Ontology-based protein-protein interactions extraction from literature using the hidden vector state model

This paper proposes a novel framework of incorporating protein-protein interactions (PPI) ontology knowledge into PPI extraction from biomedical literature in order to address the emerging challenges of deep natural language understanding. It is built upon the existing work on relation extraction using the Hidden Vector State (HVS) model. The HVS model belongs to the category of statistical learning methods. It can be trained directly from un-annotated data in a constrained way whilst at the same time being able to capture the underlying named entity relationships. However, it is difficult to incorporate background knowledge or non-local information into the HVS model. This paper proposes to represent the HVS model as a conditionally trained undirected graphical model in which non-local features derived from PPI ontology through inference would be easily incorporated. The seamless fusion of ontology inference with statistical learning produces a new paradigm to information extraction.

Revolution or evolution:the challenges of conceptualizing patient and public involvement in a consumerist world

Background Changing the relationship between citizens and the state is at the heart of current policy reforms. Across England and the developed world, from Oslo to Ontario, Newcastle to Newquay, giving the public a more direct say in shaping the organization and delivery of healthcare services is central to the current health reform agenda. Realigning public services around those they serve, based on evidence from service user's experiences, and designed with and by the people rather than simply on their behalf, is challenging the dominance of managerialism, marketization and bureaucratic expertise. Despite this attention there is limited conceptual and theoretical work to underpin policy and practice. Objective This article proposes a conceptual framework for patient and public involvement (PPI) and goes on to explore the different justifications for involvement and the implications of a rights-based rather than a regulatory approach. These issues are highlighted through exploring the particular evolution of English health policy in relation to PPI on the one hand and patient choice on the other before turning to similar patterns apparent in the United States and more broadly. Conclusions A framework for conceptualizing PPI is presented that differentiates between the different types and aims of involvement and their potential impact. Approaches to involvement are different in those countries that adopt a rights-based rather than a regulatory approach. I conclude with a discussion of the tension and interaction apparent in the globalization of both involvement and patient choice in both policy and practice. © 2009 Blackwell Publishing Ltd.

Perspectives of carers on medication management in dementia:lessons from collaboratively developing a research proposal

Background: The need for carers to manage medication-related problems for people with dementia living in the community raises dilemmas, which can be identified by carers and people with dementia as key issues for developing carer-relevant research projects.A research planning Public Patient Involvement (PPI) workshop using adapted focus group methodology was held at the Alzheimer's Society's national office, involving carers of people with dementia who were current members of the Alzheimer's Society Research Network (ASRN) in dialogue with health professionals aimed to identify key issues in relation to medication management in dementia from the carer viewpoint. The group was facilitated by a specialist mental health pharmacist, using a topic guide developed systematically with carers, health professionals and researchers. Audio-recordings and field notes were made at the time and were transcribed and analysed thematically. The participants included nine carers in addition to academics, clinicians, and staff from DeNDRoN (Dementias and Neurodegenerative Diseases Research Network) and the Alzheimer's Society. Findings. Significant themes, for carers, which emerged from the workshop were related to: (1) medication usage and administration practicalities, (2) communication barriers and facilitators, (3) bearing and sharing responsibility and (4) weighing up medication risks and benefits. These can form the basis for more in-depth qualitative research involving a broader, more diverse sample. Discussion. The supported discussion enabled carer voices and perspectives to be expressed and to be linked to the process of identifying problems in medications management as directly experienced by carers. This was used to inform an agenda for research proposals which would be meaningful for carers and people with dementia. © 2014 Poland et al.; licensee BioMed Central Ltd.

Proton pump inhibitor prescribing following Endoscopic diagnosis in a district general hospital

Focal points: A systematic review of the use of proton pump inhibitors was conducted among patients undergoing diagnostic fibreoptic endoscopic examination of the upper gastrointestinal tract during the period July 2001 to February 2002 inclusive A total of 2,557 patients received a PPI following endoscopy and healing doses were prescribed to 75.3 per cent of these patients An “unknown indication” was stated as a diagnosis in 958 patients (37.5 per cent) of patients studied Although endoscopic diagnosis does not appear possible in all cases, the present study demonstrates that NICE guidance to employ the lowest appropriate dose of PPI is followed

Individual Proton Pump Inhibitors and Outcomes in Patients With Coronary Artery Disease on Dual Antiplatelet Therapy: A Systematic Review.

