Computational problems in perfect phylogeny haplotyping: typing without calling the allele.

A haplotype is an m-long binary vector. The XOR-genotype of two haplotypes is the m-vector of their coordinate-wise XOR. We study the following problem: Given a set of XOR-genotypes, reconstruct their haplotypes so that the set of resulting haplotypes can be mapped onto a perfect phylogeny (PP) tree. The question is motivated by studying population evolution in human genetics, and is a variant of the perfect phylogeny haplotyping problem that has received intensive attention recently. Unlike the latter problem, in which the input is "full" genotypes, here we assume less informative input, and so may be more economical to obtain experimentally. Building on ideas of Gusfield, we show how to solve the problem in polynomial time, by a reduction to the graph realization problem. The actual haplotypes are not uniquely determined by that tree they map onto, and the tree itself may or may not be unique. We show that tree uniqueness implies uniquely determined haplotypes, up to inherent degrees of freedom, and give a sufficient condition for the uniqueness. To actually determine the haplotypes given the tree, additional information is necessary. We show that two or three full genotypes suffice to reconstruct all the haplotypes, and present a linear algorithm for identifying those genotypes.

General clas of inhomogeneous perfect-fluid solutions

We present a general class of solutions to Einstein's field equations with two spacelike commuting Killing vectors by assuming the separation of variables of the metric components. The solutions can be interpreted as inhomogeneous cosmological models. We show that the singularity structure of the solutions varies depending on the different particular choices of the parameters and metric functions. There exist solutions with a universal big-bang singularity, solutions with timelike singularities in the Weyl tensor only, solutions with singularities in both the Ricci and the Weyl tensors, and also singularity-free solutions. We prove that the singularity-free solutions have a well-defined cylindrical symmetry and that they are generalizations of other singularity-free solutions obtained recently.

Stability of repeated student evaluations of teaching in the second preclinical year of a medical curriculum

RESUME L'étude de la médecine à la Faculté de l'Université de Lausanne est un cursus de six ans. Depuis la réforme générale du curriculum en octobre 1995, le programme de la deuxième année consacrée à l'étude de l'être humain sain a été transformé. L'enseignement intégré par système ou organe a été introduit en remplaçant l'enseignement par discipline. Parallèlement, un système d'évaluation de l'enseignement par les étudiants a été proposé. Il a été amélioré au fil des années et depuis l'année académique 1998-99, l'évaluation est devenue systémique et régulière. Notre étude présente et compare les résultats des évaluations de l'enseignement et des enseignants de neuf cours intégrés dispensés en deuxième année durant deux années académiques (1998-99 et 1999-2000). Une forte corrélation entre les résultats des deux années consécutives ainsi qu'une importante disparité des estimations à l'intérieure de chacune de deux années ont été observées. Ceci démontre un engagement sérieux des étudiants dans le processus d'évaluation, révèle la pertinence de leur analyse et leur bonne capacité de discernement. L'analyse de nos résultats montre que les évaluations effectuées par les étudiants peuvent constituer une source fiable d'informations et contribuer à l'amélioration du processus d'enseignement.

Petrou type-D perfect-fluid solutions in generalized Kerr-Schild form.

Generalized KerrSchild space-times for a perfect-fluid source are investigated. New Petrov type D perfect fluid solutions are obtained starting from conformally flat perfect-fluid metrics.

Petrou types D and II perfect-fluid solutions in generalized Kerr-Schild form.

Petrov types D and II perfect-fluid solutions are obtained starting from conformally flat perfect-fluid metrics and by using a generalized KerrSchild ansatz. Most of the Petrov type D metrics obtained have the property that the velocity of the fluid does not lie in the two-space defined by the principal null directions of the Weyl tensor. The properties of the perfect-fluid sources are studied. Finally, a detailed analysis of a new class of spherically symmetric static perfect-fluid metrics is given.

Online teaching of inflammatory skin pathology by a French-speaking international university network

