bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid detection of the cisAB allele consisting of a chimera of normal A and B alleles by PCR‐RFLPs
Authors: Fukumori Y. , Ohnoki S. , Yoshimura K. , Nagao N. , Shibata H. , Tomita T. , Okubo Y. , Yamaguchi H. 
Published: April 2008

Summary. DNA samples were analysed from Japanese individuals with the very rare ABO variant phenotype, cisAB (A2B3), which is characterized by the apparent inheritance of both A and B genes on one chromosome. The nature of the bases present at nucleotide positions (nps) 261, 526, 703, 796 and 803 is important for the specificity of the alleles at the ABO locus and the DNA from the cis AB donors was analysed by polymerase chain reaction ‐ restriction fragment length polymorphism (PCR‐RFLP) to determine which nucleotides are present at these positions.The results indicated that the cisAB allele had the AAAB‐structure, which was a chimera of normal A and B alleles, when the expression ‘AAAA’ and ‘BBBB’ indicated the nucleotides of normal A (C, G, C and G) and B (G, A, A and C) genes at nps 526, 703, 796 and 803, respectively. The AAAB allele was found in all 27 individuals (17 families) with the cisAB including three phenotypes A2B3, A1B3 and A2B and no other chimeric gene was found. The causative gene of cisAB was the AAAB allele, and the A and B alleles were not on one chromosome.The cisAB allele appeared to be a product of the normal A allele due to a point mutation at nucleotide position 803, from G to C. The AAAB allele is thought to be normally transcribed and translated to produce an unusual transferase polypeptide, which has weak A‐ and weaker B‐specific activity.PCR‐RFLP is a rapid and useful means of detecting the cisAB allele (the AAAB allele) without a family study, even when they have A1B3 and A2B phenotypes, because trans‐type A1B3 and A2B samples have obviously different PCR‐RFLP profiles.
Design of a village breeding programme for a llama population in the High Andes of Bolivia
Authors: Wurzinger M. , Willam A. , Delgado J. , Nürnberg M. , Zárate A.V. , Stemmer A. , Ugarte G. , Sölkner J. 
Published: April 2008

SummaryNo national breeding programme for llamas is in place in Bolivia. Initiatives for genetic improvement are rarely found and are usually carried out by NGOs working in rural development or improvement of livestock production or research stations. Farmers in the Province of Ayopaya in the District of Cochabamba have formed a breeders’ organization with the aim of improving fibre production. In this study, a detailed outline of a breeding programme with a focus on organizational and technical details is described. Facing constraints like illiteracy of farmers, bad infrastructure and lack of finances, a simple breeding programme is set up. The breeding goal is a higher fleece weight while keeping the fleece quality at the current high level. Greasy fleece weight and fibre diameter are identified as main selection criteria. Mass selection of males is carried out. Selected males are either exchanged between farmers and used in the herds or are kept during the mating season in a central mating station owned by the breeders’ organization. Model calculations were carried out with the program zplan, which is based on a deterministic approach. zplan evaluates the genetic and economic efficiency of breeding strategies considering one cycle of selection. Scenarios with only intra‐herd use, using only the central mating station or combinations of those were compared in terms of expected genetic gain and expected increase of inbreeding. Fastest genetic progress is achieved when the males are kept in a central mating station as the selection intensity is on a high level. Rates of inbreeding vary between 0.08 and 0.32% per generation.
QTL detection for milk production traits in goats using a longitudinal model
Authors: Roldán D.L. , Rabasa A.E. , Saldaño S. , Holgado F. , Poli M.A. , Cantet R.J.C. 
Published: April 2008

