Tumor architecture exerts no bias on nuclear grading in breast cancer diagnosis.

We recently reported that nuclear grading in prostate cancer is subject to a strong confirmation bias induced by the tumor architecture. We now wondered whether a similar bias governs nuclear grading in breast carcinoma. An unannounced test was performed at a pathology conference. Pathologists were asked to grade nuclei in a PowerPoint presentation. Circular high power fields of 27 invasive ductal carcinomas were shown, superimposed over low power background images of either tubule-rich or tubule-poor carcinomas. We found (a) that diagnostic reproducibility of nuclear grades was poor to moderate (weighed kappa values between 0.07 and 0.54, 27 cases, 44 graders), but (b) that nuclear grades were not affected by the tumor architecture. We speculate that the categorized grading in breast cancer, separating tubule formation, nuclear pleomorphism, and mitotic figure counts in a combined three tier score, prevents the bias that architecture exerts on nuclear grades in less well-controlled situations.

Evolutionary simulations to detect functional lineage-specific genes.

MOTIVATION: Supporting the functionality of recent duplicate gene copies is usually difficult, owing to high sequence similarity between duplicate counterparts and shallow phylogenies, which hamper both the statistical and experimental inference. RESULTS: We developed an integrated evolutionary approach to identify functional duplicate gene copies and other lineage-specific genes. By repeatedly simulating neutral evolution, our method estimates the probability that an ORF was selectively conserved and is therefore likely to represent a bona fide coding region. In parallel, our method tests whether the accumulation of non-synonymous substitutions reveals signatures of selective constraint. We show that our approach has high power to identify functional lineage-specific genes using simulated and real data. For example, a coding region of average length (approximately 1400 bp), restricted to hominoids, can be predicted to be functional in approximately 94-100% of cases. Notably, the method may support functionality for instances where classical selection tests based on the ratio of non-synonymous to synonymous substitutions fail to reveal signatures of selection. Our method is available as an automated tool, ReEVOLVER, which will also be useful to systematically detect functional lineage-specific genes of closely related species on a large scale. AVAILABILITY: ReEVOLVER is available at http://www.unil.ch/cig/page7858.html.

Activity assessment of eosinophilic esophagitis.

The activity of eosinophilic esophagitis (EoE) can be assessed with patient-reported outcomes and biologic measures. Patient-reported outcomes include symptoms and quality of life, whereas biologic measures refer to endoscopic, histologic, and biochemical activity (e.g. blood biomarkers). So far, a validated tool to assess EoE activity in the above-mentioned dimensions is lacking. Given the lack of a standardized way to assess EoE activity in the various dimensions, the results of different clinical trials may be difficult to compare. For symptom assessment in adult patients, the symptom 'dysphagia' should be evaluated according to different standardized food consistencies. Furthermore, symptom assessment should take into account the following items: avoidance of specific food categories, food modification, and time to eat a regular meal. A distinct symptom recall period (e.g. 2 weeks) has to be defined for symptom assessment. Performing an 'esophageal stress test' with ingestion of a standardized meal to measure symptom severity bears the potential risk of acute food bolus impaction and should therefore be avoided. The description of endoscopic findings in EoE has meanwhile been standardized. Histologic evaluation of EoE activity should report either the size of the high-power field used or count the eosinophils per mm(2). There is a current lack of blood biomarkers demonstrating a good correlation with histologic activity in esophageal biopsies. The development and validation of an adult and pediatric EoE activity index is urgently needed not only for clinical trials and observational studies, but also for daily practice.

What Was I Thinking? Eye-Tracking Experiments Underscore the Bias that Architecture Exerts on Nuclear Grading in Prostate Cancer.

We previously reported that nuclear grade assignment of prostate carcinomas is subject to a cognitive bias induced by the tumor architecture. Here, we asked whether this bias is mediated by the non-conscious selection of nuclei that "match the expectation" induced by the inadvertent glance at the tumor architecture. 20 pathologists were asked to grade nuclei in high power fields of 20 prostate carcinomas displayed on a computer screen. Unknown to the pathologists, each carcinoma was shown twice, once before a background of a low grade, tubule-rich carcinoma and once before the background of a high grade, solid carcinoma. Eye tracking allowed to identify which nuclei the pathologists fixated during the 8 second projection period. For all 20 pathologists, nuclear grade assignment was significantly biased by tumor architecture. Pathologists tended to fixate on bigger, darker, and more irregular nuclei when those were projected before kigh grade, solid carcinomas than before low grade, tubule-rich carcinomas (and vice versa). However, the morphometric differences of the selected nuclei accounted for only 11% of the architecture-induced bias, suggesting that it can only to a small part be explained by the unconscious fixation on nuclei that "match the expectation". In conclusion, selection of « matching nuclei » represents an unconscious effort to vindicate the gravitation of nuclear grades towards the tumor architecture.

