Nucleic acid structure and sequence probing using fluorescent base analogue tC^o

The fluorescent cytosine analog tC(o) is on average the brightest probe of its kind and, moreover, it introduces minimal perturbations to the normal secondary structure of DNA. Here several ways of how tC(o), with an advantage, can be used as a local fluorescent probe in nucleic acid systems are presented. Most importantly, we show that tCo is an excellent probe for the detection of individual melting processes of complex nucleic acid structures containing a large number of separate secondary structure motifs. Since conventional UV-melting investigations merely monitor the global melting process of the whole nucleic acid structure, e.g. multi-hairpin systems in RNA/DNA, and thus is incapable of estimating individual melting transitions of such systems, tC(o) represents a new method of characterization. Furthermore, we find that tCo may be used to detect bulges and loops in nucleic acids as well as to distinguish a matched base-pair from several of the mismatched

Characterization of Nucleobase Analogue FRET Acceptor tC(nitro)

The fluorescent nucleobase analogues of the tricyclic cytosine (tC) family, tC and tC(O), possess high fluorescence quantum yields and single fluorescence lifetimes, even after incorporation into double-stranded DNA, which make these base analogues particularly useful as fluorescence resonance energy transfer (FRET) probes. Recently, we reported the first all-nucleobase FRET pair consisting of tC(O) as the donor and the novel tC(nitro) as the acceptor. The rigid and well-defined position of this FRET pair inside the DNA double helix, and consequently excellent control of the orientation factor in the FRET efficiency, are very promising features for future studies of nucleic acid structures. Here, we provide the necessary spectroscopic and photophysical characterization Of tC(nitro) needed in order to utilize this probe as a FRET acceptor in nucleic acids. The lowest energy absorption band from 375 to 525 nm is shown to be the result of a single in-plane polarized electronic transition oriented similar to 27 degrees from the molecular long axis, This band overlaps the emission bands of both tC and tC(O), and the Forster characteristics of these donor-acceptor pairs are calculated for double-stranded DNA scenarios. In addition, the UV-vis absorption of tC(nitro) is monitored in a broad pH range and the neutral form is found to be totally predominant under physiological conditions with a pK(a) of 11.1. The structure and electronic spectrum Of tC(nitro) is further characterized by density functional theory calculations

Where does all the phosphorus go? Mass balance modelling of phosphorus in the Swedish long-term soil fertility experiments

To gain insights into phosphorus (P) dynamics in soils and the ability to predict soil responses to varying fertilizer inputs, mass balance models prove to be valuable tools. In this study, a new dynamic mass balance model, PBalD8, was used to describe the change in extracted P in the A horizon of soils subjected to diverse fertilizer treatments over a period of 50 to 60 years in five soil fertility experiments. The model employed a Freundlich equation to describe soil-solution partitioning of P and assumed that acid-lactate-extractable P represented a labile pool of P in instant equilibrium with soil solution P. Additionally, oxalate-extractable inorganic P was presumed to comprise the sum of the labile and stable pools of P, with mass flux to and from the latter described by Fick's first law. The model was evaluated using results from extractions and P K-edge XANES spectroscopy. Notably, organic P, as revealed by P K-edge XANES, did not substantially contribute to long-term changes in soil P content and was therefore excluded from consideration. In general, the model offered reasonable fits to the extracted P concentrations. However, for the P-depleted treatments, a prerequisite was that the P removal through harvest was lower compared to measurements. Conversely, in three of the soils, the modelled fertilizer inputs needed to be reduced to 70 % to 85 % of the known additions. These discrepancies may be attributed to the involvement of deeper soil horizons, including deep crop uptake and mixing with lower soil layers, although other factors such as lateral dispersion and inaccuracies in estimating applied fertilizers cannot be discounted. These results underscore the necessity of gaining a more comprehensive understanding of how deeper soil horizons influence P mass balances in agricultural soils. In one of the soils, Fja center dot rdingslo center dot v, P K-edge XANES results demonstrated the formation of calcium phosphate over time in the highest fertilization treatment, consistent with the model. Additionally, in two soils, Kungsa center dot ngen and the P-depleted Vreta Kloster soil, the model predicted a significant contribution from mineral weathering. However, the PBalD8 model also projected higher P leaching rates than those observed, suggesting that the model may not fully capture this P output term

