MIMAS 3.0 is a Multiomics Information Management and Annotation System.

BACKGROUND: DNA sequence integrity, mRNA concentrations and protein-DNA interactions have been subject to genome-wide analyses based on microarrays with ever increasing efficiency and reliability over the past fifteen years. However, very recently novel technologies for Ultra High-Throughput DNA Sequencing (UHTS) have been harnessed to study these phenomena with unprecedented precision. As a consequence, the extensive bioinformatics environment available for array data management, analysis, interpretation and publication must be extended to include these novel sequencing data types. DESCRIPTION: MIMAS was originally conceived as a simple, convenient and local Microarray Information Management and Annotation System focused on GeneChips for expression profiling studies. MIMAS 3.0 enables users to manage data from high-density oligonucleotide SNP Chips, expression arrays (both 3'UTR and tiling) and promoter arrays, BeadArrays as well as UHTS data using MIAME-compliant standardized vocabulary. Importantly, researchers can export data in MAGE-TAB format and upload them to the EBI's ArrayExpress certified data repository using a one-step procedure. CONCLUSION: We have vastly extended the capability of the system such that it processes the data output of six types of GeneChips (Affymetrix), two different BeadArrays for mRNA and miRNA (Illumina) and the Genome Analyzer (a popular Ultra-High Throughput DNA Sequencer, Illumina), without compromising on its flexibility and user-friendliness. MIMAS, appropriately renamed into Multiomics Information Management and Annotation System, is currently used by scientists working in approximately 50 academic laboratories and genomics platforms in Switzerland and France. MIMAS 3.0 is freely available via http://multiomics.sourceforge.net/.

Comparison between precipitin and ELISA tests in the bloodmeal detection of Aedes aegypti (Linnaeus) and Aedes fluviatilis (Lutz) mosquitoes experimentally fed on feline, canine and human hosts

The identification of arthropod bloodmeals is important in many epidemiological studies, as, the understanding of the life cycle of vectors and the patogens they transmit, as well as helping to define arthropods' control strategies. The precipitin test has been used for decades, but ELISA is slowly becoming more popular. To compare the two tests for sensitivity, specificity and accuracy to detect small insect bloodmeals, Aedes aegypti or Ae. fluviatilis mosquitoes were fed either on feline, canine or human hosts. Mosquitoes were frozen at 6, 12, 24, 48 or 72 h after feeding. Precipitin test showed better specificity and accuracy and ELISA test showed higher sensitivity. Better results with both tests were achieved when mosquitoes were frozen within 48 h from feeding.

Isolation of Leishmania infantum, zymodeme MON-1 from canine and human visceral leishmaniasis on Margarita Island, Venezuela

An increase in the incidence of human visceral leishmaniasis (HVL) has been detected in recent years on Margarita Island, located off the NE coast of Venezuela. Recent studies have revealed reactivity to rK39 antigen (Leishmania chagasi) in 20% of 541 sera from domestic dogs in endemic communities; PCR reactions were positive using primers for the L. donovani complex. Here we report that isolates from human and canine infection, identified by isoenzyme analysis, correspond to L. infantum, zymodeme MON-1. This appears to be the first isolation and identification of an isolate from HVL on Margarita Island and demonstrates the presence of this zymodeme in the canine population.

CFPP 01-01 Management And Decontamination Of Surgical Instruments(PDF 848KB)

Part D:Washer-disinfectors

CFPP 01-01 Management And Decontamination Of Surgical Instruments(PDF 234KB)

Part E:Alternatives to steam for the sterilization of reusable medical devices

The Nursing and Midwifery Resource - Towards Workforce Planning

The Nursing and Midwifery Resource – Towards Workforce Planning The past five years have seen a dramatic change in the composition and organisation of the nursing and midwifery workforce in Ireland. For many years we had a constant supply of newly qualified nurses and midwives, with strong competition for every available post. Click here to download PDF 1.5mb

The Nursing and Midwifery Resource - Interim Report of the Steering Group

This project arises from the need for an enhanced focus on workforce planning having regard, in particular, to the availability of sufficient nurses now and in the future. For a country which historically has had an abundance of nurses, the recruitment difficulties now being experienced by the health services are unprecedented. Up to the mid 1990s, there was a surplus of registered nurses here and other countries sent recruitment teams to Ireland in order to address their own shortages. As will be seen in this report, the concern of the professional interest groups at the time was the high levels of unemployment among nurses. The conventional wisdom was that the health services were training too many nurses for the jobs available. However, there has been a sea change in the situation over the past five years and the stage has now been reached where Irish health care agencies, particularly the major acute Dublin hospitals, are actively seeking to recruit nurses from abroad. Download the Report here

Mutations in Eml1 lead to ectopic progenitors and neuronal heterotopia in mouse and human.