SummaryEight paternal half‐sib families were used to identify chromosomal regions associated with variation in the lactation curves of dairy goats. DNA samples from 162 animals were amplified by PCR for 37 microsatellite markers, from Capra hircus autosomes CHI3, CHI6, CHI14 and CHI20. Milk samples were collected during 6 years, and there were 897 records for milk yield (MY) and 814 for fat (FP) and protein percentage (PP). The analysis was conducted in two stages. First, a random regression model with several fixed effects was fitted to describe the lactation function, using a scale (α) plus four shape parameters: β and γ, both associated with a decrease in the slope of the curve, and δ and φ that are related to the increase in slope. Predictions of α, β, γ, δ and φ were regressed using an interval mapping model, and F‐tests were used to test for quantitative trait loci (QTL) effects. Significant (p < 0.05) QTLs were found for: (i) MY: CHI6 at 70–80 cM for all parameters; CHI14 at 14 cM for δ and φ; (ii) FP: CHI14, at 63 cM was associated with β; CHI20, at 72 cM, showed association with α; (iii) PP: chromosomal regions associated with β were found at 59 cM in CHI3 and at 55 cM in CHI20 with α and γ. Analyses using more families and more animals will be useful to confirm or to reject these findings.
Plasma leptin levels in pigs with different leptin and leptin receptor genotypes
Authors: Amills M. , Villalba D. , Tor M. , Mercadé A. , Gallardo D. , Cabrera B. , Jiménez N. , Noguera J.L. , Sànchez A. , Estany J. 
Published: April 2008

SummaryA C3469T mutation at exon 3 of the pig leptin (Lep) gene has been genotyped in diverse pig breeds yielding controversial results with regard to its association with growth, fatness and carcass traits. A similar situation has been reported for a HpaII restriction fragment length polymorphism (RFLP) in the pig leptin receptor (Lepr) gene, where associations were found depending on the statistical model employed. The main objective of our work was to investigate if leptin plasma concentrations differ in pigs with different C3469T and Lepr HpaII RFLP genotypes. With this aim, we have measured plasma leptin levels at 160 days in 68 Landrace pigs with different Lep C3469T and Lepr HpaII RFLP genotypes. Neither Lep (TT: 11.68 ng/ml, TC: 10.71 ng/ml) nor Lepr (AA: 12.6 ng/ml, AB: 10.93 ng/ml, BB: 11.74 ng/ml) genotypes influenced significantly plasma Lep concentration. Moreover, we did not find any association between Lep and Lepr genotypes and phenotypic variation at growth and fatness traits in a commercial population of 320 Landrace pigs.
Use of a test day model for dairy goat milk yield across lactations in Germany
Authors: Zumbach B. , Tsuruta S. , Misztal I. , Peters K.J. 
Published: April 2008

SummaryBreeding value prediction for dairy goats in Germany is still based on herd mate comparison within breeding society. The objective of this study was to estimate genetic parameters for milk yield based on a test day model. For the analysis 35 308, 30 551 and 23 640 test day records from lactations 1, 2 and 3 from 5079, 4118 and 3132 animals, respectively, were used. The data between 1987 and 2003 were obtained from six German breeding societies. The multiple trait (lactations 1, 2 and 3) repeatability model (RPT) included the fixed effects of breeding society–breed–herd–year, litter size, lambing season, and days in milk of third‐order Legendre polynomials nested within herd–year, and the random effects of animal additive and permanent environment. The three‐trait random regression model (RR) also included the random regressions based on second‐order Legendre polynomials for animal additive and permanent environmental effects. Heritability estimates in RPT were 0.27 ± 0.02, 0.20 ± 0.02 and 0.37 ± 0.02 for the first, second and third lactation, respectively. The genetic correlation between the first and second lactation was 0.69, between the second and third lactation 0.79, and between the first and third lactation 0.45. Heritability estimates from the RR in the first and second lactations decreased from the beginning to the end of the lactation, with average values of 0.28 and 0.27, respectively. Estimates in the third lactation showed a maximum in the middle of lactation, averaging 0.37. Genetic correlations between the first and second lactation averaged 0.64, between the second and third lactation 0.72, and between the first and third lactation 0.46. Despite the small data set and restricted relationship structure the estimates were reasonable with the exception of estimates from the third lactation, which seemed inflated. RR could be used for genetic evaluation of dairy goats in Germany.
Ex situ cultivation of Aplysinaaerophoba close to in situ conditions: ecological, biochemical and histological aspects
Authors: Klöppel Anne , Pfannkuchen Martin , Putz Annika , Proksch Peter , Brümmer Franz 
Published: April 2008

