Analysis of Affymetrix GeneChip Data Using Amplified RNA

The standard method of target synthesis for hybridization to Affymetrix GeneChip® expression microarrays requires a relatively large amount of input total RNA (1-15 micrograms). When small biological samples are collected by microdissection or other methods, amplification techniques are required to provide sufficient target for hybridization to expression arrays. One amplification technique used is to perform two successive rounds of T7-based in vitro transcription. However, the use of random primers required to re-generate cDNA from the first round transcription reaction results in shortened copies of the cDNA, and ultimately the cRNA, transcripts from which the 5\u27 end is missing. In this paper we describe an experiment designed to compare the quality of data obtained from labeling small RNA samples using the Affymetrix Small Sample Target Labeling Protocol V 2 to that of data obtained using the standard protocol. We utilized different preprocessing algorithms to compare the data generated using both labeling methods and present a new algorithm that improves upon existing ones in this setting

Prevalence of Psychosocial Risk Factors in Selected Industries in Latvia

Publisher Copyright: © 2016 Lasma Kozlova et al., published by De Gruyter Open 2016.The hypothesis of the study was that psychosocial risk factors are more common in industries involving intellectual work, such as education and public administration (Group 1), rather than in industries like construction, agriculture, and forestry where physical work is more common (Group 2). This hypothesis was confirmed and the important findings were that the most common psychosocial risk factors in Group 1 were staff conflicts, conflicts with managers and clients, also lack of time and having to communicate with clients during the working day. Violence, especially physical and psychological violence was a common risk factor in Group 1; mostly the client caused the violence. In Group 2 the most common psychosocial risk factors were overtime work, conflicts with managers, lack of time and having to communicate with clients during the working day. Overtime work was the most common risk factor in construction, agriculture, and forestry industries.publishersversionPeer reviewe

Impact of the Phytoestrogen Content of Laboratory Animal Feed on the Gene Expression Profile of the Reproductive System in the Immature Female Rat

The effect of the dietary background of phytoestrogens on the outcome of rodent bioassays used to identify and assess the reproductive hazard of endocrine-disrupting chemicals is controversial. Phytoestrogens, including genistein, daidzein, and coumestrol, are fairly abundant in soybeans and alfalfa, common ingredients of laboratory animal diets. These compounds are weak agonists for the estrogen receptor (ER) and, when administered at sufficient doses, elicit an estrogenic response in vivo. In this study, we assessed the potential estrogenic effects of dietary phytoestrogens at the gene expression level, together with traditional biologic end points, using estrogen-responsive tissues of the immature female rat. We compared the gene expression profile of the uterus and ovaries, as a pool, obtained using a uterotrophic assay protocol, from intact prepubertal rats fed a casein-based diet (free from soy and alfalfa) or a regular rodent diet (Purina 5001) containing soy and alfalfa. Estrogenic potency of the phytoestrogen-containing diet was determined by analyzing uterine wet weight gain, luminal epithelial cell height, and gene expression profile in the uterus and ovaries. These were compared with the same parameters evaluated in animals exposed to a low dose of a potent ER agonist [0.1 μg/kg/day 17α-ethynyl estradiol (EE) for 4 days]. Exposure to dietary phytoestrogens or to a low dose of EE did not advance vaginal opening, increase uterine wet weight, or increase luminal epithelial cell height in animals fed either diet. Although there are genes whose expression differs in animals fed the soy/alfalfa-based diet versus the casein diet, those genes are not associated with estrogenic stimulation. The expression of genes well known to be estrogen regulated, such as progesterone receptor, intestinal calcium-binding protein, and complement component 3, is not affected by consumption of the soy/alfalfa-based diet when assessed by microarray or quantitative reverse transcriptase–polymerase chain reaction analysis. Our results indicate that although diet composition has an impact on gene expression in uterus and ovaries, it does not contribute to the effects of an ER agonist

Design of a Microsphere-Based High-Throughput Gene Expression Assay to Determine Estrogenic Potential

Recently gene expression studies have been multiplied at an accelerated rate by the use of high-density microarrays. By assaying thousands of transcripts at a time, microarrays have led to the discovery of dozens of genes involved in particular biochemical processes, for example, the response of a tissue/organ to a given chemical with therapeutic or toxic properties. The next step in these studies is to focus on the response of a subset of relevant genes to verify or refine potential therapeutic or toxic properties. We have developed a sensitive, high-throughput gene expression assay for this purpose. In this assay, based on the Luminex xMAP system, carefully selected oligonucleotides were covalently linked to fluorescently coded microspheres that are hybridized to biotinylated cRNA followed by amplification of the signal, which results in a rapid, sensitive, multiplexed assay platform. Using this system, we have developed an RNA expression profiling assay specific for 17 estrogen-responsive transcripts and three controls. This assay can evaluate up to 100 distinct analytes simultaneously in a single sample, in a 96-well plate format. This system has improved sensitivity versus existing microsphere-based assays and has sensitivity and precision comparable with or better than microarray technology. We have achieved detection levels down to 1 amol, detecting rare messages in complex cRNA samples, using as little as 2.5 μg starting cRNA. This assay offers increased throughput with decreased costs compared with existing microarray technologies, with the trade-off being in the total number of transcripts that can be analyzed

