Novel Synthetic Procedures in Organocatalysis

The main aim of my PhD project was the design and the synthesis of new pyrrolidine organocatalysts. New effective ferrocenyl pyrrolidine catalysts, active in benchmark organocatalytic reactions, has been developed. The ferrocenyl moiety, in combination with simple ethyl chains, is capable of fixing the enamine conformation addressing the approach trajectory of the nucleophile in the reaction. The results obtained represent an interesting proof-of-concept, showing for the first time the remarkable effectiveness of the ferrocenyl moiety in providing enantioselectivity through conformational selection. This approach could be viably employed in the rational design of ligands for metal or organocatalysts. Other hindered secondary amines has been prepared from alkylation of acyclic chiral nitroderivatives with alcohols in a highly diastereoselective fashion, giving access to functionalized, useful organocatalytic chiral pyrrolidines. A family of new pyrrolidines bearing sterogenic centers and functional groups can be readily accessible by this methodology. The second purpose of the project was to study in deep the reactivity of stabilized carbocations in new metal-free and organocatalytic reactions. By taking advantage of the results from the kinetic studies described by Mayr, a simple and effective procedure for the direct formylation of aryltetrafluoroborate salts, has been development. The coupling of a range of aryl- and heteroaryl- trifluoroborate salts with 1,3-benzodithiolylium tetrafluoroborate, has been attempted in moderate to good yields. Finally, a simple and general methodology for the enamine-mediated enantioselective α-alkylation of α-substituted aldehydes with 1,3-benzodithiolylium tetrafluoroborate has been reported. The introduction of the benzodithiole moiety permit the installation of different functional groups due to its chameleonic behaviour.

Bioconjugation and synthetic approach towards enantioenriched gem-difluoromethylene compounds through carbenium ions

Bioconjugation of peptides and asymmetric synthesis of gem-difluoromethylene compounds are areas of the modern organic chemistry for which mild and selective methods continue to be developed. This thesis reports new methodologies for these two areas based on the use of stabilized carbenium ions. The reaction that makes the bioconjugation of peptides possible takes place via the direct nucleophilic substitution of alcohols and is driven by the spontaneous formation of stabilized carbenium ions in water. By reacting with the thiol group of cysteine in very mild conditions and with a high selectivity, these carbenium ions allow the site-specific ligation of polypeptides containing cysteine and their covalent derivatization with functionalized probes. The ligation of the indole ring of tryptophan, an emerging target in bioconjugation, is also shown and takes place in the same conditions. The second area investigated is the challenging access to optically active gem-difluoromethylene compounds. We describe a methodology relying on the synthesis of enantioenriched 1,3-benzodithioles intermediates that are shown to be precursors of the corresponding gem-difluoromethylene analogues by oxidative desulfurization-fluorination. This synthesis takes advantage of the highly enantioselective organocatalytic α-alkylation of aldehydes with the benzodithiolylium ion and of the wide possibilities of synthetic transformations offered by the 1,3-benzodithiole group. This approach allows the asymmetric access to complex gem-difluoromethylene compounds through a late-stage fluorination step, thus avoiding the use of fluorinated building blocks.

The Swiss IMRT dosimetry intercomparison using a thorax phantom

In 2008, a national intensity modulated radiation therapy (IMRT) dosimetry intercomparison was carried out for all 23 radiation oncology institutions in Switzerland. It was the aim to check the treatment chain focused on the planning, dose calculation, and irradiation process.

Contamination of Alpine snow and ice at Colle Gnifetti, Swiss/Italian Alps, from nuclear weapons tests