AbstractSponges provide the largest number of biologically active natural products known from the marine environment and continue to be a very well studied phylum of marine fauna. The Mediterranean sponge Aplysina aerophoba accumulates brominated isoxazoline alkaloids such as Aplysinamisin‐1, Aerophobin‐2, Isofistularin‐3 and the biotransformation product Aeroplysinin‐1, which possesses, for example, antibiotic and cytotoxic properties. Until now, it is still being discussed which organisms – the sponge itself or associated microorganisms – are responsible for metabolite production. For cultivating Aplysina individuals under ex situ conditions, we surveyed relevant ecological factors in situ and controlled them in our aquarium system. We maintained A. aerophoba for more than 9 months and analysed changes of metabolite content and composition, microbial association as well as morphology in situ and ex situ under different light exposure. Although sponges showed slight reduction during maintenance, ex situ cultivation similar to in situ conditions provides a promising method to keep sponges and obtain their bioactive metabolites.
Oxygen‐dependent autoaggregation in Shewanella oneidensis MR‐1
Authors: McLean J. S. , Pinchuk G. E. , Geydebrekht O. V. , Bilskis C. L. , Zakrajsek B. A. , Hill E. A. , Saffarini D. A. , Romine M. F. , Gorby Y. A. , Fredrickson J. K. , Beliaev A. S. 
Published: April 2008

SummaryIn aerobic chemostat cultures maintained at 50% dissolved O2 tension (3.5 mg l−1 dissolved O2), Shewanella oneidensis strain MR‐1 rapidly aggregated upon addition of 0.68 mM CaCl2 and retained this multicellular phenotype at high dilution rates. Confocal microscopy analysis of the extracellular matrix material contributing to the stability of the aggregate structures revealed the presence of extracellular DNA, protein and glycoconjugates. Upon onset of O2‐limited growth (dissolved O2 below detection) however, the Ca2+‐supplemented chemostat cultures of strain MR‐1 rapidly disaggregated and grew as motile dispersed cells. Global transcriptome analysis comparing aerobic aggregated to O2‐limited unaggregated cells identified genes encoding cell‐to‐cell and cell‐to‐surface adhesion factors whose transcription increased upon exposure to increased O2 concentrations. The aerobic aggregated cells also revealed increased expression of putative anaerobic electron transfer and homologues of metal reduction genes, including mtrD (SO1782), mtrE (SO1781) and mtrF (SO1780). Our data indicate that mechanisms involved in autoaggregation of MR‐1 are dependent on the function of pilD gene which encodes a putative prepilin peptidase. Mutants of S. oneidensis strain MR‐1 deficient in PilD and associated pathways, including type IV and Msh pili biogenesis, displayed a moderate increase in sensitivity to H2O2. Taken together, our evidence indicates that aggregate formation in S. oneidensis MR‐1 may serve as an alternative or an addition to biochemical detoxification to reduce the oxidative stress associated with production of reactive oxygen species during aerobic metabolism while facilitating the development of hypoxic conditions within the aggregate interior.
A new global biome reconstruction and data‐model comparison for the Middle Pliocene
Authors: Salzmann U. , Haywood A. M. , Lunt D. J. , Valdes P. J. , Hill D. J. 
Published: April 2008

ABSTRACTAim  To produce a robust, comprehensive global biome reconstruction for the Middle Pliocene (c. 3.6–2.6 Ma), which is based on an internally consistent palaeobotanical data set and a state‐of‐the‐art coupled climate–vegetation model. The reconstruction gives a more rigorous picture of climate and environmental change during the Middle Pliocene and provides a new boundary condition for future general circulation model (GCM) studies.Location  Global.Methods  Compilation of Middle Pliocene vegetation data from 202 marine and terrestrial sites into the comprehensive GIS data base TEVIS (Tertiary Environmental Information System). Translation into an internally consistent classification scheme using 28 biomes. Comparison and synthesis of vegetation reconstruction from palaeodata with the outputs of the mechanistically based BIOME4 model forced by climatology derived from the HadAM3 GCM.Results  The model results compare favourably with available palaeodata and highlight the importance of employing vegetation–climate feedbacks and the anomaly method in biome models. Both the vegetation reconstruction from palaeobotanical data and the BIOME4 prediction indicate a general warmer and moister climate for the Middle Pliocene. Evergreen taiga as well as temperate forest and grassland shifted northward, resulting in much reduced tundra vegetation. Warm‐temperate forests (with subtropical taxa) spread in mid and eastern Europe and tropical savannas and woodland expanded in Africa and Australia at the expense of deserts. Discrepancies which occurred between data reconstruction and model simulation can be related to: (1) poor spatial model resolution and data coverage; (2) uncertainties in delimiting biomes using climate parameters; or (3) uncertainties in model physics and/or geological boundary conditions.Main conclusions  The new global biome reconstruction combines vegetation reconstruction from palaeobotanical proxies with model simulations. It is an important contribution to the further understanding of climate and vegetation changes during the Middle Pliocene warm interval and will enhance our knowledge about how vegetation may change in the future.
The Problem of Free Riding in Voluntary Generic Advertising: Parallelism and Possible Solutions from the Lab
Authors: Messer Kent D. , Kaiser Harry M. , Schulze William D. 
Published: April 2008