BACKGROUND: Observational studies evaluating the possible interaction between proton pump inhibitors (PPIs) and clopidogrel have shown mixed results. We conducted a systematic review comparing the safety of individual PPIs in patients with coronary artery disease taking clopidogrel. METHODS AND RESULTS: Studies performed from January 1995 to December 2013 were screened for inclusion. Data were extracted, and study quality was graded for 34 potential studies. For those studies in which follow-up period, outcomes, and multivariable adjustment were comparable, meta-analysis was performed.The adjusted odds or hazard ratios for the composite of cardiovascular or all-cause death, myocardial infarction, and stroke at 1 year were reported in 6 observational studies with data on individual PPIs. Random-effects meta-analyses of the 6 studies revealed an increased risk for adverse cardiovascular events for those taking pantoprazole (hazard ratio 1.38; 95% CI 1.12-1.70), lansoprazole (hazard ratio 1.29; 95% CI 1.09-1.52), or esomeprazole (hazard ratio 1.27; 95% CI 1.02-1.58) compared with patients on no PPI. This association was not significant for omeprazole (hazard ratio 1.16; 95% CI 0.93-1.44). Sensitivity analyses for the coronary artery disease population (acute coronary syndrome versus mixed) and exclusion of a single study due to heterogeneity of reported results did not have significant influence on the effect estimates for any PPIs. CONCLUSIONS: Several frequently used PPIs previously thought to be safe for concomitant use with clopidogrel were associated with greater risk of adverse cardiovascular events. Although the data are observational, they highlight the need for randomized controlled trials to evaluate the safety of concomitant PPI and clopidogrel use in patients with coronary artery disease.

Reproductive Patterns and Birth Seasonality in a South-American Breeding Colony of Common Marmosets, Callithrix jacchus

SOUSA,M.B.C. et al. Reproductive Patterns and Birth Seasonality in a South-American Breeding Colony of Common Marmosets, Callithrix jacchus. Primates, v.40, n.2, p. 327-336, Apr. 1999.

Reproductive Patterns and Birth Seasonality in a South-American Breeding Colony of Common Marmosets, Callithrix jacchus

SOUSA,M.B.C. et al. Reproductive Patterns and Birth Seasonality in a South-American Breeding Colony of Common Marmosets, Callithrix jacchus. Primates, v.40, n.2, p. 327-336, Apr. 1999.

Hipertensión intra-abdominal y síndrome abdominal compartamental prevalencia postlaparotomía por abdomen agudo, HVCM Cuenca 2010-2011 /

La hipertensión intra-abdominal (HIA) y el síndrome compartamental abdominal (SCA) son causa importante de morbi-mortalidad postoperatoria. Avances en su diagnóstico y tratamiento oportuno han proporcionado mejor sobrevida en estos pacientes. Objetivo. Determinar la prevalencia de HIA, SCA y asociarla con (hallazgos quirúrgicos, presión de perfusión Intra-abdominal (PPI), obesidad) intervenidos por abdomen agudo en el Departamento de Cirugía del Hospital Vicente Corral Moscoso de Cuenca. Metodología. Se realizó un estudio transversal analítico en pacientes mayores de 16 años que ameritaron laparotomía de septiembre de 2010 hasta agosto de 2011 y que cumplieron criterios de exclusión, la PIA fue medida mediante método indirecto y la información se recopilo en un formulario elaborado para el estudio. Resultados: 347 Pacientes fueron incluidos en el estudio, la media de edad se ubicó en 46.72 ± 22.30 años, presentaron sobrepeso el 5.2%, en el estadio pre-quirúrgico se encontró Hipertensión Intra-abdominal en 41.2% y 10.4% de síndrome compartamental; luego de la laparotomía la hipertensión intra-abdominal disminuyó a 37.7% y el síndrome compartamental a 8.4%. La PIA iguales o mayores a 12mmHg aumentan el riesgo de hipo-perfusión intestinal en 3.56 veces (IC 95%: 1.81-6.99), p menor que 0.05; la obesidad se comportó como factor de riesgo con un RP de 1.73 (1.451-2.13); los hallazgo quirúrgico encontrados fueron significativos para Abdomen agudo perforativo: 2.45 con IC 95% 1.91-3.13; Abdomen agudo hemorrágico 1.83 con IC 95% 1.46-2.30 y Abdomen agudo oclusivo intestinal 2.32 con IC 95% 2.05-2.64. Conclusión: La Hipertensión intra-abdominal disminuye progresivamente en el postoperatorio, mientras que en quienes se manifiesta el SCA permaneció elevado por mayor tiempo. Se evidencio que la Obesidad influye incrementando la PIA, la misma que produce disminución de la PPI prediciendo peor pronóstico; los hallazgos quirúrgicos representativos para el incremento de la PIA fueron el abdomen agudo perforativo y oclusivo .au

