bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determination of Free Glycerol in Biodiesel via Solid‐Phase Extraction and Spectrophotometric Analysis
Authors: Mercer Erin Jo , Halaweish Fathi 
Published: November 2010

AbstractTo date, the standardized method for glycerol quantification in biodiesel production utilizes gas chromatography (GC); however, availability to manufacturers and instrumentation cost limits GC as an analytical method for general quality enforcement among producers. The method developed here is a bench top technique for quantitative determination of glycerol in biodiesel, with practical application in pharmaceutical and environmental quality control. The method extracts the glycerol contaminant from biodiesel using a normal phase solid phase extraction column (SPE). The protocol proceeds by rinsing with hexane to remove residual methyl esters, then collecting the glycerol with water. The aqueous extract is analyzed spectrophotometrically by an anthrone coloring reagent. Use of 2‐g SPE columns and the solvent system developed has achieved 85% glycerol recovery. The assay applied has a detection range of 0.004–0.400% free glycerol, comparable to the established American Society of Testing and Materials (ASTM) D 6584‐07 GC technique. Results were confirmed by GC and high‐pressure liquid chromatography (HPLC). The bench top technique reduces the costs of operation relative to current methods, completes analysis in proficient time, requires minimal labor, and has analytical limits comparable to existing standard methods of biofuel analysis.
Volumetric MRI analysis of hippocampal subregions in Cushing's disease: A model for glucocorticoid neural modulation
Authors: Toffanin T. , Nifosì F. , Follador H. , Passamani A. , Zonta F. , Ferri G. , Scanarini M. , Amistà P. , Pigato G. , Scaroni C. , Mantero F. , Carollo C. , Perini G.I. 
Published: November 2010

AbstractSeveral preclinical studies have demonstrated neuronal effects of glucocorticoids on the hippocampus (HC), a limbic structure with anterior–posterior anatomical and functional segmentation. We propose a volumetric magnetic resonance imaging analysis of hippocampus head (HH), body (HB) and tail (HT) using Cushing's disease (CD) as model, to investigate whether there is a differential sensitivity to glucocorticoid neuronal damage in these segments. We found a significant difference in the HH bilaterally after 12 months from trans-sphenoidal surgical selective resection of the adrenocorticotropic hormone (ACTH)-secreting pituitary micro-adenomas. This pre–post surgery difference could contribute to better understand the pathopysiology of CD as an in vivo model for stress-related hypercortisolemic neuropsychiatric disorders.
Telling Policy Stories: An Ethnographic Study of the Use of Evidence in Policy-making in the UK
Authors: STEVENS ALEX 
Published: November 2010

AbstractBased on participant observation in a team of British policy-making civil servants carried out in 2009, this article examines the use that is made of evidence in making policy. It shows that these civil servants displayed a high level of commitment to the use of evidence. However, their use of evidence was hampered by the huge volume of various kinds of evidence and by the unsuitability of much academic research in answering policy questions. Faced with this deluge of inconclusive information, they used evidence to create persuasive policy stories. These stories were useful both in making acceptable policies and in advancing careers. They often involved the excision of methodological uncertainty and the use of ‘killer charts’ to boost the persuasiveness of the narrative. In telling these stories, social inequality was ‘silently silenced’ in favour of promoting policies which were ‘totemically’ tough. The article concludes that this selective, narrative use of evidence is ideological in that it supports systematically asymmetrical relations of power.
Disease outbreaks associated with untreated recreational water use
Authors: SCHETS F. M. , DE RODA HUSMAN A. M. , HAVELAAR A. H. 
Published: November 2010