Highly efficient incorporation of the fluorescent nucleotide analogs tC and tCO by Klenow fragment

Studies of the mechanisms by which DNA polymerases select the correct nucleotide frequently employ fluorescently labeled DNA to monitor conformational rearrangements of the polymerase–DNA complex in response to incoming nucleotides. For this purpose, fluorescent base analogs play an increasingly important role because they interfere less with the DNA–protein interaction than do tethered fluorophores. Here we report the incorporation of the 5′-triphosphates of two exceptionally bright cytosine analogs, 1,3-diaza-2-oxo-phenothiazine (tC) and its oxo-homolog, 1,3-diaza-2-oxo-phenoxazine (tCO), into DNA by the Klenow fragment. Both nucleotide analogs are polymerized with slightly higher efficiency opposite guanine than cytosine triphosphate and are shown to bind with nanomolar affinity to the DNA polymerase active site, according to fluorescence anisotropy measurements. Using this method, we perform competitive binding experiments and show that they can be used to determine the dissociation constant of any given natural or unnatural nucleotide. The results demonstrate that the active site of the Klenow fragment is flexible enough to tolerate base pairs that are size-expanded in the major groove. In addition, the possibility to enzymatically polymerize a fluorescent nucleotide with high efficiency complements the tool box of biophysical probes available to study DNA replication

Characterization of photophysical and base-mimicking properties of a novel fluorescent adenine analogue in DNA

To increase the diversity of fluorescent base analogues with improved properties, we here present the straightforward click-chemistry-based synthesis of a novel fluorescent adenine-analogue triazole adenine (AT) and its photophysical characterization inside DNA. AT shows promising properties compared to the widely used adenine analogue 2-aminopurine. Quantum yields reach >20% and >5% in single- and double-stranded DNA, respectively, and show dependence on neighbouring bases. Moreover, AT shows only a minor destabilization of DNA duplexes, comparable to 2-aminopurine, and circular dichroism investigations suggest that AT only causes minimal structural perturbations to normal B-DNA. Furthermore, we find that AT shows favourable base-pairing properties with thymine and more surprisingly also with normal adenine. In conclusion, AT shows strong potential as a new fluorescent adenine analogue for monitoring changes within its microenvironment in DNA

Risk profiles and one-year outcomes of patients with newly diagnosed atrial fibrillation in India: Insights from the GARFIELD-AF Registry.

BACKGROUND: The Global Anticoagulant Registry in the FIELD-Atrial Fibrillation (GARFIELD-AF) is an ongoing prospective noninterventional registry, which is providing important information on the baseline characteristics, treatment patterns, and 1-year outcomes in patients with newly diagnosed non-valvular atrial fibrillation (NVAF). This report describes data from Indian patients recruited in this registry. METHODS AND RESULTS: A total of 52,014 patients with newly diagnosed AF were enrolled globally; of these, 1388 patients were recruited from 26 sites within India (2012-2016). In India, the mean age was 65.8 years at diagnosis of NVAF. Hypertension was the most prevalent risk factor for AF, present in 68.5% of patients from India and in 76.3% of patients globally (P < 0.001). Diabetes and coronary artery disease (CAD) were prevalent in 36.2% and 28.1% of patients as compared with global prevalence of 22.2% and 21.6%, respectively (P < 0.001 for both). Antiplatelet therapy was the most common antithrombotic treatment in India. With increasing stroke risk, however, patients were more likely to receive oral anticoagulant therapy [mainly vitamin K antagonist (VKA)], but average international normalized ratio (INR) was lower among Indian patients [median INR value 1.6 (interquartile range {IQR}: 1.3-2.3) versus 2.3 (IQR 1.8-2.8) (P < 0.001)]. Compared with other countries, patients from India had markedly higher rates of all-cause mortality [7.68 per 100 person-years (95% confidence interval 6.32-9.35) vs 4.34 (4.16-4.53), P < 0.0001], while rates of stroke/systemic embolism and major bleeding were lower after 1 year of follow-up. CONCLUSION: Compared to previously published registries from India, the GARFIELD-AF registry describes clinical profiles and outcomes in Indian patients with AF of a different etiology. The registry data show that compared to the rest of the world, Indian AF patients are younger in age and have more diabetes and CAD. Patients with a higher stroke risk are more likely to receive anticoagulation therapy with VKA but are underdosed compared with the global average in the GARFIELD-AF. CLINICAL TRIAL REGISTRATION-URL: http://www.clinicaltrials.gov. Unique identifier: NCT01090362

