bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impacts and lessons from BSE episodes.
Authors: Roy D. G. le , Klein K. K. 
Published: February 2009

Abstract
This review provides an overview of consumer and government responses to bovine serum encephalopathy (BSE) and draws lessons for industry stakeholders. The approaches taken around the world to contain the risk of BSE where it was discovered reveal important patterns, differences and difficulties. Important lessons are drawn in three areas: (1) the paramount position of consumers of beef with respect to production, processing and regulatory activities; (2) the importance of clearly communicating relative risks of infection to the public; and (3) the critical role of improved international trade rules to mitigate financial impacts of animal disease outbreaks.
Legal, policy and institutional aspects of urban and peri-urban forestry and greening: the case of West and Central Asia.
Authors: Knuth L. , Randrup T. B. , Gauthier M. 
Published: February 2009

Abstract
Owing to increased global urbanization, Food and Agriculture Organization of the United Nations (FAO) initiated a study on the relationship between the urban green resource, with a primary focus on urban and peri-urban forests and greening (UPFG), and urban livelihood and poverty alleviation in West and Central Asia (WECA). The present study is based primarily on a comprehensive review of scientific literature and legal, policy and institutional documents found via the Internet. Policies at national and sub-national levels related to UPFG focus mainly on environmental aspects. The present study found no policies promoting UPFG as a source of income for the livelihood of the urban and peri-urban poor. However, UPFG in the context of poverty alleviation might be addressed by related policies, such as forestry policies. Further, this study found that no particular national or international law governs UPFG; however, most countries of the WECA region are parties to the international conventions related to UPFG. It is concluded that UPFG is not comprehensively addressed at a country level but various laws exist that address UPFG in a fragmentary way. This may be because of the lack of awareness of UPFG as a multisectoral, multifaceted discipline. It is important to pursue the objective to turn degraded elements of urban green resources into environments that can be put to productive use by poor families, thereby offering them income opportunities and/or food for household use. Decentralization is becoming increasingly important in the WECA region. In this context, responsibilities related to UPFG tend to shift to lower government levels. The effect of decentralization policies will also lead to greater involvement of local community groups, municipalities and grass-root organizations in the various aspects of UPFG development and management. However, this requires capacity building and awareness-raising campaigns and sufficient financial resources.
A review of synbiotic supplements on faecal immunoglobulin A in bovine neonates.
Authors: Terrill S. J. , Heinrichs A. J. , Long M. R. 
Published: February 2009

Abstract
Antibiotics have been used with excellent results for over 50 years in livestock industries. The numerous benefits associated with antibiotic treatment have led to widespread subtherapeutic use in raising dairy calves. In recent years, interest in antibiotic alternatives has grown as concerns about antibiotic resistance in animals and humans have been publicized. One alternative is supplementation of calf diets with prebiotics, probiotics or some combination of the two (known as synbiotics). The major benefit of treatment with these products is increased proliferation and growth of healthy gut bacteria. The presence of a healthy intestinal microflora has been shown to benefit the whole body, including increased weight gain, decreased presence of pathogens and enhanced immune function. Although limited research has been done in calves, work with other species has shown that addition of these products to an animal's diet can improve mucosal immune system function, increasing levels of immunoglobulin A (IgA), both in the serum and intestinal mucosa. As the antibody secreted by mucosal surfaces, IgA is considered the first line of defence against infections entering the body. Multiple explanations exist for the mechanism of how probiotic bacteria (and, in turn, prebiotic supplements) increase IgA secretion. It has been proposed that bacterial cell components such as peptidoglycan, cytoplasmic contents and techoic acids may elicit this immune reaction. As more research focuses on mechanisms, and not simply results, of pre-, pro- and synbiotic supplementation, products will be able to be fine-tuned to enhance their function and improve results when fed to calves.
Characteristics of integrated 18F-FDG PET/CT in pulmonary cryptococcosis
Authors: Huang Chung-Jen , You Dong-Ling , Lee Pei-Ing , Hsu Li-Han , Liu Chia-Chuan , Shih Chih-Shiun , Shih Chiang-Ching , Tseng Hsiu-Chin 
Published: February 2009

