Design of Optical Systems With Extended Depth of Field: an Educational Approach to Wavefront Coding Techniques

A practical activity designed to introduce wavefront coding techniques as a method to extend the depth of field in optical systems is presented. The activity is suitable for advanced undergraduate students since it combines different topics in optical engineering such as optical system design, aberration theory, Fourier optics, and digital image processing. This paper provides the theoretical background and technical information for performing the experiment. The proposed activity requires students able to develop a wide range of skills since they are expected to deal with optical components, including spatial light modulators, and develop scripts to perform some calculations.

Design of surface forces apparatus for tribology studies combined with nonlinear optical spectroscopy

We describe the design, calibration, and performance of surface forces apparatus with the capability of illumination of the contact interface for spectroscopic investigation using optical techniques. The apparatus can be placed in the path of a Nd-YAG laser for studies of the linear response or the second harmonic and sum-frequency generation from a material confined between the two surfaces. In addition to the standard fringes of equal chromatic order technique, which we have digitized for accurate and fast analysis, the distance of separation can be measured with a fiber-optic interferometer during spectroscopic measurements (2 Å resolution and 10 ms response time). The sample approach is accomplished through application of a motor drive, piezoelectric actuator, or electromagnetic lever deflection for variable degrees of range, sensitivity, and response time. To demonstrate the operation of the instrument, the stepwise expulsion of discrete layers of octamethylcyclotetrasiloxane from the contact is shown. Lateral forces may also be studied by using piezoelectric bimorphs to induce and direct the motion of one surface.

Rational design of 4-aryl-1,2,3-triazoles for indoleamine 2,3-dioxygenase 1 inhibition.

Indoleamine 2,3-dioxygenase 1 (IDO1) is an important therapeutic target for the treatment of diseases such as cancer that involve pathological immune escape. Starting from the scaffold of our previously discovered IDO1 inhibitor 4-phenyl-1,2,3-triazole, we used computational structure-based methods to design more potent ligands. This approach yielded highly efficient low molecular weight inhibitors, the most active being of nanomolar potency both in an enzymatic and in a cellular assay, while showing no cellular toxicity and a high selectivity for IDO1 over tryptophan 2,3-dioxygenase (TDO). A quantitative structure-activity relationship based on the electrostatic ligand-protein interactions in the docked binding modes and on the quantum chemically derived charges of the triazole ring demonstrated a good explanatory power for the observed activities.

Optimal priming of poxvirus vector (NYVAC)-based HIV vaccine regimens requires 3 DNA injections. Results of the EV03/ANRS Vac20 Phase I/II Trial

Background: Two or three DNA primes have been used in previous smaller clinical trials, but the number required for optimal priming of viral vectors has never been assessed in adequately powered clinical trials. The EV03/ANRS Vac20 phase I/II trial investigated this issue using the DNA prime/poxvirus NYVAC boost combination, both expressing a common HIV-1 clade C immunogen consisting of Env and Gag-Pol-Nef polypeptide. Methods: 147 healthy volunteers were randomly allocated through 8 European centres to either 3xDNA plus 1xNYVAC (weeks 0, 4, 8 plus 24; n¼74) or to 2xDNA plus 2xNYVAC (weeks 0, 4 plus 20, 24; n¼73), stratified by geographical region and sex. T cell responses were quantified using the interferon g Elispot assay and 8 peptide pools; samples from weeks 0, 26 and 28 (time points for primary immunogenicity endpoint), 48 and 72 were considered for this analysis. Results: 140 of 147 participants were evaluable at weeks 26 and/ or 28. 64/70 (91%) in the 3xDNA arm compared to 56/70 (80%) in the 2xDNA arm developed a T cell response (P¼0.053). 26 (37%) participants of the 3xDNA arm developed a broader T cell response (Env plus at least to one of the Gag, Pol, Nef peptide pools) versus 15 (22%) in the 2xDNA arm (P¼0.047). At week 26, the overall magnitude of responses was also higher in the 3xDNA than in the 2xDNA arm (similar at week 28), with a median of 545 versus 328 SFUs/106 cells at week 26 (P<0.001). Preliminary overall evaluation showed that participants still developed T-cell response at weeks 48 (78%, n¼67) and 72 (70%, n¼66). Conclusion: This large clinical trial demonstrates that optimal priming of poxvirus-based vaccine regimens requires 3 DNA regimens and further confirms that the DNA/NYVAC prime boost vaccine combination is highly immunogenic and induced durable T-cell responses.

