Microarray based real-time analysis of nucleic acid hybridization kinetics and thermodynamics

Ziel dieser Dissertation ist die experimentelle Charakterisierung und quantitative Beschreibung der Hybridisierung von komplementären Nukleinsäuresträngen mit oberflächengebundenen Fängermolekülen für die Entwicklung von integrierten Biosensoren. Im Gegensatz zu lösungsbasierten Verfahren ist mit Microarray Substraten die Untersuchung vieler Nukleinsäurekombinationen parallel möglich. Als biologisch relevantes Evaluierungssystem wurde das in Eukaryoten universell exprimierte Actin Gen aus unterschiedlichen Pflanzenspezies verwendet. Dieses Testsystem ermöglicht es, nahe verwandte Pflanzenarten auf Grund von geringen Unterschieden in der Gen-Sequenz (SNPs) zu charakterisieren. Aufbauend auf dieses gut studierte Modell eines House-Keeping Genes wurde ein umfassendes Microarray System, bestehend aus kurzen und langen Oligonukleotiden (mit eingebauten LNA-Molekülen), cDNAs sowie DNA und RNA Targets realisiert. Damit konnte ein für online Messung optimiertes Testsystem mit hohen Signalstärken entwickelt werden. Basierend auf den Ergebnissen wurde der gesamte Signalpfad von Nukleinsärekonzentration bis zum digitalen Wert modelliert. Die aus der Entwicklung und den Experimenten gewonnen Erkenntnisse über die Kinetik und Thermodynamik von Hybridisierung sind in drei Publikationen zusammengefasst die das Rückgrat dieser Dissertation bilden. Die erste Publikation beschreibt die Verbesserung der Reproduzierbarkeit und Spezifizität von Microarray Ergebnissen durch online Messung von Kinetik und Thermodynamik gegenüber endpunktbasierten Messungen mit Standard Microarrays. Für die Auswertung der riesigen Datenmengen wurden zwei Algorithmen entwickelt, eine reaktionskinetische Modellierung der Isothermen und ein auf der Fermi-Dirac Statistik beruhende Beschreibung des Schmelzüberganges. Diese Algorithmen werden in der zweiten Publikation beschrieben. Durch die Realisierung von gleichen Sequenzen in den chemisch unterschiedlichen Nukleinsäuren (DNA, RNA und LNA) ist es möglich, definierte Unterschiede in der Konformation des Riboserings und der C5-Methylgruppe der Pyrimidine zu untersuchen. Die kompetitive Wechselwirkung dieser unterschiedlichen Nukleinsäuren gleicher Sequenz und die Auswirkungen auf Kinetik und Thermodynamik ist das Thema der dritten Publikation. Neben der molekularbiologischen und technologischen Entwicklung im Bereich der Sensorik von Hybridisierungsreaktionen oberflächengebundener Nukleinsäuremolekülen, der automatisierten Auswertung und Modellierung der anfallenden Datenmengen und der damit verbundenen besseren quantitativen Beschreibung von Kinetik und Thermodynamik dieser Reaktionen tragen die Ergebnisse zum besseren Verständnis der physikalisch-chemischen Struktur des elementarsten biologischen Moleküls und seiner nach wie vor nicht vollständig verstandenen Spezifizität bei.

Electronic structure and physical properties of Heusler compounds for thermoelectric and spintronic applications

