide at 150 p. p. m. There was an interaction (P< 0·05) between lactose level and both avilamycin and inulin on average daily gain (ADG) during the starter period (days 0 to 21). The pigs receiving 295 g/kg lactose level had a higher overall ADG than pigs receiving 175 g/kg lactose level. However, there was no difference between 295 g/kg lactose and 175 g/kg lactose in ADG when the diets were supplemented with avilamycin or inulin. There was an interaction between lactose level and inulin in the apparent digestibility of gross energy (GE) and nitrogen (N) (P< 0·05). The inclusion of inulin with 175 g/kg lactose increased GE digestibility compared with the 175 g/kg lactose only diet. However, the inclusion of inulin with 295 g/kg lactose had no effect on GE digestibility. The inclusion of inulin with 295 g/kg lactose reduced N digestibility compared with the inclusion of inulin at 175 g/kg lactose. However, there was no difference in N digestibility between 175 and 295 g/kg lactose only diets. In conclusion, there was no benefit in terms of pig growth rate to supplementing diets high in lactose with either inulin or avilamycin. However, the inclusion of inulin improved the energy digestibility of diets low in lactose.
Costs of the major endemic diseases of sheep in Great Britain and the potential benefits of reduction in disease impact
Authors: Nieuwhof G. J. , Bishop S. C. 
Published: February 2006

AbstractThe costs of three major endemic sheep diseases in Great Britain, gastro-intestinal (GI) parasites, footrot and scab, were estimated and compared with costs for other diseases from another study. Disease costs include lost performance, preventive measures and treatment of affected animals. The most costly disease, of those studied, for the British sheep industry is infestation with GI parasites, with estimated annual costs of £84 million. Annual costs for the other two diseases are £24 million for footrot and £8 million for sheep scab. This compares with literature estimates of £20 million for Chlamydial abortions and £12 million for toxoplasmosis. For sheep scab most costs are for preventive measures, therefore, short of eradication, a reduction in incidence will have a limited effect on costs. For GI parasites, costs are linearly related to the severity of the infestation and a reduction of the disease will have a proportional effect on the costs to the industry. For footrot about half the costs are for preventive measures, the other half is for lost production and treatment. A reduction in the incidence of footrot has a proportional effect on the £10 million associated with loss of production and treatment of infected animals. It is concluded that gastro-intestinal parasites and footrot are two sheep diseases in Britain for which a reduction of severity or incidence will have a large impact on costs of production.
Effect of drinking saline water on food and water intake, food digestibility, and nitrogen and mineral balances of rusa deer stags (Cervus timorensis russa)
Authors: Kii W. Yape , Dryden G. McL. 
Published: February 2006

AbstractThe salinity tolerance of Javan rusa deer (Cervus timorensis russa) was investigated with seven stags, aged 4·5 years. Animals were offered a medium-quality chaffed lucerne hay and given five different levels of water salinity: (a) control (570 mg/kg of total dissolved salts (TDS)) and (b) ‘saline’ water with TDS contents of 1000, 3500, 6000 and 8500 mg/kg. Food intake, food digestibility and nitrogen balance were not affected by increasing salt concentration in drinking water, however the drinking water (DW) intake, the total (food plus drinking) water intake and the DW:dry-matter ratio increased with increasing salt concentration. Some deer given water containing 8500 mg TDS per kg showed signs of stress which included large between-day fluctuations in water intake, opening of the orbital gland, head shaking, and rapid breathing. Rusa deer can tolerate drinking water containing 6000 mg TDS per kg for at least 9 days without harmful effect but may be unable to tolerate water with 8500 mg TDS per kg.
Intake, growth and meat quality of steers given diets based on varying proportions of maize silage and grass silage
Authors: Juniper D. T. , Browne E. M. , Fisher A. V. , Bryant M. J. , Nute G. R. , Beever D. E. 
Published: February 2006