Population based estimates of non-fatal injuries in the capital of Iran

<p>Abstract</p> <p>Background</p> <p>Fatal injuries are at the top of the injury pyramid; however, non-fatal injuries are quite common and impose huge medical expenses on the population. Relying on hospital data will underestimate the incidence of non-fatal injuries. The aim of this study was to estimate the annual incidence and out of pocket medical expenses of all injuries in urban population of Tehran (the capital city of Iran).</p> <p>Methods</p> <p>Using the cluster random sampling approach, a household survey of residents of greater Tehran was performed on April 2008. At randomly selected residential locations, interviewers asked one adult person to report all injuries which have occurred during the past year for all household members, as well as the type of injury, place of occurrence, the activity, cause of accidents resulting in injuries, the amount of out of pocket medical expenses for injury, and whether they referred to hospital.</p> <p>Results</p> <p>This study included 2,450 households residing in Tehran during 2007-8. The annual incidence of all injuries was 188.7 (180.7-196.9), significant injuries needing any medical care was 68.8 (63.7-74.2), fractures was 19.3 (16.6 - 22.4), and injuries resulted in hospitalization was 16.7 (14.2 - 19.6) per 1000 population. The annual incidence of fatal injuries was 33 (7-96) per 100,000 Population. In children aged 15 or less, the annual incidence of all injuries was 137.2 (120.0 - 155.9), significant injuries needing any medical care was 64.2 (52.2 - 78.0), fractures was 21.8 (15.0 - 30.7), and injuries resulted in hospitalization was 6.8 (3.3 - 12.5) per 1000 population. The mean out of pocket medical expense for injuries was 19.9 USD.</p> <p>Conclusion</p> <p>This population based study showed that the real incidence of non-fatal injuries in the capital of Iran is more than the formal hospital-based estimates. These injuries impose non trivial medical and indirect cost on the community. The out of pocket medical expense of non-fatal injuries to Tehran population is estimated as 27 million USD per year. Effective strategies should be considered to minimize these injuries and decrease the great financial burden to public and the health system.</p

The role of trade unions in supporting victims of domestic violence in the workplace

This article explores the effects that domestic violence has on victims in their workplace and how trade unions respond. Focussing on the experiences of union representatives, the research highlights the support offered to victims, the barriers representatives face and the under-acknowledged personal impact that these cases can have upon representatives

Injury in China: a systematic review of injury surveillance studies conducted in Chinese hospital emergency departments

<p>Abstract</p> <p>Background</p> <p>Injuries represent a significant and growing public health concern in China. This <it>Review </it>was conducted to document the characteristics of injured patients presenting to the emergency department of Chinese hospitals and to assess of the nature of information collected and reported in published surveillance studies.</p> <p>Methods</p> <p>A systematic search of MEDLINE and China Academic Journals supplemented with a hand search of journals was performed. Studies published in the period 1997 to 2007 were included and research published in Chinese was the focus. Search terms included emergency, injury, medical care.</p> <p>Results</p> <p>Of the 268 studies identified, 13 were injury surveillance studies set in the emergency department. Nine were collaborative studies of which eight were prospective studies. Of the five single centre studies only one was of a prospective design. Transport, falls and industrial injuries were common mechanisms of injury. Study strengths were large patient sample sizes and for the collaborative studies a large number of participating hospitals. There was however limited use of internationally recognised injury classification and severity coding indices.</p> <p>Conclusion</p> <p>Despite the limited number of studies identified, the scope of each highlights the willingness and the capacity to conduct surveillance studies in the emergency department. This <it>Review </it>highlights the need for the adoption of standardized injury coding indices in the collection and reporting of patient health data. While high level injury surveillance systems focus on population-based priority setting, this <it>Review </it>demonstrates the need to establish an internationally comparable trauma registry that would permit monitoring of the trauma system and would by extension facilitate the optimal care of the injured patient through the development of informed quality assurance programs and the implementation of evidence-based health policy.</p

Targeted Therapies in Liver Fibrosis:Combining the Best Parts of Platelet-Derived Growth Factor BB and Interferon Gamma

Cytokines, growth factors and other locally produced mediators play key roles in the regulation of disease progression. During liver fibrosis, these mediators orchestrate the balance between pro- and antifibrotic activities as exerted by the hepatic cells. Two important players in this respect are the profibrotic mediator platelet derived growth factor BB (PDGF-BB) and the antifibrotic cytokine interferon gamma (IFNγ). PDGF-BB, produced by many resident and infiltrating cells, causes extensive proliferation, migration and contraction of hepatic stellate cells (HSCs) and myofibroblasts. These cells are the extracellular matrix producing hepatic cells and they highly express the PDGFβ-receptor. On the other hand, IFNγ is produced by natural killer cells in fibrotic livers and is endowed with pro-inflammatory, antiviral and antifibrotic activities. This cytokine attracted much attention as a possible therapeutic compound in fibrosis. However, clinical trials yielded disappointing results because of low efficacy and adverse effects, most likely related to the dual role of IFNγ in fibrosis. In our studies, we targeted the antifibrotic IFNγ to the liver myofibroblasts. For that, we altered the cell binding properties of IFNγ, by delivery of the IFNγ-nuclear localization sequence to the highly expressed PDGFβ-receptor using a PDGFβ-receptor recognizing peptide, thereby creating a construct referred to as Fibroferon (i.e. fibroblast-targeted interferon γ). In recent years, we demonstrated that HSC-specific delivery of IFNγ increased its antifibrotic potency and improved its general safety profile in vivo, making Fibroferon highly suitable for the treatment of (fibrotic) diseases associated with elevated PDGFβ-receptor expression. The present review summarizes the knowledge on these two key mediators, PDGF-BB and IFNγ, and outlines how we used this knowledge to create the cell-specific antifibrotic compound Fibroferon containing parts of both of these mediators