Microscòpia d'alta resolució aplicada a anàlisis traceològiques, tafonòmiques i zooarqueològiques

El projecte Microscòpia d'alta resolució aplicada a anàlisis traceològiques, tafonòmiques y zooarqueològiques ha permès donar continuïtat i ampliar la xarxa científica posada en marxa gràcies a dos projectes PBR anteriors entre l’IPHES i quatre centres anglesos: l’Institute of Archaeology del University College of London, el Dept of Prehistory and Europe del British Museum, el Dept of Palaeontology del Natural History Museum, i el Lithic Microwear Research Laboratory de la University of Bradford. El tema tractat ha estat l’avaluació de la resolució i de la possible complementarietat de diferents tècniques avançades de microscòpia per a l’anàlisi de les superfícies d’ossos i eines de pedra prehistòriques: microscòpia òptica, electrònica (SEM i ESEM), microscòpia làser confocal (LSCM) i el sistema Alicona 3D Infinite Imaging. Les diverses accions de mobilitat entre Catalunya i el Regne Unit realitzades han permès satisfactòriament posar en comú els procediments emprats pels diferents especialistes de cada centre. Les proves realitzades sobre materials de jaciments arqueològics clau tant britànics com de l’estat espanyol han permès avaluar els avantatges i limitacions que cada tècnica presentava segons la mostra estudiada (eines de pedra, ossos, dents...) i segons els requeriments específics de l’estudi plantejat. En termes generals, s’ha posat en evidència que les diferents tècniques explorades són força complementàries. És a dir, la gran capacitat d’augments i de resolució d’imatge dels microscopis electrònics es complementa amb unes meravelloses prestacions quant anàlisi de textures, de perfils i de reconstrucció 3D dels altres aparells. La principal conclusió que podem extreure, doncs, és que l’estudi d’aquest tipus d’objectes arqueològics requereix de l’ús combinat de diferents aparells de microscòpia. Tant els treballs realitzats com els contactes entre especialistes establerts al llarg del projecte s’han plasmat ja en treballs concrets, alguns d’ells ja publicats o en fase final de publicació.

Further evidence on the statistical properties of real GNP

The well-known lack of power of unit root tests has often been attributed to the shortlength of macroeconomic variables and also to DGP s that depart from the I(1)-I(0)alternatives. This paper shows that by using long spans of annual real GNP and GNPper capita (133 years) high power can be achieved, leading to the rejection of both theunit root and the trend-stationary hypothesis. This suggests that possibly neither modelprovides a good characterization of these data. Next, more flexible representations areconsidered, namely, processes containing structural breaks (SB) and fractional ordersof integration (FI). Economic justification for the presence of these features in GNP isprovided. It is shown that the latter models (FI and SB) are in general preferred to theARIMA (I(1) or I(0)) ones. As a novelty in this literature, new techniques are appliedto discriminate between FI and SB models. It turns out that the FI specification ispreferred, implying that GNP and GNP per capita are non-stationary, highly persistentbut mean-reverting series. Finally, it is shown that the results are robust when breaksin the deterministic component are allowed for in the FI model. Some macroeconomicimplications of these findings are also discussed.

Correlative light and electron microscopy in parasite research.

The interaction of a parasite and a host cell is a complex process, which involves several steps: (1) attachment to the plasma membrane, (2) entry inside the host cell, and (3) hijacking of the metabolism of the host. In biochemical experiments, only an event averaged over the whole cell population can be analyzed. The power of microscopy, however, is to investigate individual events in individual cells. Therefore, parasitologists frequently perform experiments with fluorescence microscopy using different dyes to label structures of the parasite or the host cell. Though the resolution of light microscopy has greatly improved, it is not sufficient to reveal interactions at the ultrastructural level. Furthermore, only specifically labeled structures can be seen and related to each other. Here, we want to demonstrate the additional value of electron microscopy in this area of research. Investigation of the different steps of parasite-host cell interaction by electron microscopy, however, is often hampered by the fact that there are only a few cells infected, and therefore it is difficult to find enough cells to study. A solution is to profit from low magnification, hence large overview, and specific location of the players by fluorescence labels in a light microscope with the high power resolution and structural information provided by an electron microscope, in short by correlative light and electron microscopy.