Politiska granskare. Den kommunala revisionens roll för politiskt ansvarsutkrävande

De kommunala revisorerna är den institution som enligt kommunallagen ska granska den verksamhet som bedrivs inom en nämnds verksamhetsområde och av en fullmäktigeberedning. Revisorer är förtroendevalda partipolitiker, och kommunal revision handlar alltså om politiker som granskar andra politiker. De kommunala revisorernas komplexa roll och deras opartiskhet i förhållande till de granskade har diskuterats under lång tid, men forskningen om institutionen har varit mycket begränsad. I denna rapport angrips kärnfrågorna i debatten om den kommunala revisionen: Hur hanterar revisorerna den diskrepans som uppstår när fullmäktige är ovillig att följa revisionens rekommendationer om ansvarsprövning och i vilken grad kan partipolitiska överväganden förklara fullmäktiges beslut i ansvarsfrågan? Förvaltningshögskolan vid Göteborgs universitet är en ackrediterad medlem av The European Association for Public Administration Accreditation. Varje år producerar våra studenter ett antal masteruppsatser av hög kvalitet. I rapporten ”Politiska granskare” ingår två exempel på excellenta masteruppsatser i offentlig förvaltning från 2012: Angelica Börjessons ”Revidera i motvind” och Marcus Starckes ”Den kommunala revisionens partipolitiska dimension”. Angelica Börjesson är verksam vid Förvaltningshögskolan och Marcus Starcke är verksam i Kungälvs kommun

The psychology of risk and safety in the military: A balancing act

The primary purpose of this thesis was to examine how individual, leadership, group, and situational factors affect the risk and safety perceptions and behaviors of military personnel. A secondary purpose was to examine how first-line military leaders perceive and deal with risk and safety issues in their leadership roles.  The thesis comprises three articles. The first article reports on a longitudinal study of conscripts during their compulsory military training. Results show that individual characteristics, safety beliefs, leadership behaviors, and group cohesion all do have an impact on the risk and safety attitudes of the conscripts. Significant differences in ratings of risk and safety attitudes between basic training and unit training were also found. The second article includes two different samples of rank and file and officers and shows that personality traits and socio-demographic factors are related to negative safety beliefs, as well as to the degree of risk propensity. The third article is based on interviews with military leaders with experience of high-risk military missions. A core theme identified in the study concerns the balancing of risk and safety as a key aspect of the role of the first-line military leadership. The interviews demonstrate how this balancing act underpins several challenges, related to individual, group, leadership, situational and organizational factors.  In conclusion, this thesis shows the significant impact that individual, leadership, group, and situational factors can have on the perceptions of risk and safety held by military personnel. The thesis identifies factors that jointly could create a “vulnerability-chain” for maladaptive risk-taking, and factors that jointly form a “strengthening-chain” for adaptive risk-taking and safety efforts.  The findings have practical implications for military selection, team composition, leadership education, and military training. The human ability to deal with risks has increasingly been coming into focus in our society. However, the research has to a great extent focused on everyday or social risks. Considerably less attention has been directed towards the individuals and groups that have to deal with dangerous and extreme environments in their professional roles, such as the military.  The primary purpose of this thesis was to examine how individual, leadership, group, and situational factors affect the risk and safety perceptions and behaviors of military personnel. A secondary purpose was to examine how first-line military leaders perceive and deal with risk and safety issues in their leadership roles.  The thesis comprises three articles that show the significant impact that both internal and external factors can have on the perceptions of risk and safety held by military personnel. Factors are identified that jointly could create a “vulnerability-chain” for maladaptive risk-taking, and others that jointly form a “strengthening-chain” for adaptive risk-taking and safety efforts.  The findings have practical implications for military selection, team composition, leadership education, and military training.

