Association between proton pump inhibitor therapy and clostridium difficile infection: a contemporary systematic review and meta-analysis.

Abstract Introduction Emerging epidemiological evidence suggests that proton pump inhibitor (PPI) acid-suppression therapy is associated with an increased risk of Clostridium difficile infection (CDI). Methods Ovid MEDLINE, EMBASE, ISI Web of Science, and Scopus were searched from 1990 to January 2012 for analytical studies that reported an adjusted effect estimate of the association between PPI use and CDI. We performed random-effect meta-analyses. We used the GRADE framework to interpret the findings. Results We identified 47 eligible citations (37 case-control and 14 cohort studies) with corresponding 51 effect estimates. The pooled OR was 1.65, 95% CI (1.47, 1.85), I2 = 89.9%, with evidence of publication bias suggested by a contour funnel plot. A novel regression based method was used to adjust for publication bias and resulted in an adjusted pooled OR of 1.51 (95% CI, 1.26–1.83). In a speculative analysis that assumes that this association is based on causality, and based on published baseline CDI incidence, the risk of CDI would be very low in the general population taking PPIs with an estimated NNH of 3925 at 1 year. Conclusions In this rigorously conducted systemic review and meta-analysis, we found very low quality evidence (GRADE class) for an association between PPI use and CDI that does not support a cause-effect relationship

Fast and Accurate Resonance Assignment of Small-to-Large Proteins by Combining Automated and Manual Approaches

The process of resonance assignment is fundamental to most NMR studies of protein structure and dynamics. Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization. Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins. Here, we address this by introducing the software COMPASS, which, by combining automated resonance assignment with manual intervention, is able to achieve accuracy approaching that from manual assignments at greatly accelerated speeds. Moreover, by including the option to compensate for isotope shift effects in deuterated proteins, COMPASS is far more accurate for larger proteins than existing automated methods. COMPASS is an open-source project licensed under GNU General Public License and is available for download from http://www.liu.se/forskning/foass/tidigare-foass/patrik-lundstrom/software?l=en. Source code and binaries for Linux, Mac OS X and Microsoft Windows are available.Funding Agencies|Swedish Research Council [Dnr. 2012-5136]</p

Problems Concerning External Data Incorporation in Data Warehouses

Data warehouses (DWs) have become one of the largest investments in the past years for organisations, and incorporating external data into a DW can give organisations huge possibilities. Organisations that successfully manage to incorporate external data into a DW have an advantage over those who do not, but there are problems with incorporating data acquired from outside the organisation, and there is a lack of research aimed at these problems. The comprehensive aim of this dissertation is to characterise and categorise problems with incorporating external data. The available literature was scanned to find problems and an interview study was conducted to validate the problems found in the literature. Respondents from five well-known organisations in Sweden participated and the result is a list of problems backed up by both literature and empirical finding