Background: Pulmonary cryptococcosis is an uncommon cause of pulmonary nodules found by 18F-fluorodeoxyglucose positron emission tomography/computed tomography (18F-FDG PET/CT) scans. It is rarely reported but may mislead interpretation. Purpose: To describe the 18F-FDG PET/CT findings of pulmonary cryptococcosis. Material and Methods: The 18F-FDG PET/CT images of seven patients with pulmonary cryptococcosis were evaluated. Results: The 18F-FDG PET/CT exams showed single or multiple nodular lesions. The standardized uptake values (SUV) in early images varied significantly for the seven patients (ranging from 2.2 to 11.6). Delayed SUVs showed significant increases in four patients. Conclusion: Pulmonary cryptococcosis mimics primary or metastatic lung cancer on 18F-FDG PET/CT scan. Tissue confirmation should be considered for any suspicious pulmonary nodules found on 18F-FDG PET/CT scan with an SUV score higher than 2.5, in order to avoid overdiagnosis or overstaging.
Development of a Flexible, Computerized Database to Prioritize, Record, and Report Influenza Vaccination Rates for Healthcare Personnel
Authors: Melia Michael , O'Neill Sarah , Calderon Sherry , Hewitt Sandra , Orlando Kelly , Bithell-Taylor Karen , Affeln Dieter , Conti Carolyn , Wright Sharon B. 
Published: February 2009

Objective.To describe the method used to develop a flexible, computerized database for recording and reporting rates of influenza vaccination among healthcare personnel who were classified by their individual levels (hereafter, “tiers”) of direct patient contact.Design.Three-year descriptive summary.Setting.Large, academic, tertiary care medical center in the United States.Participants.All of the medical center's healthcare personnel.Methods.The need to develop a computer-based system to record direct patient care tiers and vaccination data for healthcare personnel was identified. A plan that was to be implemented in stages over several seasons was developed.Results.Direct patient care tiers were defined by consensus opinion on the basis of the extent, frequency, and intensity of direct contact with patients. The definitions of these tiers evolved over 3 seasons. Direct patient care classifications were assigned and recorded in a computerized database, and data regarding the receipt of vaccination were tracked by using the same database. Data were extracted to generate reports of individual, departmental, and institutional vaccination rates, both overall and according to direct patient care tiers.Conclusions.Development of a computerized database to record direct patient care tiers for individual healthcare workers is a daunting but manageable task. Widespread use of these direct patient care definitions will facilitate uniform comparisons of vaccination rates between institutions. This computerized database can easily be used by infection control personnel to accomplish several other key tasks, including vaccination triage in the context of shortage or delay, prioritization of personnel to receive interventions in times of crisis, and monitoring the status of other employee health or occupational health measures.
BISEN: Biochemical Simulation Environment
Authors: Vanlier J. , Wu F. , Qi F. , Vinnakota K. C. , Han Y. , Dash R. K. , Yang F. , Beard D. A. 
Published: February 2009

Abstract
Summary: The Biochemical Simulation Environment (BISEN) is a suite of tools for generating equations and associated computer programs for simulating biochemical systems in the MATLAB® computing environment. This is the first package that can generate appropriate systems of differential equations for user-specified multi-compartment systems of enzymes and transporters accounting for detailed biochemical thermodynamics, rapid equilibria of multiple biochemical species and dynamic proton and metal ion buffering.
Availability: The software and a user manual (including several tutorial examples) are available at bbc.mcw.edu/BISEN.
Contact: dbeard@mcw.edu
PLATINUM: a web tool for analysis of hydrophobic/hydrophilic organization of biomolecular complexes
Authors: Pyrkov Timothy V. , Chugunov Anton O. , Krylov Nikolay A. , Nolde Dmitry E. , Efremov Roman G. 
Published: February 2009

AbstractSummary: The PLATINUM (Protein–Ligand ATtractions Investigation NUMerically) web service is designed for analysis and visualization of hydrophobic/hydrophilic properties of biomolecules supplied as 3D-structures. Furthermore, PLATINUM provides a number of tools for quantitative characterization of the hydrophobic/hydrophilic match in biomolecular complexes e.g. in docking poses. These complement standard scoring functions. The calculations are based on the concept of empirical Molecular Hydrophobicity Potential (MHP).Availability: The PLATINUM web tool as well as detailed documentation and tutorial are available free of charge for academic users at http://model.nmr.ru/platinum/. PLATINUM requires Java 5 or higher and Adobe Flash Player 9.Contact: pyrkov@nmr.ruSupplementary information: Supplementary data are available at Bioinformatics online.
Statistical inferences for isoform expression in RNA-Seq
Authors: Jiang Hui , Wong Wing Hung 
Published: February 2009