Efficacy of an adjunctive brief psychodynamic psychotherapy to usual inpatient treatment of depression: rationale and design of a randomized controlled trial.

BACKGROUND: A few recent studies have found indications of the effectiveness of inpatient psychotherapy for depression, usually of an extended duration. However, there is a lack of controlled studies in this area and to date no study of adequate quality on brief psychodynamic psychotherapy for depression during short inpatient stay exists. The present article describes the protocol of a study that will examine the relative efficacy, the cost-effectiveness and the cost-utility of adding an Inpatient Brief Psychodynamic Psychotherapy to pharmacotherapy and treatment-as-usual for inpatients with unipolar depression. METHODS/DESIGN: The study is a one-month randomized controlled trial with a two parallel group design and a 12-month naturalistic follow-up. A sample of 130 consecutive adult inpatients with unipolar depression and Montgomery-Asberg Depression Rating Scale score over 18 will be recruited. The study is carried out in the university hospital section for mood disorders in Lausanne, Switzerland. Patients are assessed upon admission, and at 1-, 3- and 12- month follow-ups. Inpatient therapy is a manualized brief intervention, combining the virtues of inpatient setting and of time-limited dynamic therapies (focal orientation, fixed duration, resource-oriented interventions). Treatment-as-usual represents the best level of practice for a minimal treatment condition usually proposed to inpatients. Final analyses will follow an intention-to-treat strategy. Depressive symptomatology is the primary outcome and secondary outcome includes measures of psychiatric symptomatology, psychosocial role functioning, and psychodynamic-emotional functioning. The mediating role of the therapeutic alliance is also examined. Allocation to treatment groups uses a stratified block randomization method with permuted block. To guarantee allocation concealment, randomization is done by an independent researcher. DISCUSSION: Despite the large number of studies on treatment of depression, there is a clear lack of controlled research in inpatient psychotherapy during the acute phase of a major depressive episode. Research on brief therapy is important to take into account current short lengths of stay in psychiatry. The current study has the potential to scientifically inform appropriate inpatient treatment. This study is the first to address the issue of the economic evaluation of inpatient psychotherapy. TRIAL REGISTRATION: Australian New Zealand Clinical Trial Registry (ACTRN12612000909820).

History and Design of Iowa's Highway Maintenance and Weighing Facilities, 2003

In June 2001, the Iowa Department of Transportation announced the imminent closure and disposal of selected highway maintenance facilities as part of cost-cutting measures mandated by the Iowa legislature, an action that was to be completed by July 31, 2001. The DOT recognized that some of these facilities might be "historical sites," which in the Iowa Code are defined as any district, site, building or structure listed on the National Register of Historic Places or identified as eligible for listing in the National Register by the State Historic Preservation Office. Section 303 of the Code requires state agencies to "enter into an agreement with the Department of Cultural Affairs [in which the SHPO is located] to ensure the proper management, maintenance and development of historical sites." The DOT saw this disposal action as an opportunity to compile information about its highway maintenance facilities that could be employed in development of a management program for historic highway maintenance facilities in the future. Subsequently, the DOT authorized a similar study of highway weigh stations.

Structural Analysis and Overlay Design of Pavements Using the Road Rater, MLR-84-3, 1986

In recent years the Iowa DOT has shifted emphasis from the construction of new roads to the maintenance and preservation of existing highways. A need has developed for analyzing pavements structurally to select the correct rehabilitation strategy and to properly design a pavement overlay if necessary. This need has been fulfilled by Road Rater testing which has been used successfully on all types of pavements to evaluate pavement and subgrade conditions and to design asphaltic concrete overlays. The Iowa Road Rater Design Method has been simplified so that it may be easily understood and used by the widely diverse groups of individuals which may be involved in pavement restoration and management. Road Rater analysis techniques have worked well to date and have been verified by pavement coring, soils sampling and testing, and pavement removal by block sampling. Void detection testing has also been performed experimentally in Iowa, and results indicate that the Road Rater can be used to locate pavement voids and that Road Rater analysis techniques are reasonably accurate. The success of Road Rater research and development has made deflection test data one of the most important pavement management inputs.