Plutonium is present in the environment as a consequence of atmospheric nuclear tests, nuclear weapons production and industrial releases over the past 50 years. To study temporal trends, a high resolution Pu record was obtained by analyzing 52 discrete samples of an alpine firn/ice core from Colle Gnifetti (Monte Rosa, 4450 m a.s.l.), dating from 1945 to 1990. The 239Pu signal was recorded directly, without decontamination or preconcentration steps, using an Inductively Coupled Plasma - Sector Field Mass Spectrometer (ICP-SFMS) equipped with an high efficiency sample introduction system, thus requiring much less sample preparation than previously reported methods. The 239Pu profile reflects the three main periods of atmospheric nuclear weapons testing: the earliest peak lasted from 1954/55 to 1958 and was caused by the first testing period reaching a maximum in 1958. Despite a temporary halt of testing in 1959/60, the Pu concentration decreased only by half with respect to the 1958 peak due to long atmospheric residence times. In 1961/62 Pu concentrations rapidly increased reaching a maximum in 1963, which was about 40% more intense than the 1958 peak. After the signing of the "Limited Test Ban Treaty" between USA and USSR in 1964, Pu deposition decreased very sharply reaching a minimum in 1967. The third period (1967-1975) is characterized by irregular Pu concentrations with smaller peaks (about 20-30% of the 1964 peak) which might be related to the deposition of Saharan dust contaminated by the French nuclear tests of the 1960s. The data presented are in very good agreement with Pu profiles previously obtained from the Col du Dome ice core (by multi-collector ICP-MS) and Belukha ice core (by Accelerator Mass Spectrometry, AMS). Although a semi-quantitative method was employed here, the results are quantitatively comparable to previously published results.

Change in dust variability in the Atlantic sector of Antarctica at the end of the last deglaciation

We present a Rare Earth Elements (REE) record determined on the EPICA ice core drilled at Dronning Maud Land (EDML) in the Atlantic sector of the East Antarctic Plateau. The record covers the transition from the last glacial stage (LGS) to the early Holocene (26 600–7500 yr BP) at decadal to centennial resolution. Additionally, samples from potential source areas (PSAs) for Antarctic dust were analyzed for their REE characteristics. The dust provenance is discussed by comparing the REE fingerprints in the ice core and the PSA samples. We find a shift in variability in REE composition at ~15 000 yr BP in the ice core samples. Before 15 000 yr BP, the dust composition is very uniform and its provenance was most certainly dominated by a South American source. After 15 000 yr BP, multiple sources such as Australia and New Zealand become relatively more important, although South America remains the major dust source. A similar change in the dust characteristics was observed in the EPICA Dome C ice core at around ~15 000 yr BP, accompanied by a shift in the REE composition, thus suggesting a change of atmospheric circulation in the Southern Hemisphere.

Liver repopulation with bone marrow derived cells improves the metabolic disorder in the Gunn rat

BACKGROUND: Reversible ischaemia/reperfusion (I/R) liver injury has been used to induce engraftment and hepatic parenchymal differentiation of exogenous beta2-microglubulin(-)/Thy1(+) bone marrow derived cells. AIM: To test the ability of this method of hepatic parenchymal repopulation, theoretically applicable to clinical practice, to correct the metabolic disorder in a rat model of congenital hyperbilirubinaemia. METHODS AND RESULTS: Analysis by confocal laser microscopy of fluorescence labelled cells and by immunohistochemistry for beta2-microglubulin, 72 hours after intraportal delivery, showed engraftment of infused cells in liver parenchyma of rats with I/R, but not in control animals with non-injured liver. Transplantation of bone marrow derived cells obtained from GFP-transgenic rats into Lewis rats resulted in the presence of up to 20% of GFP positive hepatocytes in I/R liver lobes after one month. The repopulation rate was proportional to the number of transplanted cells. Infusion of GFP negative bone marrow derived cells into GFP positive transgenic rats resulted in the appearance of GFP negative hepatocytes, suggesting that the main mechanism underlying parenchymal repopulation was differentiation rather than cell fusion. Transplantation of wild type bone marrow derived cells into hyperbilirubinaemic Gunn rats with deficient bilirubin conjugation after I/R damage resulted in 30% decrease in serum bilirubin, the appearance of bilirubin conjugates in bile, and the expression of normal UDP-glucuronyltransferase enzyme evaluated by polymerase chain reaction. CONCLUSIONS: I/R injury induced hepatic parenchymal engraftment and differentiation into hepatocyte-like cells of bone marrow derived cells. Transplantation of bone marrow derived cells from non-affected animals resulted in the partial correction of hyperbilirubinaemia in the Gunn rat.