This thesis focuses on synthesis as well as investigations of the electronic structure and properties of Heusler compounds for spintronic and thermoelectric applications.rnThe first part reports on the electronic and crystal structure as well as the mechanical, magnetic, and transport properties of the polycrystalline Heusler compound Co2MnGe. The crystalline structure was examined in detail by extended X-ray absorption fine structure spectroscopy and anomalous X-ray diffraction. The low-temperature magnetic moment agrees well with the Slater-Pauling rule and indicates a half-metallic ferromagnetic state of the compound, as is predicted by ab-initio calculations. Transport measurements and hard X-ray photoelectron spectroscopy (HAXPES) were performed to explain the electronic structure of the compound.rnA major part of the thesis deals with a systematical investigation of Heusler compounds for thermoelectric applications. Few studies have been reported on thermoelectric properties of p-type Heusler compounds. Therefore, this thesis focuses on the search for new p-type Heusler compounds with high thermoelectric efficiency. The substitutional series NiTi1−xMxSn and CoTi1−xMxSb (where M = Sc, V and 0 ≤ x ≤ 0.2) were synthesized and investigated theoretically and experimentally with respect to electronic structure and transport properties. The results show the possibility to create n-type and p-type thermoelectrics within one Heusler compound. The pure compounds showed n-type behavior, while under Sc substitution the system switched to p-type behavior. A maximum Seebeck coefficient of +230 μV/K (at 350 K) was obtained for NiTi0.26Sc0.04Zr0.35Hf0.35Sn, which is one of the highest values for p-type thermoelectric compounds based on Heusler alloys up to now. HAXPES valence band measurement show massive in gap states for the parent compounds NiTiSn, CoTiSb and NiTi0.3Zr0.35Hf0.35Sn. This proves that the electronic states close to the Fermi energy play a key role for the behavior of the transport properties. Furthermore, the electronic structure of the gapless Heusler compounds PtYSb, PtLaBi and PtLuSb were investigated by bulk sensitive HAXPES. The linear behavior of the spectra close to εF proves the bulk origin of Dirac-cone type density of states. Furthermore, a systematic study on the optical and transport properties of PtYSb is presented. The compound exhibits promising thermoelectric properties with a high figure of merit (ZT = 0.2) and a Hall mobility μh of 300 cm2/Vs at 350 K.rnThe last part of this thesis describes the linear dichroism in angular-resolved photoemission from the valence band of NiTi0.9Sc0.1Sn and NiMnSb. High resolution photoelectron spectroscopy was performed with an excitation energy of hν = 7.938 keV. The linear polarization of the photons was changed using an in-vacuum diamond phase retarder. Noticeable linear dichroism is found in the valence bands and this allows for a symmetry analysis of the contributing states. The differences in the spectra are found to be caused by symmetry dependent angular asymmetry parameters, and these occur even in polycrystalline samples without preferential crystallographic orientation.rnIn summary, Heusler compounds with 1:1:1 and 2:1:1 stoichiometry were synthesized and examined by chemical and physical methods. Overall, this thesis shows that the combination of first-principle calculations, transport measurements and high resolution high energy photoelectron spectroscopy analysis is a very powerful tool for the design and development of new materials for a wide range of applications from spintronic applications to thermoelectric applications.rn

Prognostic factors in apical surgery with root-end filling: a meta-analysis

INTRODUCTION: Apical surgery has seen continuous development with regard to equipment and surgical technique. However, there is still a shortage of evidence-based information regarding healing determinants. The objective of this meta-analysis was to review clinical articles on apical surgery with root-end filling in order to assess potential prognostic factors. METHODS: An electronic search of PubMed and Cochrane databases was performed in 2008. Only studies with clearly defined healing criteria were included, and data for at least two categories per prognostic factor had to be reported. Prognostic factors were divided into patient-related, tooth-related, or treatment-related factors. The reported percentages of healed teeth ("the healed rate") were pooled per category. The statistical method of Mantel-Haenszel was applied to estimate the odds ratios and their 95% confidence intervals. RESULTS: With regard to tooth-related factors, the following categories were significantly associated with higher healed rates: cases without preoperative pain or signs, cases with good density of root canal filling, and cases with absence or size < or = 5 mm of periapical lesion. With regard to treatment-related factors, cases treated with the use of an endoscope tended to have higher healed rates than cases without the use of an endoscope. CONCLUSIONS: Although the clinician may be able to control treatment-related factors (by choosing a certain technique), patient- and tooth-related factors are usually beyond the surgeon's power. Nevertheless, patient- and tooth-related factors should be considered as important prognostic determinants when planning or weighing apical surgery against treatment alternatives.