Abstract
Summary: The development of RNA sequencing (RNA-Seq) makes it possible for us to measure transcription at an unprecedented precision and throughput. However, challenges remain in understanding the source and distribution of the reads, modeling the transcript abundance and developing efficient computational methods. In this article, we develop a method to deal with the isoform expression estimation problem. The count of reads falling into a locus on the genome annotated with multiple isoforms is modeled as a Poisson variable. The expression of each individual isoform is estimated by solving a convex optimization problem and statistical inferences about the parameters are obtained from the posterior distribution by importance sampling. Our results show that isoform expression inference in RNA-Seq is possible by employing appropriate statistical methods.
Contact: whwong@stanford.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Computer Simulation of the Dynamic Behavior of the Glutathione-Ascorbate Redox Cycle in Chloroplasts
Authors: Valero Edelmira , González-Sánchez María I. , Maciá Hermenegilda , García-Carmona Francisco 
Published: February 2009

AbstractThe glutathione-ascorbate redox pathway in chloroplasts is a complex network of spontaneous, photochemical, and enzymatic reactions for detoxifying hydrogen peroxide. This article presents a comprehensive sensitivity analysis of the system. A model has been constructed to simulate oxidative stress conditions, enabling steady-state concentrations of the metabolites involved in the pathway and photochemical and enzymatic fluxes to be calculated. The model includes an electron source whose flux is distributed among three competitive routes (photogeneration of \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathrm{O}_{2}^{{-}}\) \end{document}, photoreduction of NADP+ to NADPH, and photoreduction of monodehydroascorbate to ascorbate) and that allows the simulation of variations in NADPH concentration with time. Each enzyme considered is introduced in the model, taking into account its particular catalytic mechanism, including the inactivation of ascorbate peroxidase in the presence of low-ascorbate concentrations. Computer simulations pointed to the great sensitivity of the system to the ratio among fluxes corresponding to ascorbate and NADPH photoproduction and NADPH consumption by the Calvin cycle. Under oxidative stress conditions, the model shows a sequential depletion of antioxidant power in chloroplasts in the order NADPH, glutathione, ascorbate and their recovery in the reverse order. Decreasing levels of glutathione reductase, ascorbate peroxidase, and superoxide dismutase led to the irreversible photoinactivation of ascorbate peroxidase and the subsequent increase in hydrogen peroxide concentration, preceded by a maximum in dehydroascorbate reductase activity.
Preferential Up-Regulation of G2/M Phase-Specific Genes by Overexpression of the Hyperactive Form of NtmybA2 Lacking Its Negative Regulation Domain in Tobacco BY-2 Cells
Authors: Kato Kiichi , Gális Ivan , Suzuki Shiori , Araki Satoshi , Demura Taku , Criqui Marie-Claire , Potuschak Thomas , Genschik Pascal , Fukuda Hiroo , Matsuoka Ken , Ito Masaki 
Published: February 2009