Circulating miRNAs: a new generation of anti-doping biomarkers

MicroRNAs (miRNAs) are small non-coding RNAs that regulate a variety of biological processes. Cell-free miRNAs detected in blood plasma are used as specific and sensitive markers of physiological processes and some diseases. Circulating miRNAs are highly stable in body fluids, for example plasma. Therefore, profiles of circulating miRNAs have been investigated for potential use as novel, non-invasive anti-doping biomarkers. This review describes the biological mechanisms underlying the variation of circulating miRNAs, revealing that they have great potential as a new class of biomarker for detection of doping substances. The latest developments in extraction and profiling technology, and the technical design of experiments useful for anti-doping, are also discussed. Longitudinal measurements of circulating miRNAs in the context of the athlete biological passport are proposed as an efficient strategy for the use of these new markers. The review also emphasizes potential challenges for the translation of circulating miRNAs from research into practical anti-doping applications.

Development of Preliminary Load and Resistance Factor Design of Drilled Shafts in Iowa, RB03-012, 2014

The Federal Highway Administration (FHWA) mandated utilizing the Load and Resistance Factor Design (LRFD) approach for all new bridges initiated in the United States after October 1, 2007. To achieve part of this goal, a database for Drilled Shaft Foundation Testing (DSHAFT) was developed and reported on by Garder, Ng, Sritharan, and Roling in 2012. DSHAFT is aimed at assimilating high-quality drilled shaft test data from Iowa and the surrounding regions. DSHAFT is currently housed on a project website (http://srg.cce.iastate.edu/dshaft) and contains data for 41 drilled shaft tests. The objective of this research was to utilize the DSHAFT database and develop a regional LRFD procedure for drilled shafts in Iowa with preliminary resistance factors using a probability-based reliability theory. This was done by examining current design and construction practices used by the Iowa Department of Transportation (DOT) as well as recommendations given in the American Association of State Highway and Transportation Officials (AASHTO) LRFD Bridge Design Specifications and the FHWA drilled shaft guidelines. Various analytical methods were used to estimate side resistance and end bearing of drilled shafts in clay, sand, intermediate geomaterial (IGM), and rock. Since most of the load test results obtained from O-cell do not pass the 1-in. top displacement criterion used by the Iowa DOT and the 5% of shaft diameter for top displacement criterion recommended by AASHTO, three improved procedures are proposed to generate and extend equivalent top load-displacement curves that enable the quantification of measured resistances corresponding to the displacement criteria. Using the estimated and measured resistances, regional resistance factors were calibrated following the AASHTO LRFD framework and adjusted to resolve any anomalies observed among the factors. To illustrate the potential and successful use of drilled shafts in Iowa, the design procedures of drilled shaft foundations were demonstrated and the advantages of drilled shafts over driven piles were addressed in two case studies.

Design of Piles for Integral Abutment Bridges, HR-252, 1984

More and more, integral abutment bridges are being used in place of the more traditional bridge designs with expansion releases. In this study, states which use integral abutment bridges were surveyed to determine their current practice in the design of these structures. To study piles in integral abutment bridges, a finite element program for the soil-pile system was developed (1) with materially and geometrically nonlinear, two and three dimensional beam elements and (2) with a nonlinear, Winkler soil model with vertical, horizontal, and pile tip springs. The model was verified by comparison to several analytical and experimental examples. A simplified design model for analyzing piles in integral abutment bridges is also presented. This model grew from previous analytical models and observations of pile behavior. The design model correctly describes the essential behavioral characteristics of the pile and conservatively predicts the vertical load-carrying capacity. Analytical examples are presented to illustrate the effects of lateral displacements on the ultimate load capacity of a pile. These examples include friction and end-bearing piles; steel, concrete, and timber piles; and bending about the weak, strong, and 45° axes for H piles. The effects of cyclic loading are shown for skewed and nonskewed bridges. The results show that the capacity of friction piles is not significantly affected by lateral displacements, but the capacity of end-bearing piles is reduced. Further results show that the longitudinal expansion of the bridge can introduce a vertical preload on the pile.