Oesophagite à éosinophiles [Eosinophilic esophagitis].

Eosinophilic esophagitis is a recent diagnosis, of growing interest and prevalence. It has to be considered by every physician when facing any adult or pediatric case of dysphagia, food impaction, and symptoms of GERD (gastroesophageal reflux disease) resistant to proton-pump inhibitor treatment. The diagnosis is made by combining clinical symptoms and endoscopic signs, supported by biopsies of the mucosa, which should show more than 15 eosinophils per high power field. The etiology seems to be of allergic origin, and a full immuno-allergic testing should be made. Recommendations for the treatment are to calm down the inflammatory process by proton-pump inhibitors, and to give topical steroids, keeping the systemic treatment for acute severe cases. In cases of esophageal stenoses, dilations can be undertaken, but with a high risk of recurrence.

Seismic detection and characterization of landslides and other mass movements

Seismic methods used in the study of snow avalanches may be employed to detect and characterize landslides and other mass movements, using standard spectrogram/sonogram analysis. For snow avalanches, the spectrogram for a station that is approached by a sliding mass exhibits a triangular time/frequency signature due to an increase over time in the higher-frequency constituents. Recognition of this characteristic footprint in a spectrogram suggests a useful metric for identifying other mass-movement events such as landslides. The 1 June 2005 slide at Laguna Beach, California is examined using data obtained from the Caltech/USGS Regional Seismic Network. This event exhibits the same general spectrogram features observed in studies of Alpine snow avalanches. We propose that these features are due to the systematic relative increase in high-frequency energy transmitted to a seismometer in the path of a mass slide owing to a reduction of distance from the source signal. This phenomenon is related to the path of the waves whose high frequencies are less attenuated as they traverse shorter source-receiver paths. Entrainment of material in the course of the slide may also contribute to the triangular time/frequency signature as a consequence of the increase in the energy involved in the process; in this case the contribution would be a source effect. By applying this commonly observed characteristic to routine monitoring algorithms, along with custom adjustments for local site effects, we seek to contribute to the improvement in automatic detection and monitoring methods of landslides and other mass movements.

Hiiliteräspalkin kuitulaserhitsaus

Hitsaavassa teollisuudessa kilpailukyvyn säilyttäminen ja mahdollinen parantaminen edellyttää hitsauksen tehokkuuden nostoa. Laserhitsauksen nopeus, tarkkuus, tasainen laatu ja aikaansaatava syvä tunkeuma ovatkin vakiinnuttaneet menetelmän vankan aseman tehokkaana valmistusmenetelmänä. Sähkön ja heliumin hinnan nousu ovat pakottaneet teollisuuden miettimään entistä tehokkaampien ja ympäristöystävällisempien laserlähteiden hankkimista. Kuitulaserin korkea hyötysuhde, hyvä säteenlaatu, suuri teho ja matalat käyttökustannukset ovat herättäneet kiinnostusta laserhitsaavassa teollisuudessa. Diplomityössä keskityttiin kuitulaserhitsauksen soveltamiseen. Työn tavoitteena oli parantaa kuitulaserhitsausmenetelmän ymmärrystä ja saada käsitys siitä, miten valitaan hitsausparametrien arvot, ja soveltuuko kuitulaser teolliseen tuotantoon. Tutkimuksessa pyrittiin löytämään peruskokeilla optimaaliset hitsausparametrit, joilla syntyy hyvin tunkeutunut, vähän huokosia sisältävä, ja ulkoisesti laadukas hitsi, sekä optimaalinen hitsin tunkeumaprofiili. Lopuksi hitsausparametreja testattiin tuotteen hitsauksessa. Kuitulaser soveltuu erinomaisesti hiiliteräksen hitsaukseen ja hyvin erikoislujien terästen hitsaukseen, kun teräksen hiili- ja rikkipitoisuudet ovat matalia. Sillä on laaja parametrialue. Yleisimmät hitsausvirheet ovat vajaa hitsautumissyvyys ja huokoset. Tässä diplomityössä keskityttiin etsimään yhdelle valmistettavalle tuotteelle optimaaliset kuitulaserhitsausparametrit. Kuitulaserin laser- ja prosessiparametrien vaikutusta hitsiin ei ole juurikaan tutkittu. Diplomityön kokeiden perusteella olisi hyvä tehdä eri materiaalien jatkotutkimusta railonvalmistuksen, kuten liitoksen oksidikerroksen ja ilmaraon sekä suojakaasun, vaikutuksesta hitsiin. Kuitulaserin hyvä säteenlaatu ja muut laser-parametrit ovat tuoneet mukanaan prosessiin uusia ilmiöitä, joita on syytä tutkia lisää.