Abstract
Many G2/M phase-specific genes in plants contain mitosis-specific activator (MSA) elements, which act as G2/M phase-specific enhancers and bind with R1R2R3-Myb transcription factors. Here, we examined the genome-wide effects of NtmybA2 overexpression, one of the R1R2R3-Myb transcription factors in tobacco (Nicotiana tabacum). We used a custom-made 16-K cDNA microarray for comparative transcriptome analysis of transgenic tobacco BY-2 cell lines that overexpress NtmybA2 or its truncated hyperactive form. The microarray was also used to determine the transcript profile during the cell cycle in synchronized cultures of BY-2 cells. Combined microarray data from transgenic lines and synchronized cells revealed that overexpression of the truncated hyperactive form of NtmybA2, but not its full-length form, preferentially up-regulated many G2/M phase-specific genes in BY-2 cells. We determined promoter sequences of several such up-regulated genes and showed that all contain MSA-like motifs in the proximal regions of their promoters. One of the up-regulated genes, NtE2C, encoding for cyclin-specific ubiquitin carrier proteins, contained a single functional MSA-like motif, which specifically controlled the expression of a reporter gene in the G2/M phase in BY-2 cells. Furthermore, a genomic footprint experiment showed that the MSA element in the NtE2C promoter interacted with nuclear proteins in vivo. Therefore, we propose that the transcription of many G2/M phase-specific genes in tobacco is positively regulated by NtmybA2, in most cases through direct binding to the MSA elements.
Isoflavone, polymorphisms in estrogen receptor genes and breast cancer risk in case‐control studies in Japanese, Japanese Brazilians and non‐Japanese Brazilians
Authors: Iwasaki Motoki , Hamada Gerson Shigeaki , Nishimoto Inês Nobuko , Netto Mario Mourão , Motola Jr Juvenal , Laginha Fábio Martins , Kasuga Yoshio , Yokoyama Shiro , Onuma Hiroshi , Nishimura Hideki , Kusama Ritsu , Kobayashi Minatsu , Ishihara Junko , Yamamoto Seiichiro , Hanaoka Tomoyuki , Tsugane Shoichiro 
Published: February 2009

Epidemiologic studies have shown an inverse association between isoflavones and breast cancer risk. Because isoflavones bind estrogen receptors, we hypothesized that polymorphisms in the estrogen receptor genes might modify the association between isoflavone intake and breast cancer risk. We conducted hospital‐based case‐control studies of patients aged 20–74 years with primary, incident, histologically confirmed invasive breast cancer, and matched controls from among medical checkup examinees in Nagano, Japan, and from cancer‐free patients in São Paulo, Brazil. A total of 846 pairs (388 Japanese, 79 Japanese Brazilians and 379 non‐Japanese Brazilians) completed validated food frequency questionnaires, and provided blood samples. Five single nucleotide polymorphisms in the estrogen receptor alpha (rs9340799, rs1913474, and rs2234693) and beta (rs4986938 and rs1256049) genes were genotyped. We found no consistent association between the five single nucleotide polymorphisms and breast cancer risk among the three populations. In analyses of combinations of isoflavone intake and single nucleotide polymorphisms, an inverse association between intake and risk was limited to women with the GG genotype of the rs4986938 polymorphism for postmenopausal Japanese (odds ratio for highest versus lowest tertile = 0.47; P for trend = 0.01), Japanese Brazilians (odds ratio for highest versus lowest median = 0.31) and non‐Japanese Brazilians (odds ratio for consumers versus non‐consumers = 0.37) (P for interaction = 0.11, 0.08, and 0.21, respectively). We found no remarkable difference for the other four polymorphisms. Our findings suggest that polymorphisms in the estrogen receptor beta gene may modify the association between isoflavone intake and breast cancer risk. (Cancer Sci 2009; 100: 927–933)
Comparing patients' and healthcare professionals' ADR reports after media attention: the broadcast of a Dutch television programme about the benefits and risks of statins as an example
Authors: Van Hunsel Florence , Passier Anneke , Van Grootheest Kees 
Published: February 2009

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT• More and more countries accept patient reporting in their spontaneous reporting systems.• Media exposure about drugs can influence patients and health professionals.• Evaluation of patient reporting of adverse drug reactions is needed to provide further evidence of its benefits.WHAT THIS STUDY ADDS• Patient reporting compared with reporting by health professionals after media attention about statins.• Patient reports provide additional insight into impact on daily life, the patient–health professional relationship and general worries next to health professionals' reports.AIMSTo compare adverse drug reaction (ADR) reports from patients and health professionals after the broadcast of a Dutch television consumer programme about the benefits and risks of statins.METHODSWe performed a quantitative and qualitative analysis on patients' and health professionals' reports of ADRs to statins. These reports were received by the Netherlands Pharmacovigilance Centre Lareb between March 2007 and August 2007. Quantitative data consisted of patient age and gender, number of received reports and characteristics of the report (most frequently reported ADRs, seriousness, drug discontinuation and outcome of the reported reaction). Open text fields in the ADR reporting form were categorized and a content analysis was carried out.RESULTSMedia attention led to a peak in patient reporting of ADRs but not in reporting by health professionals. There were no differences between patient and health professional reports in seriousness of the ADRs and drug cessation. Patients reported nonrecovery more often than health professionals. The TV programme is mentioned as a reason for drug discontinuation in almost 30 reports. Patients often felt that they did not receive sufficient information and that their concerns were not adequately addressed by healthcare professionals.CONCLUSIONSMedia attention affects drug use and ADR reporting by patients. Patient reports can provide additional information, making them a useful source of information next to health professional reports. Content analysis provides vital insights into the impact of statins on daily life, and patients' concerns about adverse reactions should be recognized in reports to national pharmacovigilance centres.
Insulin resistance as a predictor of incident asthma‐like symptoms in adults
Authors: Thuesen B. H. , Husemoen L. L. N. , Hersoug L.‐G. , Pisinger C. , Linneberg A. 
Published: February 2009