Maintenance and Design of Steel Abutment Piles in Iowa Bridges, TR-622, 2014

Soil consolidation and erosion caused by roadway runoff have exposed the upper portions of steel piles at the abutments of numerous bridges, leaving them susceptible to accelerated corrosion rates due to the abundance of moisture, oxygen, and chlorides at these locations. This problem is compounded by the relative inaccessibility of abutment piles for close-up inspection and repair. The objective of this study was to provide bridge owners with recommendations for effective methods of addressing corrosion of steel abutment piles in existing and future bridges A review of available literature on the performance and protection of steel piles exposed to a variety of environments was performed. Eight potential coating systems for use in protecting existing and/or new piles were selected and subjected to accelerated corrosion conditions in the laboratory. Two surface preparation methods were evaluated in the field and three coating systems were installed on three piles at an existing bridge where abutment piles had been exposed by erosion. In addition, a passive cathodic protection (CP) system using sacrificial zinc anodes was tested in the laboratory. Several trial flowable mortar mixes were evaluated for use in conjunction with the CP system. For existing abutment piles, application of a protective coating system is a promising method of mitigating corrosion. Based on its excellent performance in accelerated corrosion conditions in the laboratory on steel test specimens with SSPC-SP3, -SP6, and -SP10 surface preparations, glass flake polyester is recommended for use on existing piles. An alternative is epoxy over organic zinc rich primer. Surface preparation of existing piles should include abrasive blast cleaning to SSPC-SP6. Although additional field testing is needed, based on the results of the laboratory testing, a passive CP system could provide an effective means of protecting piles in existing bridges when combined with a pumped mortar used to fill voids between the abutment footing and soil. The addition of a corrosion inhibitor to the mortar appears to be beneficial. For new construction, shop application of thermally sprayed aluminum or glass flake polyester to the upper portion of the piles is recommended.

Randomized comparison of biodegradable polymer sirolimus-eluting stents versus durable polymer everolimus-eluting stents for percutaneous coronary revascularization: Rationale and design of the BIOSCIENCE trial.

BACKGROUND: Biodegradable polymers for release of antiproliferative drugs from metallic drug-eluting stents aim to improve long-term vascular healing and efficacy. We designed a large scale clinical trial to compare a novel thin strut, cobalt-chromium drug-eluting stent with silicon carbide-coating releasing sirolimus from a biodegradable polymer (O-SES, Orsiro; Biotronik, Bülach, Switzerland) with the durable polymer-based Xience Prime/Xpedition everolimus-eluting stent (EES) (Xience Prime/Xpedition stent, Abbott Vascular, IL) in an all-comers patient population. DESIGN: The multicenter BIOSCIENCE trial (NCT01443104) randomly assigned 2,119 patients to treatment with biodegradable polymer sirolimus-eluting stents (SES) or durable polymer EES at 9 sites in Switzerland. Patients with chronic stable coronary artery disease or acute coronary syndromes, including non-ST-elevation and ST-elevation myocardial infarction, were eligible for the trial if they had at least 1 lesion with a diameter stenosis >50% appropriate for coronary stent implantation. The primary end point target lesion failure (TLF) is a composite of cardiac death, target vessel myocardial infarction, and clinically driven target lesion revascularization within 12 months. Assuming a TLF rate of 8% at 12 months in both treatment arms and accepting 3.5% as a margin for noninferiority, inclusion of 2,060 patients would provide more than 80% power to detect noninferiority of the biodegradable polymer SES compared with the durable polymer EES at a 1-sided type I error of 0.05. Clinical follow-up will be continued through 5 years. CONCLUSION: The BIOSCIENCE trial will determine whether the biodegradable polymer SES is noninferior to the durable polymer EES with respect to TLF.

EADock : design of a new molecular docking algorithm and some of its applications