Effect of Shielding Gases in Laser Welding of Aluminium Alloys

High reflectivity to laser light, alloying element evaporation during high power laser welding makes aluminium alloys highly susceptibility to weld defects such as porosity, cracking and undercutting. The dynamic behaviour of the keyhole, due to fluctuating plasma above the keyhole and the vaporization ofthe alloying elements with in the keyhole, is the key problem to be solved for the improvement of the weld quality and stabilization of the keyhole dynamics isperhaps the single most important development that can broaden the application of laser welding of aluminium alloys. In laser welding, the shielding gas is commonly used to stabilize the welding process, to improve the welded joint features and to protect the welded seam from oxidation. The chemicalcomposition of the shielding gas is a key factor in achieving the final qualityof the welded joints. Wide range of shielding gases varying from the pure gasesto complex mixtures based on helium, argon, nitrogen and carbon dioxide are commercially available. These gas mixtures should be considered in terms of their suitability during laser welding of aluminium alloys to produce quality welds. The main objective of the present work is to study the effect of the shielding gascomposition during laser welding of aluminium alloys. Aluminium alloy A15754 was welded using 3kW Nd-YAG laser (continuous wave mode). The alloy samples were butt welded with different shielding gases (pure and mixture of gases) so that high quality welds with high joint efficiencies could be produced. It was observed that the chemical composition of the gases influenced the final weld quality and properties. In general, the mixture gases, in correct proportions, enabled better utilisation of the properties of the mixing gases, stabilized the welding process and produced better weld quality compared to the pure shielding gases.

Moniensiöinen muuntaja taajuudenmuuttajakäytössä

Suuritehoisissa pumppu- ja puhallinkäytöissä käytetään usein suurnopeusmoottoria,jota syötetään välijännitteellä. Suurjännitetaajuudenmuuttajat ovat kalliita, eikä niitä ole aina edes mahdollista valmistaa. Tutkimuksen kohteena on rinnakkaisilla pienjännitetaajuudenmuuttajilla toteutettu sähkökäyttö, jossa pienjännite nostetaan moniensiöisellä muuntajalla suurjännitteeksi (6,6 kV) ja syötetään edelleen kuormana olevalle suurnopeusmoottorille. Opinnäytetyössä tutkitaan moniensiöisen muuntajan syöttöä rinnakkaisilla taajuudenmuuttajilla sekä niiden aiheuttamia häiriöitä toisilleen. Työssä tutkitaan myös harmonisten yliaaltojen vaikutuksia muuntajan häviöihin ja magnetointiominaisuuksiin. Taajuudenmuuttajan lähtöjännite ja -virta suodatetaan sinisuotimella, jonka parametreja simuloidaan Simulink- ohjelmistolla. Tavoite on löytää optimaaliset parametrit taajuudenmuuttajanlähtösuotimelle käyrämuotojen ja suotimeen jäävän tehon suhteen. Työssä tarkasteltiin sinisuodinta, johon jää 3 prosenttia syöttöjännitteestä. LC-suodin kompensoi sähkökäytön loistehon lähes kokonaan, joten taajuudenmuuttajien antotehon kannalta suotimet ovat perusteltuja. Taajuudenmuuttajan näennäisteho putoaa 22 prosenttia, joten taajuudenmuuttajat voidaan vastaavasti mitoittaa pienemmiksi.

Contribution of isotope ratio mass spectrometry to the investigation of improvised explosives: isotopic study of black powders ans ammonium nitrates