Automation proposal for handling of bobbins around a washing machine

AH Automation har fått i uppdrag från Dahréntråd AB att genomföra en förstudie och ta fram ett automationskoncept för automatisk hantering av spolar runt en spoltvätt. Dahréntråd har för avsikt att upphandla en ny spoltävtt. Detta examensarbete är genomfört med avsikten att genomföra denna förstudie för AH Automation med målsättningen att det leder till ett effektivt system för automatisk hantering runt tvätten. Resultatet i denna rapport är ett koncept och kräver ytterligare arbete innan projektet kan realiseras. Många timmar arbete har spenderats på rundvandringar, diskussioner, möten, analys och ”trial &amp; error” iteration framtagning. Detta har lett fram till en helautomatiserad lösning. Resultatet innefattar en robot som lastar in spolar i tvätten och en robot på en linjärenhet som lastar spolar från tvätten. Roboten innan spoltvätten sorterar pallar och mellanlägg samtidigt som den förser roboten efter tvätten med pallar och mellanlägg. Båda robotarna är utrustade med ett vakuumgripdon som har för avsikt att kunna hantera samtliga spole modeller, pallar och mellanlägg. Konceptet tillåter att spolar kan plockas manuellt när packningen inte är kompatibel med robotplock. Resultatet presenteras som en 3D layout skapad i Inventor Autodesk.AH Automation has been commissioned by Dahréntråd AB to carry out a pilot study and develop an automation concept for automatic handling of bobbins around an industrial bobbin washer. Dahréntråd intends to buy a new bobbin washing machine. This thesis report is made with the intention of carrying out this pilot study for AH Automation with the aim that it leads to a effective automation system. The result in this report is a concept and requires further work before the project can be realized. Many hours of work have been spent on tours, discussions, meeting, analysis and trial &amp; error iteration development. These steps have led to a fully automated solution. The result includes a robot that loads bobbins into the washing machine and one robot on a linear unit, that unloads the bobbins from the washing machine. The first robot is sorting pallets and slipsheets at the same time as it supplies the other robot with pallets and slipsheets. Both robots are equipped with a vacuum gripper that aims to handle all bobbin models, pallets and slipsheets. This concept also allows bobbins to be picked manually with lifting assistance when the bobbins are packed in such a way that that the robot can’t handle it

Automation proposal for handling of bobbins around a washing machine

AH Automation har fått i uppdrag från Dahréntråd AB att genomföra en förstudie och ta fram ett automationskoncept för automatisk hantering av spolar runt en spoltvätt. Dahréntråd har för avsikt att upphandla en ny spoltävtt. Detta examensarbete är genomfört med avsikten att genomföra denna förstudie för AH Automation med målsättningen att det leder till ett effektivt system för automatisk hantering runt tvätten. Resultatet i denna rapport är ett koncept och kräver ytterligare arbete innan projektet kan realiseras. Många timmar arbete har spenderats på rundvandringar, diskussioner, möten, analys och ”trial &amp; error” iteration framtagning. Detta har lett fram till en helautomatiserad lösning. Resultatet innefattar en robot som lastar in spolar i tvätten och en robot på en linjärenhet som lastar spolar från tvätten. Roboten innan spoltvätten sorterar pallar och mellanlägg samtidigt som den förser roboten efter tvätten med pallar och mellanlägg. Båda robotarna är utrustade med ett vakuumgripdon som har för avsikt att kunna hantera samtliga spole modeller, pallar och mellanlägg. Konceptet tillåter att spolar kan plockas manuellt när packningen inte är kompatibel med robotplock. Resultatet presenteras som en 3D layout skapad i Inventor Autodesk.AH Automation has been commissioned by Dahréntråd AB to carry out a pilot study and develop an automation concept for automatic handling of bobbins around an industrial bobbin washer. Dahréntråd intends to buy a new bobbin washing machine. This thesis report is made with the intention of carrying out this pilot study for AH Automation with the aim that it leads to a effective automation system. The result in this report is a concept and requires further work before the project can be realized. Many hours of work have been spent on tours, discussions, meeting, analysis and trial &amp; error iteration development. These steps have led to a fully automated solution. The result includes a robot that loads bobbins into the washing machine and one robot on a linear unit, that unloads the bobbins from the washing machine. The first robot is sorting pallets and slipsheets at the same time as it supplies the other robot with pallets and slipsheets. Both robots are equipped with a vacuum gripper that aims to handle all bobbin models, pallets and slipsheets. This concept also allows bobbins to be picked manually with lifting assistance when the bobbins are packed in such a way that that the robot can’t handle it

Coding to cure : NMR and thermodynamic software applied to congenital heart disease research