Effect of nitric oxide donors on blood pressure and pulse pressure in acute and subacute stroke

High blood pressure (BP), pulse pressure (PP), and rate pressure product (RPP) areeach associated independently with a poor outcome in acute ischemic stroke. Whereas nitric oxide (NO) donors, such as glyceryl trinitrate (GTN), lower blood pressure in acute ischemic stroke, their effect on other hemodynamic measures is not known. We performed a systematic review of the effects of NO donors on systemic hemodynamic measures in patients with acute/subacute stroke. Randomized controlled trials were identified from searches of the Cochrane Library, Pubmed, and Embase. Information on hemodynamic measures, including systolic BP (SBP), diastolic BP (DBP), and heart rate, were assessed, and hemodynamic derivatives of these were calculated: PP (PP SBP DBP), mean arterial pressure (MAP DBP PP/3), mid blood pressure (MBP (SBP DBP)/2), pulse pressure index (PPI PP/MAP), and RPP (RPP SBP HR). The effect of treatment on hemodynamic measures was calculated as the weighted mean difference (WMD) between treated and control groups with adjustment for baseline. Results: Three trials involving 145 patients were identified; 93 patients received the NO donor, GTN, and 52 control. As compared with placebo, GTN significantly reduced SBP (WMD -9.80 mmHg, p< 0.001), DBP (WMD -4.43 mmHg, p<0.001), MAP (WMD -6.41 mmHg, p< 0.001), MBP (WMD -7.33 mmHg,p<0.001), PP (WMD -6.11 mmHg, p<0.001 ) and PPI (WMD -0.03, p=0.04 ). 3 GTN increased HR (WMD +3.87 bpm, p<0.001) and non-significantly lowered RPP (WMD -323 mmHg.bpm, p=0.14). Conclusion: The NO donor GTN reduces BP, PP and other derivatives in acute and subacute stroke whilst increasing heart rate.

A geometric study of liquid retention in open-cell metal foams

Open-cell metal foams show promise as an emerging novel material for heat exchanger applications. The high surface-area-to-volume ratio suggests increased compactness and decrease in weight of heat exchanger designs. However, the metal foam structure appears conducive to condensate retention, which would degenerate heat transfer performance. This research investigates the condensate retention behavior of aluminum open-cell metal foams through the use of static dip tests and geometrical classification via X-ray Micro-Computed Tomography. Aluminum open-cell metal foam samples of 5, 10, 20, and 40 pores per inch (PPI), all having a void fraction greater than 90%, were included in this investigation. In order to model the condensate retention behavior of metal foams, a clearer understanding of the geometry was required. After exploring the ideal geometries presented in the open literature, X-ray Micro-Computed Tomography was employed to classify the actual geometry of the metal foam samples. The images obtained were analyzed using specialized software from which geometric information including strut length and pore shapes were extracted. The results discerned a high variability in ligament length, as well as features supporting the ideal geometry known as the Weaire-Phelan unit cell. The static dip tests consisted of submerging the metal foam samples in a liquid, then allowing gravity-induced drainage until steady-state was reached and the liquid remaining in the metal foam sample was measured. Three different liquids, water, ethylene glycol, and 91% isopropyl alcohol, were employed. The behaviors of untreated samples were compared to samples subjected to a Beomite surface treatment process, and no significant differences in retention behavior were discovered. The dip test results revealed two distinct regions of condensate retention, each holding approximately half of the total liquid retained by the sample. As expected, condensate retention increased as the pores sizes decreased. A model based on surface tension was developed to predict the condensate retention in the metal foam samples and verified using a regular mesh. Applying the model to both the ideal and actual metal foam geometries showed good agreement with the dip test results in this study.