Neuronal migration disorders such as lissencephaly and subcortical band heterotopia are associated with epilepsy and intellectual disability. DCX, PAFAH1B1 and TUBA1A are mutated in these disorders; however, corresponding mouse mutants do not show heterotopic neurons in the neocortex. In contrast, spontaneously arisen HeCo mice display this phenotype, and our study revealed that misplaced apical progenitors contribute to heterotopia formation. While HeCo neurons migrated at the same speed as wild type, abnormally distributed dividing progenitors were found throughout the cortical wall from embryonic day 13. We identified Eml1, encoding a microtubule-associated protein, as the gene mutated in HeCo mice. Full-length transcripts were lacking as a result of a retrotransposon insertion in an intron. Eml1 knockdown mimicked the HeCo progenitor phenotype and reexpression rescued it. We further found EML1 to be mutated in ribbon-like heterotopia in humans. Our data link abnormal spindle orientations, ectopic progenitors and severe heterotopia in mouse and human.

Analyse de la prise en charge médicale et de l'impact économique des patients ayant présentés des coûts extrêmes dans un hôpital universitaire [Analysis of the medical management and the economic impact of patients who have represented extreme costs at a university hospital]

Les coûts de traitement de certains patients s'avèrent extrêmement élevés, et peuvent faire soupçonner une prise en charge médicale inadéquate. Comme I'évolution du remboursement des prestations hospitalières passe à des forfaits par pathologie, il est essentiel de vérifier ce point, d'essayer de déterminer si ce type de patients peut être identifié à leur admission, et de s'assurer que leur devenir soit acceptable. Pour les années 1995 et 1997. les coûts de traitement dépassant de 6 déviations standard le coût moyen de la catégorie diagnostique APDRG ont été identifiés, et les dossiers des 50 patients dont les coûts variables étaient les plus élevés ont été analysés. Le nombre total de patients dont I'hospitalisation a entraîné des coûts extrêmes a passé de 391 en 1995 à 328 patients en 1997 (-16%). En ce qui concerne les 50 patients ayant entraîné les prises en charge les plus chères de manière absolue, les longs séjours dans de multiples services sont fréquents, mais 90% des patients sont sortis de l'hôpital en vie, et près de la moitié directement à domicile. Ils présentaient une variabilité importante de diagnostics et d'interventions, mais pas d'évidence de prise en charge inadéquate. En conclusion, les patients qualifiés de cas extrêmes sur un plan économique, ne le sont pas sur un plan strictement médical, et leur devenir est bon. Face à la pression qu'exercera le passage à un mode de financement par pathologie, les hôpitaux doivent mettre au point un système de revue interne de I'adéquation des prestations fournies basées sur des caractéristiques cliniques, s'ils veulent garantir des soins de qualité. et identifier les éventuelles prestations sous-optimales qu'ils pourraient être amenés à délivrer. [Auteurs] Treatment costs for some patients are extremely high and might let think that medical care could have been inadequate. As hospital financing systems move towards reimbursement by diagnostic groups, it is essential to assess whether inadequate care is provided, to try to identify these patients upon admission, and make sure that their outcome is good. For the years 1995 and 1997, treatment costs exceeding by 6 standard deviations the average cost of their APDRG category were identified, and the charts of the 50 patients with the highest variable costs were analyzed. The total number of patients with such extreme costs diminished from 391 in 1995 to 328 in 1997 (-16%). For the 50 most expensive patients, long stays in several services were frequent, but 90% of these patients left the hospital alive, and about half directly to their home. They presented an important variation in diagnoses and operations, but no evidence for inadequate care. Thus, patients qualified as extreme from an economic perspective cannot be qualified as such from a medical perspective, and their outcome is good. To face the pressure linked with the change in financing system, hospitals must develop an internal review system for assessing the adequacy of care, based on clinical characteristics, if they want to guarantee good quality of care and identify potentially inadequate practice.

Interactions between schistosomiasis and human immunodeficiency virus in Western Kenya

For the past ten years, we have been exploring the relationship between schistosomiasis and human immunodeficiency virus (HIV-1) and how coinfection with both agents may affect the pathology and progression of each infection. To date, given the systems we have examined, the effects of HIV-1 on schistosomiasis have been more profound than the effects of schistosomiasis on HIV-1 progression. Additional key questions with important public health implications remain unanswered, but hopefully not unanswerable.