The establishment of legislative rules about explosives in the eighties has reduced the illicit use of military and civilian explosives. However, bomb-makers have rapidly taken advantage of substances easily accessible and intended for licit uses to produce their own explosives. This change in strategy has given rise to an increase of improvised explosive charges, which is moreover assisted by the ease of implementation of the recipes, widely available through open sources. While the nature of the explosive charges has evolved, instrumental methods currently used in routine, although more sensitive than before, have a limited power of discrimination and allow mostly the determination of the chemical nature of the substance. Isotope ratio mass spectrometry (IRMS) has been applied to a wide range of forensic materials. Conclusions drawn from the majority of the studies stress its high power of discrimination. Preliminary studies conducted so far on the isotopic analysis of intact explosives (pre-blast) have shown that samples with the same chemical composition and coming from different sources could be differentiated. The measurement of stable isotope ratios appears therefore as a new and remarkable analytical tool for the discrimination or the identification of a substance with a definite source. However, much research is still needed to assess the validity of the results in order to use them either in an operational prospect or in court. Through the isotopic study of black powders and ammonium nitrates, this research aims at evaluating the contribution of isotope ratio mass spectrometry to the investigation of explosives, both from a pre-blast and from a post-blast approach. More specifically, the goal of the research is to provide additional elements necessary to a valid interpretation of the results, when used in explosives investigation. This work includes a fundamental study on the variability of the isotopic profile of black powder and ammonium nitrate in both space and time. On one hand, the inter-variability between manufacturers and, particularly, the intra-variability within a manufacturer has been studied. On the other hand, the stability of the isotopic profile over time has been evaluated through the aging of these substances exposed to different environmental conditions. The second part of this project considers the applicability of this high-precision technology to traces and residues of explosives, taking account of the characteristics specific to the field, including their sampling, a probable isotopic fractionation during the explosion, and the interferences with the matrix of the site.

Induction motor versus permanent magnet synchronous motor in motion control applications: a comparative study

High dynamic performance of an electric motor is a fundamental prerequisite in motion control applications, also known as servo drives. Recent developments in the field of microprocessors and power electronics have enabled faster and faster movements with an electric motor. In such a dynamically demanding application, the dimensioning of the motor differs substantially from the industrial motor design, where feasible characteristics of the motor are for example high efficiency, a high power factor, and a low price. In motion control instead, such characteristics as high overloading capability, high-speed operation, high torque density and low inertia are required. The thesis investigates how the dimensioning of a high-performance servomotor differs from the dimensioning of industrial motors. The two most common servomotor types are examined; an induction motor and apermanent magnet synchronous motor. The suitability of these two motor types indynamically demanding servo applications is assessed, and the design aspects that optimize the servo characteristics of the motors are analyzed. Operating characteristics of a high performance motor are studied, and some methods for improvements are suggested. The main focus is on the induction machine, which is frequently compared to the permanent magnet synchronous motor. A 4 kW prototype induction motor was designed and manufactured for the verification of the simulation results in the laboratory conditions. Also a dynamic simulation model for estimating the thermal behaviour of the induction motor in servo applications was constructed. The accuracy of the model was improved by coupling it with the electromagnetic motor model in order to take into account the variations in the motor electromagnetic characteristics due to the temperature rise.

Modern Gamma Knife radiosurgery of vestibular schwannomas: treatment concept, volumetric tumor response, and functional results.

The objective of the present study was longitudinal evaluation of the volumetric tumor response and functional results after Gamma Knife radiosurgery of vestibular schwannomas, performed according to the modern standards of treatment. From October 2003 to September 2007, 133 consecutive patients with vestibular schwannomas were treated according to the concept of robotic Gamma Knife microradiosurgery, which is based on precise irradiation of the lesion, sparing adjacent structures, and delivery of the high radiation energy to the target. Multiple small-sized isocenters located within the border of the neoplasm were applied. The mean marginal dose was 11.5 Gy (range, 11-12 Gy). In total, 126 cases with a minimum posttreatment follow-up of 2 years (range, 2-7 years; median, 4 years) were analyzed. Temporary enlargement was noted in 25 % of tumors at 6 months after radiosurgery. At 3 years of follow-up, tumor shrinkage, stabilization, and increase in volume were marked in 73 %, 23 %, and 4 % of cases, respectively. All progressing lesions spontaneously stabilized later on and did not require additional management. In 3 % of patients, transitory impairment of the facial nerve function was marked; however, neither its permanent dysfunction nor trigeminal neuropathy attributed to radiosurgery was noted. Impairment of hearing compared to its pretreatment level was revealed in 4 %, 12 %, 13 %, and 16 % of patients at 6 months, 1 year, 2 years, and 3 years after radiosurgery, respectively, and this trend was statistically significant (P = 0.0042). Overall, 77 % of patients with serviceable hearing before treatment preserved it 3 years thereafter. In conclusion, modern Gamma Knife radiosurgery provides effective and safe management of vestibular schwannomas. Nevertheless, possible temporary tumor enlargement, delay of its growth arrest, transient dysfunction of the cranial nerves, and gradual deterioration of hearing after irradiation should be always taken into consideration.