AbstractSimmental × Holstein-Friesian steers were offered four forage diets. These comprised grass silage (G); proportionately 0·67 grass silage, proportionately 0·33 maize silage (GGM); 0·33 grass silage, 0·67 maize silage (MMG); maize silage (M) from 424 (s.d. = 11·5) kg to slaughter at a minimum weight of 560 kg. Forages were mixed and offered ad libitum. Steers were offered 2 kg of a concentrate daily, the concentrate being formulated such that all steers had similar crude protein intakes across dietary treatments. A sample of steers was slaughtered at the beginning of the experimental period to allow the calculation of the rate of gain of the carcass and its components. Carcass dissection of a sample of steers allowed the development of a prediction equation of carcass composition based on thoracic limb dissection of all carcasses. Forage dry matter intake and live-weight gain increased linearly as maize silage replaced grass silage in the forage mixture, resulting in improvements in food conversion ratio (allP= 0·001). Killing-out proportion increased with maize silage inclusion (P< 0·001) but fat and conformation scores did not differ significantly between diets. However, increasing maize inclusion in the diet resulted in a greater weight (P= 0·05) and proportion (P= 0·008) of fat in the carcass, and significant increases in internal fat deposition. The inclusion of maize led to a progressive increase in the daily gains of carcass (P< 0·001), and significant increases in the daily gains of both fat (P< 0·001) and lean tissue (P< 0·001). Fat colour was more yellow in cattle given diets G and GGM than diets MMG and M(P< 0·001) and colour intensity was lower on diet M than the other three diets (P< 0·001). There were no significant differences in any aspects of eating quality between diets. Therefore, maize silage has the potential to reduce the time taken for finishing beef animals to achieve slaughter weight with no apparent detrimental effects on subsequent meat quality.
Effects of restricted feeding and re-feeding of Barbarine lambs: intake, growth and non-carcass components
Authors: Mahouachi M. , Atti N. 
Published: February 2006

Abstract Fifty intact male Barbarine lambs were used to assess the effects of restricted feeding and re-alimentation on intake, growth and non-carcass components. Five lambs were slaughtered at the start of the trial, the remainder were randomly allocated into three groups. One group was offered only stubble grazing (low: L), another, also on stubble, received, indoors, an average of 80 g dry matter (DM) of soya-bean meal per day (medium: M); the third group was kept indoors and had free access to hay and 450 g of concentrate per day (high: H). At the end of this restriction period (70 days), five lambs per group were slaughtered. The 10 remaining animals in each group were divided into two groups receiving concentrate and hayad libitum. The crude protein content (CP) of the concentrate was 160 and 210 g/kg DM for the two treatments, respectively. At the end of the trial all animals were slaughtered at 37·61 ± 2·05 kg live weight.In the restriction period, sheep from the H group had a significantly higher growth rate (108 g/day) than L group (61 g/day) with M intermediate. The empty body weight (EBW) as well as carcass weight were significantly higher in H than in restricted sheep. Digestive tract components and liver weight were the same for all treatments. However, skin weight was significantly (P< 0·01) affected by dietary treatment. The heart and lungs were also heavier in H lambs than in the two other groups. Conversely, the relative weights of gut and liver as proportion of EBW increased in restricted lambs, while that of skin and red organs was not affected by diet.In the re-alimentation period and with both CP levels, the compensating animals showed the same growth rate as the previous unrestricted ones. At the end of this period, organ weights, in both absolute and relative value, were comparable among lambs of the three nutritional histories and two CP level. The absolute and proportional daily gains were similar in all animals for visceral and external organs, but they were significantly higher in H lambs than in L and M ones for the omental and mesenteric fat and testis.
An improved model for the French genetic evaluation of dairy bulls on length of productive life of their daughters
Authors: Ducrocq V. 
Published: February 2006

AbstractFunctional longevity of dairy cows has been routinely evaluated in France since 1997 using a survival analysis model. Recently, we proposed a genetic trend validation test that could be used before including national data in an international evaluation of bulls on longevity of their daughters. Its application to the French Holstein data revealed a large overestimation of the genetic trend. It was found that the bias is the result of a change in the baseline hazard rate over time. A new proportional hazards model is proposed which accounts for this change. In the new model, the baseline is described as a stratified, piecewise Weibull hazard function within lactation, i.e. a function of the number of days since the most recent calving. Stratification is within year and parity. Different Weibull hazard functions are used over four periods: 0 to 270 days, 271 to 380 days, 381 days to day when dried, dry period until the next calving. The non-genetic effects included in the model were slightly different from the previous one. In particular the interaction effects between the within herd-year class of production and lactation number × stage of lactation on the one hand and year-season were accounted for. The estimated genetic variance was smaller than with the old model. The new genetic trend is almost flat. An illustration of the efficiency of selection on the estimated breeding values for longevity is presented.