Regardless of scientific field computers have become pivotal tools for data analysis and the field of structural biology is not an exception. Here, computers are the main tools used for tasks including structural calculations of proteins, spectral analysis of nuclear magnetic resonance (NMR) spectroscopy data and fitting mathematical models to data. As results reported in papers heavily rely on software and scripts it is of key importance that the employed computational methods are robust and yield reliable results. However, as many scientific fields are niched and possess a small potential user base the task to develop necessary software often falls on researchers themselves. This can cause divergence when comparing data analyzed by different measures or by using subpar methods. Therein lies the importance of development of accurate computational methods that can be employed by the scientific community. The main theme of this thesis is software development applied to structural biology, with the purpose to aid research in this scientific field by speeding up the process of data analysis as well as to ensure that acquired data is properly analyzed. Among the original results of this thesis are three user-friendly software: COMPASS - a resonance assignment software for NMR spectroscopy data capable of analyzing chemical shifts and providing the user with suggestions to potential resonance assignments, based on a meticulous database comparison. CDpal - a curve fitting software used to fit thermal and chemical denaturation data of proteins acquired by circular dichroism (CD) spectroscopy or fluorescence spectroscopy. PINT - a line shape fitting and downstream analysis software forNMRspectroscopy data, designed with the important purpose to easily and accurately fit peaks in NMR spectra and extract parameters such as relaxation rates, intensities and volumes of peaks. This thesis also describes a study performed on variants of the life essential regulatory protein calmodulin that have been associated with the congenital life threatening heart disease long QT syndrome (LQTS). The study provided novel insights revealing that all variants are distinct from the wild type in regards to structure and dynamics on a detailed level; the presented results are useful for the interpretation of results from protein interaction studies. The underlying research of this paper makes use of all three developed software, which validates that all developed methods fulfil a scientific purpose and are capable of producing solid results

Current and future application areas for external data in data warehouses

External data is data that a company could acquire outside their internal systems. This external data could bring another dimension for the companies, and allow them to further understand the environment. External data incorporated into a data warehouse makes it possible to exploit a number of application areas. The comprehensive aim of this dissertation is to outline what application areas that companies exploits today and what the future will bring. To achieve this, an interview study among people working with external data and DWs have been conducted. Based on the information gathered through the study, the most common application areas are address updates, credit information, and marketing. Some smaller application areas have also been identified. A discussion on what application areas that will come in the future, are also to be found

Making shipping energy efficient : A study regarding implementing mandatory guidelines

Vi lever i en värld av klimatförändringar där det ständigt söks efter lösningar för att minska utsläppen av växthusgaser. IMO har infört SEEMP:en med målet att reducera utsläppen från världshandelsflottan och därmed öka dess energieffektivitet. Med denna bakgrund har syftet varit att undersöka hur svenska tankrederier implementerat och tillämpat SEEMP:en samt kartlägga åsikter kring den. En kvalitativ metod har använts för att på djupet undersöka rederiernas tillvägagångssätt. Undersökningen omfattar fyra semistrukturerade intervjuer med totalt sex personer ifrån två rederier där både ombord- och landanställda finns representerade. Resultatet visade att rederierna implementerat SEEMP:en efter IMO:s riktlinjer, i samråd med sitt klassningssällskap, där rederierna också har försökt ta tillvara möjligheten att energieffektivisera sin organisation. Båda rederierna såg positivt på införandet av SEEMP:en och menade att den borde införts tidigare. Det framkommer dock faktorer som anses motverka SEEMP:ens fulla potential, bland annat att strukturen i branschen måste ändras för att kunna applicera SEEMP:en fullt ut.We live in a world of climate change where finding a solution to reducing the emission of GHG is a continuous pursuit. To reduce the emission from global shipping IMO has adopted the SEEMP consequently making the shipping industry more energy efficient. With this in mind the purpose of this study has been to review the implementation and usage of the SEEMP among Swedish shipping companies trading oil. Furthermore, the views of the involved parties with regard to the SEEMP were also investigated. In order to deeply analyze the companies´ approach to the SEEMP a qualitative research method has been used. The study consists of four semi-structured interviews with sex persons from two shipping companies including both onshore and ship-based personnel. The result shows that the implementation has been carried out in consultation with their own classification societies and with the IMO guidelines in mind. They have also tried to take the opportunity to make their organization more energy efficient. Both companies welcomed the adoption of the SEEMP and were of the opinion that it shouldhave been introduced at an earlier stage. However, some barriers to the SEEMP have been found, for example the operational structure of the shipping industry