Effects of glucosamine, chondroitin, or placebo in patients with osteoarthritis of hip or knee: network meta-analysis

OBJECTIVE: To determine the effect of glucosamine, chondroitin, or the two in combination on joint pain and on radiological progression of disease in osteoarthritis of the hip or knee. Design Network meta-analysis. Direct comparisons within trials were combined with indirect evidence from other trials by using a Bayesian model that allowed the synthesis of multiple time points. MAIN OUTCOME MEASURE: Pain intensity. Secondary outcome was change in minimal width of joint space. The minimal clinically important difference between preparations and placebo was prespecified at -0.9 cm on a 10 cm visual analogue scale. DATA SOURCES: Electronic databases and conference proceedings from inception to June 2009, expert contact, relevant websites. Eligibility criteria for selecting studies Large scale randomised controlled trials in more than 200 patients with osteoarthritis of the knee or hip that compared glucosamine, chondroitin, or their combination with placebo or head to head. Results 10 trials in 3803 patients were included. On a 10 cm visual analogue scale the overall difference in pain intensity compared with placebo was -0.4 cm (95% credible interval -0.7 to -0.1 cm) for glucosamine, -0.3 cm (-0.7 to 0.0 cm) for chondroitin, and -0.5 cm (-0.9 to 0.0 cm) for the combination. For none of the estimates did the 95% credible intervals cross the boundary of the minimal clinically important difference. Industry independent trials showed smaller effects than commercially funded trials (P=0.02 for interaction). The differences in changes in minimal width of joint space were all minute, with 95% credible intervals overlapping zero. Conclusions Compared with placebo, glucosamine, chondroitin, and their combination do not reduce joint pain or have an impact on narrowing of joint space. Health authorities and health insurers should not cover the costs of these preparations, and new prescriptions to patients who have not received treatment should be discouraged.

Sacral neuromodulation for neurogenic lower urinary tract dysfunction: systematic review and meta-analysis

Context Treatment of neurogenic lower urinary tract dysfunction (LUTD) is a challenge, because conventional therapies often fail. Sacral neuromodulation (SNM) has become a well-established therapy for refractory non-neurogenic LUTD, but its value in patients with a neurologic cause is unclear. Objective To assess the efficacy and safety of SNM for neurogenic LUTD. Evidence acquisition Studies were identified by electronic search of PubMed, EMBASE, and ScienceDirect (on 15 April 2010) and hand search of reference lists and review articles. SNM articles were included if they reported on efficacy and/or safety of tested and/or permanently implanted patients suffering from neurogenic LUTD. Two reviewers independently selected studies and extracted data. Study estimates were pooled using Bayesian random-effects meta-analysis. Evidence synthesis Of the 26 independent studies (357 patients) included, the evidence level ranged from 2b to 4 according to the Oxford Centre for Evidence-Based Medicine. Half (n = 13) of the included studies reported data on both test phase and permanent SNM; the remaining studies were confined to test phase (n = 4) or permanent SNM (n = 9). The pooled success rate was 68% for the test phase (95% credibility interval [CrI], 50–87) and 92% (95% CrI, 81–98%) for permanent SNM, with a mean follow-up of 26 mo. The pooled adverse event rate was 0% (95% CrI, 0–2%) for the test phase and 24% (95% CrI, 6–48%) for permanent SNM. Conclusions There is evidence indicating that SNM may be effective and safe for the treatment of patients with neurogenic LUTD. However, the number of investigated patients is low with high between-study heterogeneity, and there is a lack of randomised, controlled trials. Thus, well-designed, adequately powered studies are urgently needed before more widespread use of SNM for neurogenic LUTD can be recommended.

Mobile phone technologies and advanced data analysis towards the enhancement of diabetes self-management

Advances in the area of mobile and wireless communication for healthcare (m-Health) along with the improvements in information science allow the design and development of new patient-centric models for the provision of personalised healthcare services, increase of patient independence and improvement of patient's self-control and self-management capabilities. This paper comprises a brief overview of the m-Health applications towards the self-management of individuals with diabetes mellitus and the enhancement of their quality of life. Furthermore, the design and development of a mobile phone application for Type 1 Diabetes Mellitus (T1DM) self-management is presented. The technical evaluation of the application, which permits the management of blood glucose measurements, blood pressure measurements, insulin dosage, food/drink intake and physical activity, has shown that the use of the mobile phone technologies along with data analysis methods might improve the self-management of T1DM.