Introduction: Developments in technology, webbased teaching and whole slide imaging have broadened the teaching horizon in anatomic pathology. Creating online learning material including many types of media like radiologic images, videos, clinical and macroscopic photographs and whole slides imaging is now accessible to almost every university. Unfortunately, a major limiting factor to maintain and update the learning material is the amount of work, time and resources needed. In this perspective, a French national university network was initiated in 2011 to build mutualised online teaching pathology modules with clinical cases and tests. This network has been extended to an international level in 2012-2014 (Quebec, Switzerland and Ivory Coast). Method: One of the first steps of the international project was to build a learning module on inflammatory skin pathology intended for interns and residents of pathology and dermatology. A pathology resident from Quebec spent 6 weeks in France and Switzerland to develop the contents and build the module on an e-learning Moodle platform (http: //moodle.sorbonne-paris-cite.fr) under the supervision of two dermatopathologists (BV, MB). The learning module contains text, interactive clinical cases, tests with feedback, whole slides images (WSI), images and clinical photographs. For that module, the virtual slides are decentralized in 2 universities (Bordeaux and Paris 7). Each university is responsible of its own slide scanning, image storage and online display with virtual slide viewers. Results: The module on inflammatory skin pathology includes more than 50 web pages with French original content, tests and clinical cases, links to over 45 WSI and more than 50 micro and clinical photographs. The whole learning module is currently being revised by four dermatopathologists and two senior pathologists. It will be accessible to interns and residents in spring 2014. The experience and knowledge gained from that work will be transferred to the next international fellowship intern whose work will be aimed at creating lung and breast pathology learning modules. Conclusion: The challenges of sustaining a project of this scope are numerous. The technical aspect of whole-slide imaging and storage needs to be developed by each university or group. The content needs to be regularly updated, completed and its use and existence needs to be promoted by the different actors in pathology. Of the great benefits of that kind of project are the international partnerships and connections that have been established between numerous Frenchspeaking universities and pathologists with the common goals of promoting education in pathology and the use of technology including whole slide imaging. * The Moodle website is hosted by PRES Sorbonne Paris Cité, and financial supports for hardware have been obtained from UNF3S (http://www.unf3s.org/) and PRES Sorbonne Paris Cité. Financial support for international fellowships has been obtained from CFQCU (http://www.cfqcu.org/).

Plastinated Ethmoidal Region : I. Preparation and Applications in Clinical Teaching.

Ethmoidal regions weer prepared and dissected to demonstrate regional sinus anatomy and endoscopic surgery approaches from six human heads. After perparation, the specimens were plastinated using the standard S10 technique. A CT-scan of each ethmoidal block was performed before and after preparation of the block to access shrinkage. The plastinated specimens were successfully introduced into clinical teaching of sinus anatomy and surgery. One advantage of using these specimens is their long-lasting preservation without deterioration of the tissue. The specimens were well suited for comparative radiographic and ondoscopic studies, and the CT-scans allowed an exact measurement of tissue shrinkage due to plastination. Increaseed tissue rigidity and shrionkage due to plastination has to be taken into account for subsequent endoscopic observation.

Immersion communautaire à Lausanne : une autre façon d'enseigner la santé publique [Community immersion in Lausanne: a different approach to teaching public health?].

Teaching community medicine represents a significant challenge for medical schools, which tend to struggle to promote interest in the issue among students. In 2009, the Lausanne medical school introduced a "community immersion" module specifically designed to address the issue. The new module requires students working in small groups under the supervision of a tutor to investigate a health question of their choice. The investigation involves conducting interviews with stakeholders (health professionals, patients, politicians, etc.), carrying out a survey, and presenting the results of the investigation in a "congress". An external evaluation showed that the objectives of the initiative had been largely achieved, with an increase of interest in community medicine for over 50% of students (based on a total cohort of 150 students) and a high level of satisfaction for over 90% of students and tutors. This paper presents the results of the initiative and its use for promoting community-oriented medicine.

Infective Endocarditis in a Finnish Teaching Hospital. 25 Years of Experience of Adult Patients