Testing the GlaaS algorithm for dose measurements on low- and high-energy photon beams using an amorphous silicon portal imager

The GLAaS algorithm for pretreatment intensity modulation radiation therapy absolute dose verification based on the use of amorphous silicon detectors, as described in Nicolini et al. [G. Nicolini, A. Fogliata, E. Vanetti, A. Clivio, and L. Cozzi, Med. Phys. 33, 2839-2851 (2006)], was tested under a variety of experimental conditions to investigate its robustness, the possibility of using it in different clinics and its performance. GLAaS was therefore tested on a low-energy Varian Clinac (6 MV) equipped with an amorphous silicon Portal Vision PV-aS500 with electronic readout IAS2 and on a high-energy Clinac (6 and 15 MV) equipped with a PV-aS1000 and IAS3 electronics. Tests were performed for three calibration conditions: A: adding buildup on the top of the cassette such that SDD-SSD = d(max) and comparing measurements with corresponding doses computed at d(max), B: without adding any buildup on the top of the cassette and considering only the intrinsic water-equivalent thickness of the electronic portal imaging devices device (0.8 cm), and C: without adding any buildup on the top of the cassette but comparing measurements against doses computed at d(max). This procedure is similar to that usually applied when in vivo dosimetry is performed with solid state diodes without sufficient buildup material. Quantitatively, the gamma index (gamma), as described by Low et al. [D. A. Low, W. B. Harms, S. Mutic, and J. A. Purdy, Med. Phys. 25, 656-660 (1998)], was assessed. The gamma index was computed for a distance to agreement (DTA) of 3 mm. The dose difference deltaD was considered as 2%, 3%, and 4%. As a measure of the quality of results, the fraction of field area with gamma larger than 1 (%FA) was scored. Results over a set of 50 test samples (including fields from head and neck, breast, prostate, anal canal, and brain cases) and from the long-term routine usage, demonstrated the robustness and stability of GLAaS. In general, the mean values of %FA remain below 3% for deltaD equal or larger than 3%, while they are slightly larger for deltaD = 2% with %FA in the range from 3% to 8%. Since its introduction in routine practice, 1453 fields have been verified with GLAaS at the authors' institute (6 MV beam). Using a DTA of 3 mm and a deltaD of 4% the authors obtained %FA = 0.9 +/- 1.1 for the entire data set while, stratifying according to the dose calculation algorithm, they observed: %FA = 0.7 +/- 0.9 for fields computed with the analytical anisotropic algorithm and %FA = 2.4 +/- 1.3 for pencil-beam based fields with a statistically significant difference between the two groups. If data are stratified according to field splitting, they observed %FA = 0.8 +/- 1.0 for split fields and 1.0 +/- 1.2 for nonsplit fields without any significant difference.

The exchange of radiotherapy data as part of an electronic patient-referral system

PURPOSE: To describe the implementation and use of an electronic patient-referral system as an aid to the efficient referral of patients to a remote and specialized treatment center. METHODS AND MATERIALS: A system for the exchange of radiotherapy data between different commercial planning systems and a specially developed planning system for proton therapy has been developed through the use of the PAPYRUS diagnostic image standard as an intermediate format. To ensure the cooperation of the different TPS manufacturers, the number of data sets defined for transfer has been restricted to the three core data sets of CT, VOIs, and three-dimensional dose distributions. As a complement to the exchange of data, network-wide application-sharing (video-conferencing) technologies have been adopted to provide methods for the interactive discussion and assessment of treatments plans with one or more partner clinics. RESULTS: Through the use of evaluation plans based on the exchanged data, referring clinics can accurately assess the advantages offered by proton therapy on a patient-by-patient basis, while the practicality or otherwise of the proposed treatments can simultaneously be assessed by the proton therapy center. Such a system, along with the interactive capabilities provided by video-conferencing methods, has been found to be an efficient solution to the problem of patient assessment and selection at a specialized treatment center, and is a necessary first step toward the full electronic integration of such centers with their remotely situated referral centers.

Renal artery assessment with nonenhanced steady-state free precession versus contrast-enhanced MR angiography