Efficacy of communication skills training courses in oncology: a systematic review and meta-analysis

Objective: Group training in communication skills [communication skills training (CST)] has become partly mandatory for oncology staff. However, so far, a comprehensive meta-analysis on the efficacy is lacking. Design: Included studies either compare the efficacy of a specific training with a control group or look at the additional effect of booster sessions on communication behaviour, attitudes or patient outcomes. Methods: Four electronic databases were searched up to July 2008 without language restriction, and reference lists of earlier reviews were screened. Effect sizes (ESs) were extracted and pooled in random effects meta-analyses. Results: We included 13 trials (three non-randomised), 10 with no specific intervention in the control group. Meta-analysis showed a moderate effect of CST on communication behaviour ES = 0.54. Three trials compared basic training courses with more extensive training courses and showed a small additional effect on communication skills ES = 0.37. Trials investigating participants' attitudes ES = 0.35 and patient outcomes ES = 0.13 (trend) confirmed this effect. Conclusions: Training health professionals by CST is a promising approach to change communication behaviour and attitudes. Patients might also benefit from specifically trained health professionals but strong studies are lacking. However, feasibility and economic aspects have to be kept in mind when considering providing a training of optimal length.

Association between variants of the leptin receptor gene (LEPR) and overweight: a systematic review and an analysis of the CoLaus study

Background Three non-synonymous single nucleotide polymorphisms (Q223R, K109R and K656N) of the leptin receptor gene (LEPR) have been tested for association with obesity-related outcomes in multiple studies, showing inconclusive results. We performed a systematic review and meta-analysis on the association of the three LEPR variants with BMI. In addition, we analysed 15 SNPs within the LEPR gene in the CoLaus study, assessing the interaction of the variants with sex. Methodology/Principal Findings We searched electronic databases, including population-based studies that investigated the association between LEPR variants Q223R, K109R and K656N and obesity- related phenotypes in healthy, unrelated subjects. We furthermore performed meta-analyses of the genotype and allele frequencies in case-control studies. Results were stratified by SNP and by potential effect modifiers. CoLaus data were analysed by logistic and linear regressions and tested for interaction with sex. The meta-analysis of published data did not show an overall association between any of the tested LEPR variants and overweight. However, the choice of a BMI cut-off value to distinguish cases from controls was crucial to explain heterogeneity in Q223R. Differences in allele frequencies across ethnic groups are compatible with natural selection of derived alleles in Q223R and K109R and of the ancient allele in K656N in Asians. In CoLaus, the rs10128072, rs3790438 and rs3790437 variants showed interaction with sex for their association with overweight, waist circumference and fat mass in linear regressions. Conclusions Our systematic review and analysis of primary data from the CoLaus study did not show an overall association between LEPR SNPs and overweight. Most studies were underpowered to detect small effect sizes. A potential effect modification by sex, population stratification, as well as the role of natural selection should be addressed in future genetic association studies.

Varying spin state composition by the choice of capping ligand in a family of molecular chains: detailed analysis of magnetic properties of chromium(III) horseshoes

We report a detailed physical analysis on a family of isolated, antiferro-magnetically (AF) coupled, chromium(III) finite chains, of general formula (Cr(RCO(2))(2)F)(n) where the chain length n = 6 or 7. Additionally, the chains are capped with a selection of possible terminating ligands, including hfac (= 1,1,1,5,5,5-hexafluoropentane-2,4-dionate(1-)), acac (= pentane-2,4-dionate(1-)) or (F)(3). Measurements by inelastic neutron scattering (INS), magnetometery and electron paramagnetic resonance (EPR) spectroscopy have been used to study how the electronic properties are affected by n and capping ligand type. These comparisons allowed the subtle electronic effects the choice of capping ligand makes for odd member spin 3/2 ground state and even membered spin 0 ground state chains to be investigated. For this investigation full characterisation of physical properties have been performed with spin Hamiltonian parameterisation, including the determination of Heisenberg exchange coupling constants and single ion axial and rhombic anisotropy. We reveal how the quantum spin energy levels of odd or even membered chains can be modified by the type of capping ligand terminating the chain. Choice of capping ligands enables Cr-Cr exchange coupling to be adjusted by 0, 4 or 24%, relative to Cr-Cr exchange coupling within the body of the chain, by the substitution of hfac, acac or (F)(3) capping ligands to the ends of the chain, respectively. The manipulation of quantum spin levels via ligands which play no role in super-exchange, is of general interest to the practise of spin Hamilton modelling, where such second order effects are generally not considered of relevance to magnetic properties.