Brandplan för Gotska Sandön

Föreliggande arbete är en plan för att införa skyddsavbränning som ett verktyg för att minska risken för okontrollerbara skogsbränder samt för att bibehålla naturvärdena på Gotska Sandön. Ön härbärgerar en unik fauna som starkt gynnas av brand. Tidigare undersökningar har visat att fram till år 1760 brann öns skogar med ungefär 25 års intervall, därefter har endast två större bränder inträffat (1880 och 1917). Den långa frånvaron av brand har medfört både igenväxning och ackumulering av stora bränslemängder (humus, förna, mossor och fältskiktsarter, främst ljung) över stora områden. Igenväxningen har lett till minskning av arealen öppen sandmark. De mycket speciella förhållandena på Gotska Sandön med frånvaro av naturliga brandhinder (våtmarker, öppet vatten, större dynområden) i kombination med i princip ett sammanhängande ljungtäcke skapar förutsättningar för mycket stora skogsbränder med hög trädmortalitet och stor risk för bebyggelsen på ön (fyrbyn). Bränderna 1880 och 1739 har delvis haft denna karaktär. Igenväxningen är också negativ för en stor mängd arter (skalbaggar, fjärilar, kärlväxter m fl artgrupper) som är hotade och tillbakaträngda eller överhuvudtaget inte alls finns idag på det svenska fastlandet. För att minska risken för okontrollerade bränder med katastrofala effekter samt för att vända den negativa påverkan av igenväxningen föreslås införande av kontrollerad bränslereducerande skydds­avbränningar och naturvårdsbränningar som skötselmetod på delar av ön. Tack vare öns isolerade läge i havet finns på lång sikt goda förutsättningar för en framtida i huvudsak människostyrd brandregim som kontinuerligt minskar risken för okontrollerade, oönskat stora och beståndsdödande bränder. Många unika och hotade arter gynnas av dessa skydds- och naturvårdsbränningar.   I brandplanen har ön delats in i fem olika områden utifrån ett säkerhets- och restaureringsperspektiv. 1. Områden som behöver skyddas från eld (egendom och kulturvärden, 150 ha). 2. Områden där brand skall undvikas och skall om möjligt skyddas i händelse av brand eller bränning (450 ha). 3. Skyddsavbränning i restaureringssyfte med lägre prioritet (1900 ha). 4. Skyddsavbränning i restaureringssyfte med högre prioritet (800 ha). 5. Skyddsavbränning i syfte att drastiskt reducera bränslemängderna i en bred zon runt fyrbyn som ett skydd mot okontrollerade bränder (ca 10 ha)

Biophysical characterization of the calmodulin-like domain of Plasmodium falciparum calcium dependent protein kinase 3

Calcium dependent protein kinases are unique to plants and certain parasites and comprise an N-terminal segment and a kinase domain that is regulated by a C-terminal calcium binding domain. Since the proteins are not found in man they are potential drug targets. We have characterized the calcium binding lobes of the regulatory domain of calcium dependent protein kinase 3 from the malaria parasite Plasmodium falciparum. Despite being structurally similar, the two lobes differ in several other regards. While the monomeric N-terminal lobe changes its structure in response to calcium binding and shows global dynamics on the sub-millisecond time-scale both in its apo and calcium bound states, the C-terminal lobe could not be prepared calcium-free and forms dimers in solution. If our results can be generalized to the full-length protein, they suggest that the C-terminal lobe is calcium bound even at basal levels and that activation is caused by the structural reorganization associated with binding of a single calcium ion to the N-terminal lobe.Funding Agencies|Vetenskapsradet [Dnr. 2012-5136, Dnr. 2012-5270]; Swedish e-science</p