AbstractProducers of many commodities pay for generic advertising, which is a public good for producers and, in cases like healthy foods, enhances social welfare. Though most programs were initially funded through the Voluntary Contribution Mechanism, many became mandatory to mitigate free riding. This experimental research simulates key economic and psychological details of these programs and produces donation results strikingly similar to a historic example. Because mandatory programs may be declared unconstitutional, the Provision Point Mechanism is tested as an alternative. This research also shows that refund‐by‐request donation mechanisms establish a status quo of contributing and reduce free riding.
An Incentive Compatible Conjoint Ranking Mechanism
Authors: Lusk Jayson L. , Fields Deacue , Prevatt Walt 
Published: April 2008

AbstractA simple method for making ranking‐based conjoint analysis incentive compatible is proposed. The incentive compatible mechanism involves people purchasing a product profile with a probability proportional to its assigned rank. In an empirical application related to consumer preferences for beef attributes, we find that the forecasted market share for a new pasture‐raised steak obtained using incentive‐compatible rankings was significantly greater than that implied from traditional hypothetical conjoint rankings. People's rankings of ground beef products were not affected by the mechanism or by information about pasture‐raised beef.
Immigrant Parents and Children: An Analysis of Decisions Related to Return Migration
Authors: Djajić Slobodan 
Published: April 2008

AbstractIt is not unusual for immigrants to leave the host country and resettle permanently in their country of origin. This paper examines the interaction among some of the key factors that influence the return decision of immigrant households. These include purely economic variables such as wages of the two countries and the costs and benefits of accumulating country‐specific human capital, but also subjective factors such as the intensity of the locational preferences of immigrant parents and children and of their desire to remain together in a single location. The analysis is conducted under alternative assumptions with respect to the role of parents and children in the household's decision‐making process.
Marginal Likelihood Estimation via Power Posteriors
Authors: Friel N. , Pettitt A. N. 
Published: April 2008

SummaryModel choice plays an increasingly important role in statistics. From a Bayesian perspective a crucial goal is to compute the marginal likelihood of the data for a given model. However, this is typically a difficult task since it amounts to integrating over all model parameters. The aim of the paper is to illustrate how this may be achieved by using ideas from thermodynamic integration or path sampling. We show how the marginal likelihood can be computed via Markov chain Monte Carlo methods on modified posterior distributions for each model. This then allows Bayes factors or posterior model probabilities to be calculated. We show that this approach requires very little tuning and is straightforward to implement. The new method is illustrated in a variety of challenging statistical settings.
Non-Crossing Non-Parametric Estimates of Quantile Curves
Authors: Dette Holger , Volgushev Stanislav 
Published: April 2008