782 consecutive construction work accidents: who is at risk? A 10-year analysis from a Swiss university hospital trauma unit

BACKGROUND: Mortality and morbidity are particularly high in the building industry. The annual rate of non-fatal occupational accidents in Switzerland is 1,133 per 100,000 inhabitants. METHODS: Retrospective analysis of the electronic database of a university emergency centre. Between 2001 and 2011, 782 occupational accidents to construction workers were recorded and analysed using specific demographic and medical keywords. RESULTS: Most patients were aged 30-39 (30.4%). 66.4% of the injured workers were foreigners. This is almost twice as high as the overall proportion of foreigners in Switzerland or in the Swiss labour market. 16% of the Swiss construction workers and 8% of the foreign construction workers suffered a severe injury with ISS >15. There was a trend for workers aged 60 and above to suffer an accident with a high ISS (p = 0.089). CONCLUSIONS: As in other European countries, most patients were in their thirties. Older construction workers suffered fewer injuries, although these tended to be more severe. The injuries were evenly distributed through the working days of the week. A special effort should be made that current health and safety measures are understood and applied by foreign and older construction workers.

Can falls risk prediction tools correctly identify fall-prone elderly rehabilitation inpatients? A systematic review and meta-analysis

Background Falls of elderly people may cause permanent disability or death. Particularly susceptible are elderly patients in rehabilitation hospitals. We systematically reviewed the literature to identify falls prediction tools available for assessing elderly inpatients in rehabilitation hospitals. Methods and Findings We searched six electronic databases using comprehensive search strategies developed for each database. Estimates of sensitivity and specificity were plotted in ROC space graphs and pooled across studies. Our search identified three studies which assessed the prediction properties of falls prediction tools in a total of 754 elderly inpatients in rehabilitation hospitals. Only the STRATIFY tool was assessed in all three studies; the other identified tools (PJC-FRAT and DOWNTON) were assessed by a single study. For a STRATIFY cut-score of two, pooled sensitivity was 73% (95%CI 63 to 81%) and pooled specificity was 42% (95%CI 34 to 51%). An indirect comparison of the tools across studies indicated that the DOWNTON tool has the highest sensitivity (92%), while the PJC-FRAT offers the best balance between sensitivity and specificity (73% and 75%, respectively). All studies presented major methodological limitations. Conclusions We did not identify any tool which had an optimal balance between sensitivity and specificity, or which were clearly better than a simple clinical judgment of risk of falling. The limited number of identified studies with major methodological limitations impairs sound conclusions on the usefulness of falls risk prediction tools in geriatric rehabilitation hospitals.

Analysis and Prediction of Transient Opacity Spikes Using Dimensional Modeling

Dimensional modeling, GT-Power in particular, has been used for two related purposes-to quantify and understand the inaccuracies of transient engine flow estimates that cause transient smoke spikes and to improve empirical models of opacity or particulate matter used for engine calibration. It has been proposed by dimensional modeling that exhaust gas recirculation flow rate was significantly underestimated and volumetric efficiency was overestimated by the electronic control module during the turbocharger lag period of an electronically controlled heavy duty diesel engine. Factoring in cylinder-to-cylinder variation, it has been shown that the electronic control module estimated fuel-Oxygen ratio was lower than actual by up to 35% during the turbocharger lag period but within 2% of actual elsewhere, thus hindering fuel-Oxygen ratio limit-based smoke control. The dimensional modeling of transient flow was enabled with a new method of simulating transient data in which the manifold pressures and exhaust gas recirculation system flow resistance, characterized as a function of exhaust gas recirculation valve position at each measured transient data point, were replicated by quasi-static or transient simulation to predict engine flows. Dimensional modeling was also used to transform the engine operating parameter model input space to a more fundamental lower dimensional space so that a nearest neighbor approach could be used to predict smoke emissions. This new approach, intended for engine calibration and control modeling, was termed the "nonparametric reduced dimensionality" approach. It was used to predict federal test procedure cumulative particulate matter within 7% of measured value, based solely on steady-state training data. Very little correlation between the model inputs in the transformed space was observed as compared to the engine operating parameter space. This more uniform, smaller, shrunken model input space might explain how the nonparametric reduced dimensionality approach model could successfully predict federal test procedure emissions when roughly 40% of all transient points were classified as outliers as per the steady-state training data.