SUMMARYAnnual overviews of waterborne disease outbreaks associated with untreated recreational water use provided by authorities responsible for bathing-water quality and public health in The Netherlands revealed 742 outbreaks during 1991–2007 mainly comprising of skin conditions (48%) and gastroenteritis (31%) and involving at least 5623 patients. The number of outbreaks per bathing season correlated with the number of days with temperatures over 25°C (r=0·8–0·9), but was not reduced through compliance with European bathing-water legislation (r=0·1), suggesting that monitoring of faecal indicator parameters and striving for compliance with water-quality standards may not sufficiently protect bathers. Bathing sites were prone to incidental faecal contamination events or environmental conditions that favoured the growth of naturally occurring pathogens. Identification of all possible contamination sources, awareness of changes that might negatively affect water quality, and provision of adequate information to the public are important preventive measures to protect public health.
Prevalence and risk factors for Salmonella in veal calves at Danish cattle abattoirs
Authors: NIELSEN L. R. , BAGGESEN D. L. , AABO S. , MOOS M. K. , RATTENBORG E. 
Published: November 2010

SUMMARYThe study's objectives were to determine herd- and animal-level prevalence and herd-level risk factors for Salmonella in dairy-bred veal calves at slaughter in Denmark. In total, 1296 faecal samples were collected at five cattle abattoirs in Denmark during 2007–2008. The animals came from 71 randomly selected specialized veal-calf producers that delivered more than 100 animals to slaughter per year. Salmonella Dublin bacteria were isolated from 19 samples from 12 herds and Salmonella Typhimurium was isolated from one sample. The apparent prevalence of herds delivering Salmonella-shedding animals to slaughter was 18% (95% CI 9–27). The overall estimated true prevalence of shedding calves at slaughter was 1·3%. Veal-calf herds that purchased animals from herds not classified as low risk in the Danish Salmonella surveillance programme had significantly (P=0·03) higher risk of delivering Salmonella-shedding calves to slaughter. The results emphasize the importance of efforts in the dairy industry to ensure food safety for consumers.
The Effect of Perioperative Betamethasone on Post-operative Nausea, Vomiting and Pain in Children Undergoing Tonsillar Surgery
Authors: Johansson Ulrica , Sundgren Carola , Tano Krister , van den Berg Johannes 
Published: November 2010

AbstractObjectives:To investigate if a single dose of betamethasone given perioperatively could reduce common post-operative problems such as vomiting, nausea and pain in children undergoing tonsillar surgery.Background:Post-operative nausea and vomiting (PONV) are common problems after surgery caused by several perioperative factors, such as post-operative pain. Prophylactic treatment of PONV can be effective in improving recovery after surgery. Studies have shown that the use of a single dose of dexamethasone during tonsillectomies in children was efficient against PONV. Dexamethasone is not available in Sweden for intravenous administration; betamethasone was thought to be an alternative.Method:The study was a retrospective cohort study including 69 children who underwent tonsillar surgery. A single dose of betamethasone perioperatively was introduced to a group of 32 children, to reduce PONV while 37 children did not receive betamethasone. Data were received from the medical records and from a post-operative questionnaire.Results:No significant differences for children undergoing tonsillar surgery regarding the prevalence of PONV between the betamethasone group and the non-betamethasone group were found. This was maybe due to a comparatively low dose of betamethasone. However, the given dose was sufficient to significantly reduce post-operative pain.
Inverse perturbation for optimal intervention in gene regulatory networks
Authors: Bouaynaya Nidhal , Shterenberg Roman , Schonfeld Dan 
Published: November 2010

