A Workflow for Software Development within Computational Epidemiology

A critical investigation into computational models developed for studying the spread of communicable disease is presented. The case in point is a spatially explicit micro-meso-macro model for the entire Swedish population built on registry data, thus far used for smallpox and for influenza-like illnesses. The lessons learned from a software development project of more than 100 person months are collected into a check list. The list is intended for use by computational epidemiologists and policy makers, and the workflow incorporating these two roles is described in detail.NOTICE: This is the author’s version of a work that was accepted for publication in Journal of Computationa Science. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Journal of Computational Science, VOL 2, ISSUE 3, 6 June 2011 DOI 10.1016/j.jocs.2011.05.004.</p

Los adoratorios de altura inkaicos. Una mirada desde el cerro Cuzco, Departamento de Potosí, Bolivia

In light of new data obtained at Cerro Cuzco (Potosi, Bolivia), this article deals with a group of mountains sanctified by the Inkas which intervened in the formation of the territorial jurisdiction associated with the wak’a of Porco. The articulation between the archaeological register and archival records allows for the exploration of different aspects in the high altitude Inkan shrines located in this region -well known for the exploitation of mineral deposits as well as for cults of worship dedicated to the pre-Hispanic lightning divinity.A la luz de los nuevos datos arqueológicos obtenidos en cerro Cuzco (Potosí, Bolivia), en este trabajo trataremos sobre un conjunto de montañas antiguamente sacralizadas por los inkas, las cuales intervinieron en la conformación de una jurisdicción territorial asociada con el wak’a de Porco. La articulación de los registros arqueológico e histórico permitió explorar diversos aspectos que envuelven los adoratorios de altura inkaicos de esta región, en los cuales se destacan tanto su relación con la explotación de yacimientos mineros como su vínculo con los cultos a la divinidad prehispánica del rayo

Strain driven fast osseointegration of implants

BACKGROUND: Although the bone's capability of dental implant osseointegration has clinically been utilised as early as in the Gallo-Roman population, the specific mechanisms for the emergence and maintenance of peri-implant bone under functional load have not been identified. Here we show that under immediate loading of specially designed dental implants with masticatory loads, osseointegration is rapidly achieved. METHODS: We examined the bone reaction around non- and immediately loaded dental implants inserted in the mandible of mature minipigs during the presently assumed time for osseointegration. We used threaded conical titanium implants containing a titanium2+ oxide surface, allowing direct bone contact after insertion. The external geometry was designed according to finite element analysis: the calculation showed that physiological amplitudes of strain (500–3,000 ustrain) generated through mastication were homogenously distributed in peri-implant bone. The strain-energy density (SED) rate under assessment of a 1 Hz loading cycle was 150 Jm-3 s-1, peak dislocations were lower then nm. RESULTS: Bone was in direct contact to the implant surface (bone/implant contact rate 90%) from day one of implant insertion, as quantified by undecalcified histological sections. This effect was substantiated by ultrastructural analysis of intimate osteoblast attachment and mature collagen mineralisation at the titanium surface. We detected no loss in the intimate bone/implant bond during the experimental period of either control or experimental animals, indicating that immediate load had no adverse effect on bone structure in peri-implant bone. CONCLUSION: In terms of clinical relevance, the load related bone reaction at the implant interface may in combination with substrate effects be responsible for an immediate osseointegration state

IRS-III: A broker-based approach to semantic Web services

A factor limiting the take up of Web services is that all tasks associated with the creation of an application, for example, finding, composing, and resolving mismatches between Web services have to be carried out by a software developer. Semantic Web services is a combination of semantic Web and Web service technologies that promise to alleviate these problems. In this paper we describe IRS-III, a framework for creating and executing semantic Web services, which takes a semantic broker based approach to mediating between service requesters and service providers. We describe the overall approach and the components of IRS-III from an ontological and architectural viewpoint. We then illustrate our approach through an application in the eGovernment domain