The effect of the proton pump inhibitor pantoprazole on the biology of Campylobacter jejuni

Campylobacter is a major cause of acute bacterial gastroenteritis worldwide, with the highest number of infections being attributed to Campylobacter jejuni. C. jejuni is a Gram negative, spiral, motile bacterium that belongs to the campylobacterales order and is related to both Helicobacter spp. and Wolinella sp.. It has long been established that proton pump inhibitors (PPIs) and other benzimidazole derivatives display anti-Helicobacter activity in vitro. PPIs have in the past been shown to affect Helicobacter pylori growth, survival, motility, morphology, adhesion/invasion potential and susceptibility to conventional antibiotics. PPIs are highly effective drugs that are well tolerated, safe for prolonged daily use and are therefore in high demand. Both the PPIs omeprazole and lansoprazole featured in the top ten drugs prescribed in England in 2014. In 2014 Campylobacter was also the most commonly diagnosed gastrointestinal infection in Scotland, in England and Wales and also in Europe. It has previously been generally accepted that patients who are being treated with PPIs are more susceptible to enteric infections such as Campylobacter than people not taking PPIs. The effect of PPI exposure on H. pylori has been investigated rigorously in the past. A single previous study has hinted that PPIs may also be capable of affecting the related organism C. jejuni,but investigations have been extremely limited in comparison to those investigating the effect of PPIs on H. pylori. This study has investigated the in vitro effects of direct contact with PPIs on the biology ofC. jejuni. Exposure to the PPI pantoprazole was found to affect C. jejuni growth/survival, motility, morphology, biofilm formation, invasion potential and susceptibility to some conventional antibiotics. Microarray studies showed that the cmeA and Cj0561c genes were significantly up-regulated in response to pantoprazole exposure and a CmeABC deficient mutant was found to be significantly more susceptible to killing by pantoprazole than was the parent strain. Proteomic analysis indicated that the oxidative stress response of C. jejuni was induced following exposure to sub-lethal concentrations of pantoprazole. C. jejuni gene expression was assessed using qRT-PCR and the genes encoding for thiol peroxidase and GroEL co-chaperonin (both involved in the C. jejuni oxidative stress response) were found to be around four times higher in response to exposure to sub-lethal concentrations of pantoprazole. Experiments using the oxidative stress inhibitors thiourea (a hydroxyl radical quencher) and bipyridyl (a ferrous iron chelator) showed that killing by pantoprazole was not mediated by hydroxyl radical production.

Proton-pump inhibitors adverse effects: a review of the evidence and position statement by the Sociedad Española de Patología Digestiva

Introduction: In the last few years a significant number of papers have related the use of proton-pump inhibitors (PPIs) to potential serious adverse effects that have resulted in social unrest. Objective: The goal of this paper was to provide a literature review for the development of an institutional position statement by Sociedad Española de Patología Digestiva (SEPD) regarding the safety of long-term PPI use. Material and methods: A comprehensive review of the literature was performed to draw conclusions based on a critical assessment of the following: a) current PPI indications; b) vitamin B12 deficiency and neurological disorders; c) magnesium deficiency; d) bone fractures; e) enteric infection and pneumonia; f) interactions with thienopyridine derivatives; e) complications in cirrhotic patients. Results: Current PPI indications have remained unchanged for years now, and are well established. A general screening of vitamin B12 levels is not recommended for all patients on a PPI; however, it does seem necessary that magnesium levels be measured at therapy onset, and then monitored in subjects on other drugs that may induce hypomagnesemia. A higher risk for bone fractures is present, even though causality cannot be concluded for this association. The association between PPIs and infection with Clostridium difficile is mild to moderate, and the risk for pneumonia is low. In patients with cardiovascular risk receiving thienopyridines derivatives it is prudent to adequately consider gastrointestinal and cardiovascular risks, given the absence of definitive evidence regardin potential drug-drug interactions; if gastrointestinal risk is found to be moderate or high, effective prevention should be in place with a PPI. PPIs should be cautiously indicated in patients with decompensated cirrhosis. Conclusions: PPIs are safe drugs whose benefits outweigh their potential side effects both short-term and long-term, provided their indication, dosage, and duration are appropriate.