AbstractMotivation: Analysis and intervention in the dynamics of gene regulatory networks is at the heart of emerging efforts in the development of modern treatment of numerous ailments including cancer. The ultimate goal is to develop methods to intervene in the function of living organisms in order to drive cells away from a malignant state into a benign form. A serious limitation of much of the previous work in cancer network analysis is the use of external control, which requires intervention at each time step, for an indefinite time interval. This is in sharp contrast to the proposed approach, which relies on the solution of an inverse perturbation problem to introduce a one-time intervention in the structure of regulatory networks. This isolated intervention transforms the steady-state distribution of the dynamic system to the desired steady-state distribution.Results: We formulate the optimal intervention problem in gene regulatory networks as a minimal perturbation of the network in order to force it to converge to a desired steady-state distribution of gene regulation. We cast optimal intervention in gene regulation as a convex optimization problem, thus providing a globally optimal solution which can be efficiently computed using standard toolboxes for convex optimization. The criteria adopted for optimality is chosen to minimize potential adverse effects as a consequence of the intervention strategy. We consider a perturbation that minimizes (i) the overall energy of change between the original and controlled networks and (ii) the time needed to reach the desired steady-state distribution of gene regulation. Furthermore, we show that there is an inherent trade-off between minimizing the energy of the perturbation and the convergence rate to the desired distribution. We apply the proposed control to the human melanoma gene regulatory network.Availability: The MATLAB code for optimal intervention in gene regulatory networks can be found online: http://syen.ualr.edu/nxbouaynaya/Bioinformatics2010.html.Contact: nxbouaynaya@ualr.eduSupplementary information: Supplementary data are available at Bioinformatics online.
NBC: the Naïve Bayes Classification tool webserver for taxonomic classification of metagenomic reads
Authors: Rosen Gail L. , Reichenberger Erin R. , Rosenfeld Aaron M. 
Published: November 2010

Abstract
Motivation: Datasets from high-throughput sequencing technologies have yielded a vast amount of data about organisms in environmental samples. Yet, it is still a challenge to assess the exact organism content in these samples because the task of taxonomic classification is too computationally complex to annotate all reads in a dataset. An easy-to-use webserver is needed to process these reads. While many methods exist, only a few are publicly available on webservers, and out of those, most do not annotate all reads.
Results: We introduce a webserver that implements the naïve Bayes classifier (NBC) to classify all metagenomic reads to their best taxonomic match. Results indicate that NBC can assign next-generation sequencing reads to their taxonomic classification and can find significant populations of genera that other classifiers may miss.
Availability: Publicly available at: http://nbc.ece.drexel.edu.
Contact: gailr@ece.drexel.edu
Linkage disequilibrium and historical effective population size in the Thoroughbred horse
Authors: Corbin L. J. , Blott S. C. , Swinburne J. E. , Vaudin M. , Bishop S. C. , Woolliams J. A. 
Published: November 2010

SummaryMany genomic methodologies rely on the presence and extent of linkage disequilibrium (LD) between markers and genetic variants underlying traits of interest, but the extent of LD in the horse has yet to be comprehensively characterized. In this study, we evaluate the extent and decay of LD in a sample of 817 Thoroughbreds. Horses were genotyped for over 50 000 single nucleotide polymorphism (SNP) markers across the genome, with 34 848 autosomal SNPs used in the final analysis. Linkage disequilibrium, as measured by the squared correlation coefficient (r2), was found to be relatively high between closely linked markers (>0.6 at 5 kb) and to extend over long distances, with averager2maintained above non‐syntenic levels for single nucleotide polymorphisms (SNPs) up to 20 Mb apart. Using formulae which relate expected LD to effective population size (Ne), and assuming a constant actual population size, Newas estimated to be 100 in our population. Values of historical Ne, calculated assuming linear population growth, suggested a decrease in Nesince the distant past, reaching a minimum twenty generations ago, followed by a subsequent increase until the present time. The qualitative trends observed in Necan be rationalized by current knowledge of the history of the Thoroughbred breed, and inbreeding statistics obtained from published pedigree analyses are in agreement with observed values of Ne. Given the high LD observed and the small estimated Ne, genomic methodologies such as genomic selection could feasibly be applied to this population using the existing SNP marker set.
RT‐qPCR Comparison of mast cell populations in whole blood from healthy horses and those with laminitis
Authors: Brooks S. A. , Bailey E. 
Published: November 2010