SummarySince the introduction by Koenker and Bassett, quantile regression has become increasingly important in many applications. However, many non-parametric conditional quantile estimates yield crossing quantile curves (calculated for various p ∈ (0, 1)). We propose a new non-parametric estimate of conditional quantiles that avoids this problem. The method uses an initial estimate of the conditional distribution function in the first step and solves the problem of inversion and monotonization with respect to p ∈ (0, 1) simultaneously. It is demonstrated that the new estimates are asymptotically normally distributed with the same asymptotic bias and variance as quantile estimates that are obtained by inversion of a locally constant or locally linear smoothed conditional distribution function. The performance of the new procedure is illustrated by means of a simulation study and some comparisons with the currently available procedures which are similar in spirit with the method proposed are presented.
A 71‐nucleotide deletion in the periaxin gene in a Romani patient with early‐onset slowly progressive demyelinating CMT
Authors: Baránková L. , Šišková D. , Hühne K. , Vyhnálková E. , Sakmaryová I. , Bojar M. , Rautenstrauss B. , Seeman P. 
Published: April 2008

Background:  Mutations in the periaxin (PRX) gene cause autosomal recessive demyelinating neuropathy Charcot–Marie–Tooth (CMT) type 4F. To date, 10 non‐sense or frameshift PRX mutations have been reported in patients with early‐onset neuropathy and further disease course consistent with either Dejerine–Sottas neuropathy or slow‐progressive demyelinating CMT.Methods:  We sequenced 59 patients from 55 Czech families including four unrelated patients of Romani (Gypsy) origin with early‐onset CMT displaying decreased nerve conduction velocities.Results:  We identified a novel homozygous mutation c.3286_3356del71 (K1095fsX18) in one Romani patient showing very slow disease progression. Amongst non‐Romani Czech CMT patients, PRX mutations have been proven to be very rare.
A descriptive study on constructional impairment in frontotemporal dementia and Alzheimer’s disease
Authors: Gasparini M. , Masciarelli G. , Vanacore N. , Ottaviani D. , Salati E. , Talarico G. , Lenzi G. L. , Bruno G. 
Published: April 2008

Background and purpose:  Frontotemporal dementia (FTD) is a degenerative disorder characterized, in its frontal variant, by psychiatric onset, deficits in executive functions and sparing of memory and visuo‐spatial abilities. Studies on visuo‐spatial abilities in FTD and Alzheimer’s disease (AD) have mainly focused on constructional abilities (CA) and have yielded contrasting data, often depending either on the task used or biases in the clinical selection of patients. The aim of our study was to evaluate the frequency of the CA impairment in FTD‐fv and AD patients at the early stage of the disease, and to verify if some distinctive features of this impairment can characterize each pathology.Methods:  The copy‐drawing task (Rey Complex Figure, RCF) of 41 patients with probable mild AD and 15 patients with probable mild FTD‐fv were analysed by means of quantitative and qualitative indices.Results:  Data showed that both AD and FTD patients displayed similar RCF scores, as well as execution strategies, type of errors and global analysis. The FTD group only had a significant deficit in the analysis of inner details.
Hypokalemic thyrotoxic periodic paralysis: clinical characteristics and predictors of recurrent paralytic attacks
Authors: Hsieh M.‐J. , Lyu R.‐K. , Chang W.‐N. , Chang K.‐H. , Chen C.‐M. , Chang H.‐S. , Wu Y.‐R. , Chen S.‐T. , Ro L.‐S. 
Published: April 2008

Background and purpose:  To study the clinical characteristics of hypokalemic thyrotoxic periodic paralysis (hoTPP) and identify the predictors of recurrent paralytic attacks before achieving the euthyroid status.Methods:  We retrospectively analyzed 45 hoTPP patients who were admitted during the 7‐year study period.Results:  A tendency towards male predominance was observed among the 45 patients (91.1%, 41/45). The mean onset age was 32.9 ± 10.0 years (range: 16–54 years). No significant differences were observed in the onset age between male and female patients. Precipitating factors included rest/sleep at night, hot weather, upper respiratory tract infections (URIs), and excessive physical activities. Atypical weakness was observed in nine (20%, 9/45) patients. One patient initially diagnosed with sporadic periodic paralysis eventually developed hoTPP.Discussion:  In provocative tests, hypokalemia was not a consistent finding during paralytic attacks. Before achieving the euthyroid status, the rate of recurrent attacks was as high as 62.2%, and peaked in the first 3 months after hoTPP was diagnosed. Patients with URIs exhibited a higher incidence of recurrent paralytic attacks than those without (odds ratio = 13.00; 95% confidence interval = 1.08–156.08; P = 0.04).