Practical considerations in the management of proton-pump inhibitors

Proton-pump inhibitors (PPIs) are one of the most active ingredients prescribed in Spain. In recent decades there has been an overuse of these drugs in both outpatient clinics and hospitals that has lead to a significant increase in healthcare spending and to an increase in the risk of possible side effects. It is important for health professionals to know the accepted indications and the correct doses for the use of these drugs. On the market there are different types of PPI: omeprazole, pantoprazole, lansoprazole, rabeprazole and esomeprazole. Omeprazole is the oldest and most used PPI, being also the cheapest. Although there are no important differences between PPIs in curing diseases, esomeprazole, a new-generation PPI, has proved to be more effective in eradicating H. pylori and in healing severe esophagitis compared to other PPIs. In recent years the use of generic drugs has spread; these drugs have the same bioavailability than the original drugs. In the case of PPIs, the few comparative studies available in the literature between original and generic drugs have shown no significant differences in clinical efficacy.

Enhancing legume ecosystem services through an understanding of plant–pollinator interplay

Legumes are bee-pollinated, but to a different extent. The importance of the plant– pollinator interplay (PPI), in flowering crops such as legumes lies in a combination of the importance of pollination for the production service and breeding strategies, plus the increasing urgency in mitigating the decline of pollinators through the development and implementation of conservation measures. To realize the full potential of the PPI, a multidisciplinary approach is required. This article assembles an international team of genebank managers, geneticists, plant breeders, experts on environmental governance and agro-ecology, and comprises several sections. The contributions in these sections outline both the state of the art of knowledge in the field and the novel aspects under development, and encompass a range of reviews, opinions and perspectives. The first three sections explore the role of PPI in legume breeding strategies. PPI based approaches to crop improvement can make it possible to adapt and re-design breeding strategies to meet both goals of: (1) optimal productivity, based on an efficient use of pollinators, and (2) biodiversity conservation. The next section deals with entomological aspects and focuses on the protection of the “pest control service” and pollinators in legume crops. The final section addresses general approaches to encourage the synergybetweenfoodproductionandpollinationservicesatfarmerfieldlevel.Twobasic approaches are proposed: (a) Farming with Alternative Pollinators and (b) Crop Design System.

Enhancing legume ecosystem services through an understanding of plant–pollinator interplay

Legumes are bee-pollinated, but to a different extent. The importance of the plant– pollinator interplay (PPI), in flowering crops such as legumes lies in a combination of the importance of pollination for the production service and breeding strategies, plus the increasing urgency in mitigating the decline of pollinators through the development and implementation of conservation measures. To realize the full potential of the PPI, a multidisciplinary approach is required. This article assembles an international team of genebank managers, geneticists, plant breeders, experts on environmental governance and agro-ecology, and comprises several sections. The contributions in these sections outline both the state of the art of knowledge in the field and the novel aspects under development, and encompass a range of reviews, opinions and perspectives. The first three sections explore the role of PPI in legume breeding strategies. PPI based approaches to crop improvement can make it possible to adapt and re-design breeding strategies to meet both goals of: (1) optimal productivity, based on an efficient use of pollinators, and (2) biodiversity conservation. The next section deals with entomological aspects and focuses on the protection of the “pest control service” and pollinators in legume crops. The final section addresses general approaches to encourage the synergybetweenfoodproductionandpollinationservicesatfarmerfieldlevel.Twobasic approaches are proposed: (a) Farming with Alternative Pollinators and (b) Crop Design System.