Performance evaluation of ground source heat pump heating systems in Stockholm

GSHP systems are common in Sweden but there are few evaluations quantifying the performance of the systems and highlighting problem that occurs during operations. The research project Annex 52 Long-term performance measurement of GSHP systems serving commercial, institutional and multifamily building part of IEA HPT TCP proves the need to systematically be able to evaluate GSHP systems. This thesis aims to expand the knowledge of how to evaluate GSHP systems and provide case studies for Annex 52. Three residential ground source heating systems used for heating has been evaluated and analyzed in this study. The evaluation has consisted of three parts. The first part analyzes the operation and stability of the GSHP systems. The second part consist of a detailed study of the performance of the GSHP systems. The seasonal performance factor has been calculated for different system boundaries based on the work done by SEPEMO. In addition, a method on how to evaluate the efficiency of the heat pumps based on the two temperature levels, source side temperature and the heat sink temperature, that the heat pump is operating at throughout a year has been developed within this thesis. This has included a method on how to normalize the temperatures based on the operation of the heat pump in order to quantify one temperature for each the two temperature levels. The third part consist of a comparison of the mean secondary fluid temperature between the calculated temperature using the software EED and the measured temperatures. This includes a comparison evaluation and sensitivity analysis on input parameters during the design of the borehole heat exchanger fields. This study has expanded the available reference cases of GSHP systems in Sweden. It also can be used as a guideline for those who will evaluate future GSHP systems. Designers of GSHP system will also benefit from the recommendations listed in this thesis regarding instrumentation and possible problems that may occur. The results show that the evaluation successfully managed to quantify the performance and operational issues that have occurred for each system. The method developed in this study was able to quantify the operation of the different systems based on the temperature levels and can be used for future GSHP evaluations of similar system type.Bergvärmesystem är vanligt förekommande i Sverige men trots detta finns det få studier där prestandan har utvärderats och de vanligt förekommande problemen under drift har belysts. Forskningsprojektet Annex 52 Annex 52 Long-term performance measurement of GSHP systems serving commercial, institutional and multi-family building som är en del av IEA HPT TCP visar på behovet av att systematisk utvärdera bergvärmesystem. Detta examensarbete syftar till att utveckla och bidra till kunskap om hur bergvärmesystem kan utvärderas och att bidra med exempelstudier till Annex 52. Inom detta examensarbete har tre bergvärmesystem som betjänar flerbostadshus utvärderats och analyserats. Utvärderingen bestod av tre analyser. I den första analyserades driften av bergvärmesystemen och hur stabilt systemet har varit historiskt. Detta följdes av en detaljerad analys av olika nyckeltal för bergvärmesystemen. Årsverkningsgraden har beräknats för olika gränsdragningar vilka baseras på det tidigare arbetet utfört av SEPEMO. Inom detta examensarbete har även en metod tagits fram för att utvärdera verkningsgraderna för en värmepump baserat på de två temperaturnivåerna, köldbärarsidan och värmebärarsidan, som värmepumpen arbetar med under ett år. Till detta har en metod tagits fram om hur temperaturen kan normaliserats baserat på driften av värmepumparna för att kvantifiera en temperatur vardera för de två temperaturnivåerna. I den tredje utvärderingen jämfördes den beräknade medelfluidtemperaturen av köldbäraren i borrhålen med den uppmätta temperaturen. Till detta utfördes en känslighetsanalys av hur indata av dessa beräkningar påverkar resultaten