Body-mass index and incidence of cancer: a systematic review and meta-analysis of prospective observational studies

BACKGROUND: Excess bodyweight, expressed as increased body-mass index (BMI), is associated with the risk of some common adult cancers. We did a systematic review and meta-analysis to assess the strength of associations between BMI and different sites of cancer and to investigate differences in these associations between sex and ethnic groups. METHODS: We did electronic searches on Medline and Embase (1966 to November 2007), and searched reports to identify prospective studies of incident cases of 20 cancer types. We did random-effects meta-analyses and meta-regressions of study-specific incremental estimates to determine the risk of cancer associated with a 5 kg/m2 increase in BMI. FINDINGS: We analysed 221 datasets (141 articles), including 282,137 incident cases. In men, a 5 kg/m2 increase in BMI was strongly associated with oesophageal adenocarcinoma (RR 1.52, p<0.0001) and with thyroid (1.33, p=0.02), colon (1.24, p<0.0001), and renal (1.24, p <0.0001) cancers. In women, we recorded strong associations between a 5 kg/m2 increase in BMI and endometrial (1.59, p<0.0001), gallbladder (1.59, p=0.04), oesophageal adenocarcinoma (1.51, p<0.0001), and renal (1.34, p<0.0001) cancers. We noted weaker positive associations (RR <1.20) between increased BMI and rectal cancer and malignant melanoma in men; postmenopausal breast, pancreatic, thyroid, and colon cancers in women; and leukaemia, multiple myeloma, and non-Hodgkin lymphoma in both sexes. Associations were stronger in men than in women for colon (p<0.0001) cancer. Associations were generally similar in studies from North America, Europe and Australia, and the Asia-Pacific region, but we recorded stronger associations in Asia-Pacific populations between increased BMI and premenopausal (p=0.009) and postmenopausal (p=0.06) breast cancers. INTERPRETATION: Increased BMI is associated with increased risk of common and less common malignancies. For some cancer types, associations differ between sexes and populations of different ethnic origins. These epidemiological observations should inform the exploration of biological mechanisms that link obesity with cancer.

Drug eluting and bare metal stents in people with and without diabetes: collaborative network meta-analysis

Objective To compare the effectiveness and safety of three types of stents (sirolimus eluting, paclitaxel eluting, and bare metal) in people with and without diabetes mellitus. Design Collaborative network meta-analysis. Data sources Electronic databases (Medline, Embase, the Cochrane Central Register of Controlled Trials), relevant websites, reference lists, conference abstracts, reviews, book chapters, and proceedings of advisory panels for the US Food and Drug Administration. Manufacturers and trialists provided additional data. Review methods Network meta-analysis with a mixed treatment comparison method to combine direct within trial comparisons between stents with indirect evidence from other trials while maintaining randomisation. Overall mortality was the primary safety end point, target lesion revascularisation the effectiveness end point. Results 35 trials in 3852 people with diabetes and 10 947 people without diabetes contributed to the analyses. Inconsistency of the network was substantial for overall mortality in people with diabetes and seemed to be related to the duration of dual antiplatelet therapy (P value for interaction 0.02). Restricting the analysis to trials with a duration of dual antiplatelet therapy of six months or more, inconsistency was reduced considerably and hazard ratios for overall mortality were near one for all comparisons in people with diabetes: sirolimus eluting stents compared with bare metal stents 0.88 (95% credibility interval 0.55 to 1.30), paclitaxel eluting stents compared with bare metal stents 0.91 (0.60 to 1.38), and sirolimus eluting stents compared with paclitaxel eluting stents 0.95 (0.63 to 1.43). In people without diabetes, hazard ratios were unaffected by the restriction. Both drug eluting stents were associated with a decrease in revascularisation rates compared with bare metal stents in people both with and without diabetes. Conclusion In trials that specified a duration of dual antiplatelet therapy of six months or more after stent implantation, drug eluting stents seemed safe and effective in people both with and without diabetes.