Prevalence of hepatitis-B surface antigen among blood donors and human immunodeficiency virus-infected patients in Jos, Nigeria

Information is very scarce on the prevalence of hepatitis-B virus (HBV) infection among blood donors and patients with human immunodeficiency virus (HIV) infection in Nigeria. Hepatitis-B surface antigen (HBsAg) ELISA was used to determined the prevalence of HBsAg among 175 blood donors (aged 20-40 years) and 490 HIV-infected patients (aged 17-60 years) in Jos, Nigeria. Twenty-five (14.3%) of the blood donors and 127 (25.9%) of the HIV-infected individuals were HBsAg seropositive, indicating a higher HBV infection among HIV-infected persons than among healthy blood donors. A slightly higher HBsAg seroprevalence was recorded in the males (14.6%) than females (12.9%) of the blood donors. Among the HIV-infected patients, the males had considerably higher HBsAg seroprevalence than the females (31.8 vs 22.1%) with the highest prevalence of HBsAg occurring in the 51-60 years age group (44%), followed by those of 31-40 years (28.2%). Results confirmed the high endemicity of HBV infection in Jos, Nigeria and the significantly greater prevalence of HBV infection among HIV -infected patients than among blood donors.

The role of triple infection with hepatitis B virus, hepatitis C virus, and human immunodeficiency virus (HIV) type-1 on CD4+ lymphocyte levels in the highly HIV infected population of North-Central Nigeria

We set out to determine the seroprevalence of hepatitis B and C among human immunodeficiency virus type-1 (HIV-1) infected individuals in North-Central Nigeria to define the influence of these infections on CD4+ lymphocytes cells among our patients as access to antiretroviral therapy improves across the Nigerian nation. The CD4+ values of 180 confirmed HIV-1 infected individuals were enumerated using a superior fluorescence-activated cell sorter system. These patients were tested for the presence of hepatitis B surface antigen and anti-hepatitis C virus (HCV) using third generation enzyme-linked immunosorbent assays. Fifty (27.8%) patients had active hepatitis B virus (HBV) infection while 33 (18.3%) tested positive for anti-HCV antibody. Of these infections, 110 (61.1%), 37 (20.6%), and 20 (11.1%) had HIV only, HBV/HIV-only, and HCV/HIV-only respectively. A HBV/HCV/HIV coinfection prevalence of 7.2% (13 patients) was recorded. Patients coinfected with HIV/HBV/HCV appeared to have lower CD4+ counts (mean = 107 cells/µl; AIDS defining) when compared to HBV/HIV-only (mean = 377 cells/µl), HCV/HIV-only (mean = 373 cells/µl) and patients with mono HIV infection (mean = 478 cells/µl). Coinfection with HBV or HCV is relatively common among HIV-infected patients in Nigeria and should be a big consideration in the initiation and choice of therapy.

Angiotensin II is an endogenous neurotransmitter for rat and human mesenteric resistance blood vessels

Angiotensin II (Ang II) is one of the most potent vasoconstrictors. We document here the innervation of rat and human mesenteric resistance arteries (MRA) by angiotensinergic neurons of the rat and human sympathetic coeliac ganglia. Angiotensinogen (Ang-N)-mRNA and angiotensin converting enzyme-mRNA but no renin-mRNA were detected by using quantitative real time polymerase chain reaction in total RNA extracts of rat coeliac ganglia. In the same extracts, cathepsin D-mRNA was detected: This protease also cleaves Ang I from Ang-N and could therefore account for the generation of neuronal Ang peptides in the absence of renin. In situ hybridization confirmed the presence of Ang-N-mRNA in the cytoplasm of rat coeliac ganglia. By using solid-phase extraction, high performance liquid chromatography and subsequent radioimmunoassay, Ang II and its metabolites were detected in rat and also in human coeliac ganglia. Immunoreactivity for Ang II was demonstrated in rat and human coeliac ganglia neurons and their projections innervating MRA. In addition, segmental angiotensinergic innervation of MRA was also observed. By means of confocal laser scanning microscopy we were able to demonstrate the presence of angiotensinergic synapses en passant along side of vascular smooth muscle cells. Our findings could indicate that Ang II is synthesized inside the neurons of sympathetic coeliac ganglia and may act as an endogenous neurotransmitter locally in MRA.

War and Natural Resource Exploitation

We build a theoretical framework that allows for endogenous conflict behaviour (i.e., fighting efforts) and for endogenous natural resource exploitation (i.e., speed, ownership, and investments). While depletion is spread in a balanced Hotelling fashion during peace, the presence of conflict creates incentives for rapacious extraction, as this lowers the stakes of future contest. This voracious extraction depresses total oil revenue, especially if world oil demand is relatively elastic and the government's weapon advantage is weak. Some of these political distortions can be overcome by bribing rebels or by government investment in weapons. The shadow of conflict can also make less efficient nationalized oil extraction more attractive than private extraction, as insecure property rights create a holdup problem for the private firm and lead to a lower license fee. Furthermore, the government fights less intensely than the rebels under private exploitation, which leads to more government turnover. Without credible commitment to future fighting efforts, private oil depletion is only lucrative if the government's non-oil office rents are large and weaponry powerful, which guarantees the government a stronger grip on office and makes the holdup problem less severe.