SummaryInflammatory damage to the digital laminae, a structure responsible for suspension of the distal skeleton within the hoof capsule, results in a painful and often life‐threatening disease in horses called laminitis. There can be many diverse causes of laminitis; however, previous work in the horse has suggested that in each case, the inflammation and resulting tissue damage is consistent with the action of mediators released from mast cells (MC), as well as the downstream consequences of their activation. The recent development of molecular genetics tools to characterize cells based on their transcriptional activity makes a new approach for measuring MCs possible. Healthy thoroughbred horses from a variety of age groups were used to assess the amount of variation in KIT (encoding mast cell growth factor receptor) and TPSB2 (encoding mast cell tryptase beta 2) gene expression present in the population and to establish “normal” values. Horses (n = 9) with a wider range of body condition scores (3–8), because of a more lax management setting that could predispose them to laminitis, had significantly higher KIT expression in circulating peripheral blood cells than horses under individualized management conditions (n = 10) that produced ideal body condition scores (4–6) (mean 2.573‐fold, P < 0.0005). Likewise, horses affected with acute laminitis (n = 11) had elevated expression of TPSB2 (2.760‐fold, P = 0.0011) relative to control horses (n = 15). These data suggest that investigation of MC‐related genes KIT and TPSB2 may be effective to assay MC population and activity. More work is needed to refine the diagnostic criteria to better describe at what point MC activation occurs and illustrate the use of gene expression assays in clinical cases of laminitis. Additionally, MC activation is associated with inflammatory disease in several mammalian species and may prove a valuable therapeutic target in the horse.
Transcription of LINE‐derived sequences in exercise‐induced stress in horses
Authors: Capomaccio S. , Verini‐Supplizi A. , Galla G. , Vitulo N. , Barcaccia G. , Felicetti M. , Silvestrelli M. , Cappelli K. 
Published: November 2010

SummaryA large proportion of mammalian genomes is represented by transposable elements (TE), most of them being long interspersed nuclear elements 1 (LINE‐1 or L1). An increased expression of LINE‐1 elements may play an important role in cellular stress–related conditions exerting drastic effects on the mammalian transcriptome. To understand the impact of TE on the known horse transcriptome, we masked the horse EST database, pointing out that the amount is consistent with other major vertebrates. A previously developed transcript‐derived fragments (TDFs) dataset, deriving from exercise‐stimulated horse peripheral blood mononuclear cells (PBMCs), was found to be enriched with L1 (26.8% in terms of bp). We investigated the involvement of TDFs in exercise‐induced stress through bioinformatics and gene expression analysis. Results indicate that LINE‐derived sequences are not only highly but also differentially expressed during physical effort, hinting at interesting scenarios in the regulation of gene expression in relation to exercise.
A genome‐wide association study for racing performances in Thoroughbreds clarifies a candidate region near the MSTN gene
Authors: Tozaki T. , Miyake T. , Kakoi H. , Gawahara H. , Sugita S. , Hasegawa T. , Ishida N. , Hirota K. , Nakano Y. 
Published: November 2010

SummaryUsing 1400 microsatellites, a genome‐wide association study (GWAS) was performed to identify genomic regions associated with lifetime earnings and performance ranks, as determined by the Japan Racing Association (JRA). The minimum heritability (h2) was estimated at 7–8% based on the quantitative trait model, suggesting that the racing performance is heritable. Following GWAS with microsatellites, fine mapping led to identification of three SNPs on ECA18, namely, g.65809482T>C (P = 1.05E‐18), g.65868604G>T (P = 6.47E‐17), and g.66539967A>G (P = 3.35E‐14) associated with these performance measures. The haplotype of these SNPs, together with a recently published nearby SNP, g.66493737C>T (P = 9.06E‐16) in strong linkage disequilibrium, also showed a very clear association with the performance (P < 1E‐05). The candidate genomic region contained eight genes annotated by ENSEMBL, including the myostatin gene (MSTN). These findings suggest the presence of a gene affecting the racing performance in Thoroughbred racehorses in this region on ECA18.
Refinement of quantitative trait loci on equine chromosome 10 for radiological signs of navicular disease in Hanoverian warmblood horses
Authors: Lopes M. S. , Diesterbeck U. , Da Câmara Machado A. , Distl O. 
Published: November 2010