Performance evaluation of ground source heat pump heating systems in Stockholm

GSHP systems are common in Sweden but there are few evaluations quantifying the performance of the systems and highlighting problem that occurs during operations. The research project Annex 52 Long-term performance measurement of GSHP systems serving commercial, institutional and multifamily building part of IEA HPT TCP proves the need to systematically be able to evaluate GSHP systems. This thesis aims to expand the knowledge of how to evaluate GSHP systems and provide case studies for Annex 52. Three residential ground source heating systems used for heating has been evaluated and analyzed in this study. The evaluation has consisted of three parts. The first part analyzes the operation and stability of the GSHP systems. The second part consist of a detailed study of the performance of the GSHP systems. The seasonal performance factor has been calculated for different system boundaries based on the work done by SEPEMO. In addition, a method on how to evaluate the efficiency of the heat pumps based on the two temperature levels, source side temperature and the heat sink temperature, that the heat pump is operating at throughout a year has been developed within this thesis. This has included a method on how to normalize the temperatures based on the operation of the heat pump in order to quantify one temperature for each the two temperature levels. The third part consist of a comparison of the mean secondary fluid temperature between the calculated temperature using the software EED and the measured temperatures. This includes a comparison evaluation and sensitivity analysis on input parameters during the design of the borehole heat exchanger fields. This study has expanded the available reference cases of GSHP systems in Sweden. It also can be used as a guideline for those who will evaluate future GSHP systems. Designers of GSHP system will also benefit from the recommendations listed in this thesis regarding instrumentation and possible problems that may occur. The results show that the evaluation successfully managed to quantify the performance and operational issues that have occurred for each system. The method developed in this study was able to quantify the operation of the different systems based on the temperature levels and can be used for future GSHP evaluations of similar system type.Bergvärmesystem är vanligt förekommande i Sverige men trots detta finns det få studier där prestandan har utvärderats och de vanligt förekommande problemen under drift har belysts. Forskningsprojektet Annex 52 Annex 52 Long-term performance measurement of GSHP systems serving commercial, institutional and multi-family building som är en del av IEA HPT TCP visar på behovet av att systematisk utvärdera bergvärmesystem. Detta examensarbete syftar till att utveckla och bidra till kunskap om hur bergvärmesystem kan utvärderas och att bidra med exempelstudier till Annex 52. Inom detta examensarbete har tre bergvärmesystem som betjänar flerbostadshus utvärderats och analyserats. Utvärderingen bestod av tre analyser. I den första analyserades driften av bergvärmesystemen och hur stabilt systemet har varit historiskt. Detta följdes av en detaljerad analys av olika nyckeltal för bergvärmesystemen. Årsverkningsgraden har beräknats för olika gränsdragningar vilka baseras på det tidigare arbetet utfört av SEPEMO. Inom detta examensarbete har även en metod tagits fram för att utvärdera verkningsgraderna för en värmepump baserat på de två temperaturnivåerna, köldbärarsidan och värmebärarsidan, som värmepumpen arbetar med under ett år. Till detta har en metod tagits fram om hur temperaturen kan normaliserats baserat på driften av värmepumparna för att kvantifiera en temperatur vardera för de två temperaturnivåerna. I den tredje utvärderingen jämfördes den beräknade medelfluidtemperaturen av köldbäraren i borrhålen med den uppmätta temperaturen. Till detta utfördes en känslighetsanalys av hur indata av dessa beräkningar påverkar resultaten