Infektiivinen endokardiitti yliopistollisessa keskussairaalassa vuosina 1980-2004 hoidetuilla aikuispotilailla Tausta: Infektiivinen endokardiitti on edelleen vakava sairaus. Huolimatta siitä, että taudin diagnostiikka ja hoito ovat kehittyneet, siihen liittyy edelleen merkittävää sairastuvuutta ja kuolleisuutta. Endokardiitin taudinkuvassa on viime vuosina tapahtunut muutoksia monissa maissa. Tavoitteet: Tutkia endokardiitin kliinista kuvaa ja ennustetta suomalaisessa yliopistosairaalassa vuosina 1980-2004 endokardiitin vuoksi hoidetuilla aikuispotilailla. Aineisto: Osatyössä I endokardiitin todennäköisyyttä analysoitiin 222:lla vuosina 1980-1995 endokardiittiepäilyn vuoksi hoidetulla potilaalla käyttäen apuna sekä Duken että von Reyn diagnostisia kriteereitä. Osatyössä II tutkittiin endokardiittiin liittyviä neurologisia komplikaatioita 218 varmassa tai mahdollisessa endokardiittiepisodissa. Osatyössä III tutkittiin seerumin C-reaktiivisen proteiinin (CRP) käyttökelpoisuutta hoitovasteen arvioinnissa 134:ssä varmaksi luokitellussa endokardiittiepisodissa. Osatyössä IV tutkittiin yleisbakteeri-PCRmenetelmän käyttökelpoisuutta etiologisessa diagnostiikassa 56:lla endokardiittiepäilyn vuoksi leikatulla potilaalla. Osatöissä V ja VI analysoitiin kaikki vuosina 1980-2004 hoidetut 303 endokardiittipotilasta lyhytaikais- ja 1-vuotisennusteen suhteen sekä tutkittiin endokardiitin taudinkuvassa tapahtuneita muutoksia sairaalassamme. Tulokset: Duken kriteerit osoittautuivat von Reyn kriteereitä herkemmiksi endokardiitin diagnostiikassa: 243 tutkitusta episodista 114 luokiteltiin varmoiksi endokardiiteiksi Duken kriteereillä, kun vastaavasti ainoastaan 64 luoteltiin varmoiksi von Reyn kriteereillä (p<0.001). Lisäksi peräti 115 episodissa endokardiitin diagnoosi hylättiin von Reyn kriteereillä, kun diagnoosi hylättiin Duken kriteereillä ainoastaan 37 episodissa (p<0.001). Neurologinen komplikaatio ilmeni ennen mikrobilääkehoidon aloittamista 76 %:ssa episodeja ollen ensimmäinen oire 47 %:ssa. Kuolema oli merkitsevästi yhteydessä neurologisiin komplikaatioihin. Hoitovastetta seurattaessa seerumin CRP:n lasku oli merkitsevästi nopeampaa komplikaatioitta toipuvilla potilailla kuin niillä, joille kehittyi komplikaatioita tai jotka menehtyivät tautiinsa. PCR-tutkimus poistetusta läpästä antoi ainoana menetelmänä etiologisen diagnoosin neljässä tapauksessa (2 stafylokokkilajia, 1 Streptococcus bovis,1 Bartonella quintana), joissa kaikissa mikrobilääkehoito oli ollut käytössä ennen näytteiden ottamista. Koko aineistossa kahden läpän infektio tai neurologisten komplikaatioiden, perifeeristen embolioiden tai sydämen vajaatoiminnan kehittyminen ennustivat sekä sairaalakuolleisuutta että 1-vuotiskuolleisuutta, kun taas ≥65 vuoden ikä ja sydämen ultraäänitutkimuksessa todettu vegetaatio tai Duken luokittelun mukainen pääkriteeri ennustivat kuolemaa vuoden sisällä. Korkea CRP-taso sairaalaan tullessa ennusti sekä sairaalakuolleisuutta että 1-vuotiskuolleisuutta. Huumeiden käyttäjien endokardiitit lisääntyivät tutkimusaikana merkitsevästi (p<0.001). Päätelmät: Tässä työssä vahvistetaan Duken kriteerien käyttökelpoisuus endokardiitin diagnostiikassa. Lisäksi vahvistui käsitys, että nopea diagnoosi ja mikrobilääkehoidon aloittaminen ovat parhaat keinot ehkäistä neurologisia komplikaatioita ja parantaa endokardiittipotilaiden ennustetta. CRP:n normalisoituminen on endokardiittipotilailla hyvän ennusteen merkki. Suoraan läppäkudoksesta tehty PCR-tutkimus on hyödyllinen, kun taudin aiheuttaja on kasvuominaisuuksiltaan vaativa tai potilas on saanut mikrobilääkehoitoa ennen viljelynäytteiden ottamista. Muutamat aiemmissa tutkimuksissa todetut huonon ennusteen merkit ennustavat huonoa ennustetta myös tämän tutkimuksen potilailla. Uutena löydöksenä ilmeni, että korkea CRP-arvo sairaalaan tullessa merkitsee sekä huonoa lyhyt- että pitkäaikaisennustetta. Huumeiden käyttäjien endokardiittien ilmaantuminen on tärkein epidemiologinen muutos 25 vuoden tutkimusaikana.

Enseignement de la médecine de famille: nouvelles évolutions à Lausanne [Teaching family medicine in Lausanne].

The Faculty of Biology and Medicine of Lausanne has integrated education of family medicine all along its new undergraduate medical curriculum. The Institute of general medicine is in charge to implement those offers among which two are presented hereafter. In the new module "Generalism" several courses cover the specificities of the discipline as for example medical decision in the practice. A mandatory one-month internship in the medical practice offers an experiential immersion into family medicine for all students. In a meeting at the end of their internship, students discuss in group with their peers their individual experiences and are asked to identify, based on their personal experience, the general concepts of the specialty of family medicine and general practice.