SummaryBackground
There is accumulating evidence that obesity is associated with an increased risk of asthma. It has been hypothesized that insulin resistance may be involved in obesity‐induced asthma, but till date there is no prospective data on this issue.Objective
To investigate the association of obesity and insulin resistance with the incidence of asthma‐like symptoms in adults.Methods
Out of a random sample of 12 934 persons from a general population, 6784 (52.5%) were included and participated in a health examination in 1999–2001. After 5 years they were re‐invited and 4516 (66.6%) participated at follow‐up. At baseline three obesity measures were considered: body mass index, waist circumference, and waist‐to‐hip ratio. In addition, fasting glucose and insulin were measured for determination of insulin resistance. Information on asthma‐like symptoms at baseline and follow‐up were obtained by questionnaires. A total of 3441 participants defined as non‐asthmatic at baseline and with complete information on all the considered variables were included in the analyses. Data were controlled for confounding by sex, age, social status, and smoking.Results
All obesity measures were associated with incident wheezing and asthma‐like symptoms. In addition, insulin resistance was associated with incident wheezing [odds ratio (OR) 1.87, 95% confidence interval (CI) 1.38–2.54] and asthma‐like symptoms (OR 1.61, 95% CI 1.23–2.10). The effect of insulin resistance was stronger than that of obesity and was independent of sex.Conclusion
We found that insulin resistance was associated with an increased risk of developing asthma‐like symptoms. This finding supports the hypothesis that obesity and asthma may be linked through inflammatory pathways also involved in insulin resistance.
Effects of livestock breed and grazing pressure on ground‐dwelling arthropods in Cantabrian heathlands
Authors: GARCÍA ROCÍO ROSA , JÁUREGUI BERTA M. , GARCÍA URCESINO , OSORO KOLDO , CELAYA RAFAEL 
Published: February 2009

Abstract1. The effects of different goat breeds and grazing pressures on epigeal arachnids (Lycosidae and Opiliones) and ground beetles (Carabidae) were assessed in a heath–gorse shrubland located in the north of the Iberian Peninsula. Three treatments (low grazing pressure with Cashmere breed, high grazing pressure with Cashmere breed, and high grazing pressure with local Celtiberic breed) with three replicates of each treatment were allocated randomly to nine plots.2. Arthropod fauna abundance, diversity, and species richness were estimated using pitfall trapping over 3 years (2003, 2004, and 2005). Vegetation cover, composition, and height were assessed along transects and above‐ground plant biomass was sampled in quadrats.3. Lower grazing pressure led to lower herbaceous cover and higher heather cover than high grazing pressure. Overall, it did not enhance arthropod diversity or abundance, but the abundance and species richness of carabids, and abundance of lycosids likePardosa pullata, were higher under high stocking rates, whereas Opiliones were favoured by the low stocking rates. Although it has been assumed that traditional breeds enhance biodiversity, the present study found no significant differences for both arthropod fauna and vegetation between the goat breeds.4. Arthropod–vegetation relationships were examined by constrained ordination. Fauna assemblages followed a gradient from closed canopy shrubland areas, in the lowest grazing pressure, to grassier open canopy areas resulting from higher grazing pressure, revealing the importance of grazing management as a driver of arthropod community structure of the heathland.