PURPOSE: To prospectively assess the diagnostic accuracy of nonenhanced three-dimensional (3D) steady-state free precession (SSFP) magnetic resonance (MR) angiography for detection of renal artery stenosis (RAS), with breath-hold contrast material-enhanced MR angiography performed as the reference standard. MATERIALS AND METHODS: The study was local ethics committee approved; all patients gave written informed consent. Fifty-three patients (30 male, 23 female; mean age, 58 years) with arterial hypertension and suspected of having RAS were examined with 1.5-T 3D SSFP renal MR angiography. Stenosis grade, maximal visible vessel length, and subjective image quality were compared. Sensitivity, specificity, accuracy, and negative predictive value (NPV) were calculated on artery-by-artery and patient-by-patient bases. The significance of the results was assessed with the paired two-sided t test for continuous variables and with the marginal homogeneity test for categorical variables. Cohen kappa statistics were used to estimate interobserver agreement. RESULTS: One hundred eight renal arteries with 20 significant (>or=50%) stenoses were detected with contrast-enhanced MR angiography. At artery-by-artery analysis, sensitivity, specificity, accuracy, and NPV of nonenhanced SSFP MR angiography for RAS detection were 100%, 93%, 94%, and 100%, respectively, for observer 1 and 95%, 95%, 95%, and 99%, respectively, for observer 2. Corresponding patient-by-patient values were 100%, 92%, 94%, and 100%, respectively, for observer 1 and 100%, 95%, 96%, and 100%, respectively, for observer 2. Overestimation of stenosis grade with SSFP MR angiography resulted in six and four false-positive findings for readers 1 and 2, respectively. Mean maximal visible lengths of the renal arteries were 69.9 mm at contrast-enhanced MR angiography and 61.1 mm at SSFP MR angiography (P<.001). Both techniques yielded good to excellent image quality. CONCLUSION: Slab-selective inversion-prepared 3D SSFP MR angiography had high sensitivity, specificity, accuracy, and NPV for RAS detection, without the need for contrast material. However, RAS severity was overestimated in some patients.

Iron fluxes to Talos Dome, Antarctica, over the past 200 kyr

Atmospheric fluxes of iron (Fe) over the past 200 kyr are reported for the coastal Antarctic Talos Dome ice core, based on acid leachable Fe concentrations. Fluxes of Fe to Talos Dome were consistently greater than those at Dome C, with the greatest difference observed during interglacial climates. We observe different Fe flux trends at Dome C and Talos Dome during the deglaciation and early Holocene, attributed to a combination of deglacial activation of dust sources local to Talos Dome and the reorganisation of atmospheric transport pathways with the retreat of the Ross Sea ice shelf. This supports similar findings based on dust particle sizes and fluxes and Rare Earth Element fluxes. We show that Ca and Fe should not be used as quantitative proxies for mineral dust, as they all demonstrate different deglacial trends at Talos Dome and Dome C. Considering that a 20 ppmv decrease in atmospheric CO2 at the coldest part of the last glacial maximum occurs contemporaneously with the period of greatest Fe and dust flux to Antarctica, we confirm that the maximum contribution of aeolian dust deposition to Southern Ocean sequestration of atmospheric CO2 is approximately 20 ppmv.�

Low-frequency drug-resistant HIV-1 and risk of virological failure to first-line NNRTI-based ART: a multicohort European case-control study using centralized ultrasensitive 454 pyrosequencing.

OBJECTIVES It is still debated if pre-existing minority drug-resistant HIV-1 variants (MVs) affect the virological outcomes of first-line NNRTI-containing ART. METHODS This Europe-wide case-control study included ART-naive subjects infected with drug-susceptible HIV-1 as revealed by population sequencing, who achieved virological suppression on first-line ART including one NNRTI. Cases experienced virological failure and controls were subjects from the same cohort whose viraemia remained suppressed at a matched time since initiation of ART. Blinded, centralized 454 pyrosequencing with parallel bioinformatic analysis in two laboratories was used to identify MVs in the 1%-25% frequency range. ORs of virological failure according to MV detection were estimated by logistic regression. RESULTS Two hundred and sixty samples (76 cases and 184 controls), mostly subtype B (73.5%), were used for the analysis. Identical MVs were detected in the two laboratories. 31.6% of cases and 16.8% of controls harboured pre-existing MVs. Detection of at least one MV versus no MVs was associated with an increased risk of virological failure (OR = 2.75, 95% CI = 1.35-5.60, P = 0.005); similar associations were observed for at least one MV versus no NRTI MVs (OR = 2.27, 95% CI = 0.76-6.77, P = 0.140) and at least one MV versus no NNRTI MVs (OR = 2.41, 95% CI = 1.12-5.18, P = 0.024). A dose-effect relationship between virological failure and mutational load was found. CONCLUSIONS Pre-existing MVs more than double the risk of virological failure to first-line NNRTI-based ART.