Cross-cultural clinical competence and post-graduate teaching: any impact(s) on doctors?

Context: Cross-cultural clinical competence (CCC) requires a mixtureof "knowledge" (K), "attitude" (A) and "skills" (S), in order to develop theability to give quality care to patients of different cultures. Theseattributes allow, while providing medical care, consideration of thepatient's medical, social, cultural and language needs. The LausanneUniversity Medical Policlinic (PMU) provides approximately 30000consultations per year to migrant patients and over the past five yearshas implemented a training course on CCC that focuses on trialogue,stereotypes and administrative procedures for the healthcare ofmigrants.Method: A quantitative survey of 18 new residents, was carried outusing a validated questionnaire, the "Multicultural AssessmentQuestionnaire" (the MAQ, 16 questions on K, A and S) to evaluate theimpact of CCC training. The questionnaire was distributed before theCCC course (J-1), three days after (J+3) and three months later (J+90).A descriptive univariate analysis of the difference in MAQ scoresbetween the times J-1 - J+3 and J-1 - J+90 was made. Three FocusGroups were conducted, at three months, to explore residents' thoughtsabout the course.Results: A significant increase was observed in global performancedeclared by residents. Following the intervention, the score of the MAQincreased from 31.4 points to 38.0 points at three days (p = 0.004) andto 37.7 points at three months (p = 0.003). This increase was mostnoticeable in the field of acquiring K: total score J-1: 118, J+3: 189,J+90: 190 (difference J-1 - J+3 and J-1 - J+90: p <0.005). There was nosignificant difference in acquiring A (J-1: 222, J+3: 228, J+90: 229), andS increases in a significant way at first (J-1: 222, J+3: 265, J-1 - J+3:p = 0.035), then comes back to the start value (J+90: 217). The residentswere interested by the course which they felt provides useful informationfor clinical practice. They had a great number of expectations in varyingfields (medical anthropology, cultural differences, epidemiology, etc.),hoping a "ready-made" solution for the approach of migrant patients.Conclusions: A unique training of CCC at the post-graduate level,upgraded K, and to a lesser extent A and S, for these 18 residents. Theywere interest and they had many expectations. Subsequent coursesshould consolidate these acquisitions. Future study should demonstratethe impact on patients' clinical outcome.

Online teaching of inflammatory skin pathology by a French-speaking International University Network

INTRODUCTION: Developments in technology, web-based teaching and whole slide imaging have broadened the teaching horizon in anatomic pathology. Creating online learning material including many types of media such as radiologic images, whole slides, videos, clinical and macroscopic photographs, is now accessible to most universities. Unfortunately, a major limiting factor to maintain and update the learning material is the amount of resources needed. In this perspective, a French-national university network was initiated in 2011 to build joint online teaching modules consisting of clinical cases and tests. The network has since expanded internationally to Québec, Switzerland and Ivory Coast. METHOD: One of the first steps of the project was to build a learning module on inflammatory skin pathology for interns and residents in pathology and dermatology. A pathology resident from Québec spent 6 weeks in France and Switzerland to develop the contents and build the module on an e-learning Moodle platform under the supervision of two dermatopathologists. The learning module contains text, interactive clinical cases, tests with feedback, virtual slides, images and clinical photographs. For that module, the virtual slides are decentralized in 2 universities (Bordeaux and Paris 7). Each university is responsible of its own slide scanning, image storage and online display with virtual slide viewers. RESULTS: The module on inflammatory skin pathology includes more than 50 web pages with French original content, tests and clinical cases, links to over 45 virtual images and more than 50 microscopic and clinical photographs. The whole learning module is being revised by four dermatopathologists and two senior pathologists. It will be accessible to interns and residents in the spring of 2014. The experience and knowledge gained from that work will be transferred to the next international resident whose work will be aimed at creating lung and breast pathology learning modules. CONCLUSION: The challenges of sustaining a project of this scope are numerous. The technical aspect of whole-slide imaging and storage needs to be developed by each university or group. The content needs to be regularly updated and its accuracy reviewed by experts in each individual domain. The learning modules also need to be promoted within the academic community to ensure maximal benefit for trainees. A collateral benefit of the project was the establishment of international partnerships between French-speaking universities and pathologists with the common goal of promoting pathology education through the use of multi-media technology including whole slide imaging.