SummaryNavicular disease is characterized by a progressive degenerative alteration of the equine podotrochlea. In this study, we refined a previously identified quantitative trait locus (QTL) on horse chromosome 10 for the abnormal development of canales sesamoidales (DCS) of the navicular bone in Hanoverian warmblood horses. Genotyping was done in 192 Hanoverian warmblood horses from 17 paternal half‐sib groups. The whole marker set comprised 45 markers including seven newly developed microsatellites and 13 single nucleotide polymorphisms (SNPs) within positional candidate genes. Chromosome‐wide significant QTL were confirmed and refined for DCS on horse chromosome (ECA) 10 at 0.16–2.70 Mb and at 14.45–36.37 Mb. Nine microsatellites and three SNP markers reached the highest multipoint Zmeans and LOD scores at 19.34–20.38 Mb and at 23.17–30.73 Mb with genome‐wide error probabilities of P < 0.05. In addition, a significant association of a SNP within VSTM1 and a significant haplotype‐trait association within IRF3 could be shown. These results support a possible role of the candidate genes VSTM1 and IRF3 within the QTL on ECA10 for DCS. This study is a further step towards the identification of the genes responsible for navicular disease in Hanoverian warmblood horses.
Interspersed repeats in the horse (Equus caballus); spatial correlations highlight conserved chromosomal domains
Authors: Adelson D. L. , Raison J. M. , Garber M. , Edgar R. C. 
Published: November 2010

SummaryThe interspersed repeat content of mammalian genomes has been best characterized in human, mouse and cow. In this study, we carried out de novo identification of repeated elements in the equine genome and identified previously unknown elements present at low copy number. The equine genome contains typical eutherian mammal repeats, but also has a significant number of hybrid repeats in addition to clade‐specific Long Interspersed Nuclear Elements (LINE). Equus caballus clade specific LINE 1 (L1) repeats can be classified into approximately five subfamilies, three of which have undergone significant expansion. There are 1115 full‐length copies of these equine L1, but of the 103 presumptive active copies, 93 fall within a single subfamily, indicating a rapid recent expansion of this subfamily. We also analysed both interspersed and simple sequence repeats (SSR) genome‐wide, finding that some repeat classes are spatially correlated with each other as well as with G+C content and gene density. Based on these spatial correlations, we have confirmed that recently‐described ancestral vs. clade‐specific genome territories can be defined by their repeat content. The clade‐specific Short Interspersed Nuclear Element correlations were scattered over the genome and appear to have been extensively remodelled. In contrast, territories enriched for ancestral repeats tended to be contiguous domains. To determine if the latter territories were evolutionarily conserved, we compared these results with a similar analysis of the human genome, and observed similar ancestral repeat enriched domains. These results indicate that ancestral, evolutionarily conserved mammalian genome territories can be identified on the basis of repeat content alone. Interspersed repeats of different ages appear to be analogous to geologic strata, allowing identification of ancient vs. newly remodelled regions of mammalian genomes.
Pleiotropic effects of pigmentation genes in horses
Authors: Bellone R. R. 
Published: November 2010

SummaryHorses are valued for the beauty and variety of colouration and coat patterning. To date, eleven different genes have been characterized that contribute to the variation observed in the horse. Unfortunately, mutations involving pigmentation often lead to deleterious effects in other systems, some of which have been described in the horse. This review focuses on six such pleiotropic effects or associations with pigmentation genes. These include neurological defects (lethal white foal syndrome and lavender foal syndrome), hearing defects, eye disorders (congenital stationary night blindness and multiple congenital ocular anomalies), as well as horse‐specific melanoma. The pigmentation phenotype, disorder phenotype, mode of inheritance, genetic or genomic methods utilized to identify the genes involved and, if known, the causative mutations, molecular interactions and other susceptibility loci are discussed. As our understanding of pigmentation in the horse increases, through the use of novel genomic tools, we are likely to unravel yet unknown pleiotropic effects and determine additional interactions between previously discovered loci.