3 Summary 3. 1 English The pharmaceutical industry has been facing several challenges during the last years, and the optimization of their drug discovery pipeline is believed to be the only viable solution. High-throughput techniques do participate actively to this optimization, especially when complemented by computational approaches aiming at rationalizing the enormous amount of information that they can produce. In siiico techniques, such as virtual screening or rational drug design, are now routinely used to guide drug discovery. Both heavily rely on the prediction of the molecular interaction (docking) occurring between drug-like molecules and a therapeutically relevant target. Several softwares are available to this end, but despite the very promising picture drawn in most benchmarks, they still hold several hidden weaknesses. As pointed out in several recent reviews, the docking problem is far from being solved, and there is now a need for methods able to identify binding modes with a high accuracy, which is essential to reliably compute the binding free energy of the ligand. This quantity is directly linked to its affinity and can be related to its biological activity. Accurate docking algorithms are thus critical for both the discovery and the rational optimization of new drugs. In this thesis, a new docking software aiming at this goal is presented, EADock. It uses a hybrid evolutionary algorithm with two fitness functions, in combination with a sophisticated management of the diversity. EADock is interfaced with .the CHARMM package for energy calculations and coordinate handling. A validation was carried out on 37 crystallized protein-ligand complexes featuring 11 different proteins. The search space was defined as a sphere of 15 R around the center of mass of the ligand position in the crystal structure, and conversely to other benchmarks, our algorithms was fed with optimized ligand positions up to 10 A root mean square deviation 2MSD) from the crystal structure. This validation illustrates the efficiency of our sampling heuristic, as correct binding modes, defined by a RMSD to the crystal structure lower than 2 A, were identified and ranked first for 68% of the complexes. The success rate increases to 78% when considering the five best-ranked clusters, and 92% when all clusters present in the last generation are taken into account. Most failures in this benchmark could be explained by the presence of crystal contacts in the experimental structure. EADock has been used to understand molecular interactions involved in the regulation of the Na,K ATPase, and in the activation of the nuclear hormone peroxisome proliferatoractivated receptors a (PPARa). It also helped to understand the action of common pollutants (phthalates) on PPARy, and the impact of biotransformations of the anticancer drug Imatinib (Gleevec®) on its binding mode to the Bcr-Abl tyrosine kinase. Finally, a fragment-based rational drug design approach using EADock was developed, and led to the successful design of new peptidic ligands for the a5ß1 integrin, and for the human PPARa. In both cases, the designed peptides presented activities comparable to that of well-established ligands such as the anticancer drug Cilengitide and Wy14,643, respectively. 3.2 French Les récentes difficultés de l'industrie pharmaceutique ne semblent pouvoir se résoudre que par l'optimisation de leur processus de développement de médicaments. Cette dernière implique de plus en plus. de techniques dites "haut-débit", particulièrement efficaces lorsqu'elles sont couplées aux outils informatiques permettant de gérer la masse de données produite. Désormais, les approches in silico telles que le criblage virtuel ou la conception rationnelle de nouvelles molécules sont utilisées couramment. Toutes deux reposent sur la capacité à prédire les détails de l'interaction moléculaire entre une molécule ressemblant à un principe actif (PA) et une protéine cible ayant un intérêt thérapeutique. Les comparatifs de logiciels s'attaquant à cette prédiction sont flatteurs, mais plusieurs problèmes subsistent. La littérature récente tend à remettre en cause leur fiabilité, affirmant l'émergence .d'un besoin pour des approches plus précises du mode d'interaction. Cette précision est essentielle au calcul de l'énergie libre de liaison, qui est directement liée à l'affinité du PA potentiel pour la protéine cible, et indirectement liée à son activité biologique. Une prédiction précise est d'une importance toute particulière pour la découverte et l'optimisation de nouvelles molécules actives. Cette thèse présente un nouveau logiciel, EADock, mettant en avant une telle précision. Cet algorithme évolutionnaire hybride utilise deux pressions de sélections, combinées à une gestion de la diversité sophistiquée. EADock repose sur CHARMM pour les calculs d'énergie et la gestion des coordonnées atomiques. Sa validation a été effectuée sur 37 complexes protéine-ligand cristallisés, incluant 11 protéines différentes. L'espace de recherche a été étendu à une sphère de 151 de rayon autour du centre de masse du ligand cristallisé, et contrairement aux comparatifs habituels, l'algorithme est parti de solutions optimisées présentant un RMSD jusqu'à 10 R par rapport à la structure cristalline. Cette validation a permis de mettre en évidence l'efficacité de notre heuristique de recherche car des modes d'interactions présentant un RMSD inférieur à 2 R par rapport à la structure cristalline ont été classés premier pour 68% des complexes. Lorsque les cinq meilleures solutions sont prises en compte, le taux de succès grimpe à 78%, et 92% lorsque la totalité de la dernière génération est prise en compte. La plupart des erreurs de prédiction sont imputables à la présence de contacts cristallins. Depuis, EADock a été utilisé pour comprendre les mécanismes moléculaires impliqués dans la régulation de la Na,K ATPase et dans l'activation du peroxisome proliferatoractivated receptor a (PPARa). Il a également permis de décrire l'interaction de polluants couramment rencontrés sur PPARy, ainsi que l'influence de la métabolisation de l'Imatinib (PA anticancéreux) sur la fixation à la kinase Bcr-Abl. Une approche basée sur la prédiction des interactions de fragments moléculaires avec protéine cible est également proposée. Elle a permis la découverte de nouveaux ligands peptidiques de PPARa et de l'intégrine a5ß1. Dans les deux cas, l'activité de ces nouveaux peptides est comparable à celles de ligands bien établis, comme le Wy14,643 pour le premier, et le Cilengitide (PA anticancéreux) pour la seconde.