Diffuse idiopathic skeletal hyperostosis in ancient clergymen

Diffuse idiopathic skeletal hyperostosis (DISH) is a common but often unrecognized systemic disorder observed mainly in the elderly. DISH is diagnosed when the anterior longitudinal ligament of the spine is ossified on at least four contiguous spinal levels or when multiple peripheral enthesopathies are present. The etiology of DISH is unknown but previous studies have shown a strong association with obesity and insulin-independent diabetes mellitus. DISH can lead to back pain, dysphagia, myelopathy, musculoskeletal impairment and grossly unstable spine fractures after minor trauma. In archeological studies a high prevalence of DISH has been demonstrated in ancient clergymen. The present study describes the pathological changes of human remains excavated from the abbey court (Pandhof) in the city of Maastricht, The Netherlands. Human remains of 51 individuals buried between 275 and 1795 ce were excavated and examined. The remains were investigated according to a standardized physical anthropological report and individuals demonstrating ossification of spinal ligaments and/or multiple peripheral enthesopathies were included in the study group. The authors reviewed all available material and after reaching consensus, each abnormality found was given a diagnosis and subsequently recorded. After examination, 28 individuals were considered to be adult males; 11 adult females; three adults of indeterminate sex and nine individuals were of sub adult age. The mean age at death for adults was 36.8 years. Seventeen adult individuals (40.4% of all adults), displayed ossifications of at least four contiguous spinal levels and/or multiple enthesopathies of the appendicular skeleton and were therefore, assigned the diagnosis DISH. The mean age of these individuals was 49.5 ± 13.0 years. In at least three of these individuals, DISH had led to extensive ossification and subsequent ankylosis of axial and peripheral skeletal structures. In this population of (presumably) clergymen and high-ranking citizens, DISH was observed in unusual high numbers at a relatively young age. Some of the examined cases suggest that DISH may be a seriously incapacitating disorder when the more advanced stages of the disease have been reached. It is hypothesized that “a monastic way of life” can predispose to DISH. Present demographic trends in obesity and diabetes mellitus as potential co-factors for the development of DISH warrant further study to investigate its future prevalence

CASE: A Framework for Computer Supported Outbreak Detection

Background: In computer supported outbreak detection, a statistical method is applied to a collection of cases to detect any excess cases for a particular disease. Whether a detected aberration is a true outbreak is decided by a human expert. We present a technical framework designed and implemented at the Swedish Institute for Infectious Disease Control for computer supported outbreak detection, where a database of case reports for a large number of infectious diseases can be processed using one or more statistical methods selected by the user. Results: Based on case information, such as diagnosis and date, different statistical algorithms for detecting outbreaks can be applied, both on the disease level and the subtype level. The parameter settings for the algorithms can be configured independently for different diagnoses using the provided graphical interface. Input generators and output parsers are also provided for all supported algorithms. If an outbreak signal is detected, an email notification is sent to the persons listed as receivers for that particular disease. Conclusions: The framework is available as open source software, licensed under GNU General Public License Version 3. By making the code open source, we wish to encourage others to contribute to the future development of computer supported outbreak detection systems, and in particular to the development of the CASE framewor

Y-chromosome descent clusters and male differential reproductive success: young lineage expansions dominate Asian pastoral nomadic populations

International audienceHigh-frequency microsatellite haplotypes of the male-specific Y-chromosome can signal past episodes of high reproductive success of particular men and their patrilineal descendants. Previously, two examples of such successful Y-lineages have been described in Asia, both associated with Altaic-speaking pastoral nomadic societies, and putatively linked to dynasties descending, respectively, from Genghis Khan and Giocangga. Here we surveyed a total of 5321 Y-chromosomes from 127 Asian populations, including novel Y-SNP and microsatellite data on 461 Central Asian males, to ask whether additional lineage expansions could be identified. Based on the most frequent eight-microsatellite haplotypes, we objectively defined 11 descent clusters (DCs), each within a specific haplogroup, that represent likely past instances of high male reproductive success, including the two previously identified cases. Analysis of the geographical patterns and ages of these DCs and their associated cultural characteristics showed that the most successful lineages are found both among sedentary agriculturalists and pastoral nomads, and expanded between 2100 BCE and 1100 CE. However, those with recent origins in the historical period are almost exclusively found in Altaic-speaking pastoral nomadic populations, which may reflect a shift in political organisation in pastoralist economies and a greater ease of transmission of Y-chromosomes through time and space facilitated by the use of horses

Dispensation des produits pharmaceutiques dans le service d’hospitalisation à domicile de l’hôpital de Gap dans les Hautes-Alpes

L’Hospitalisation à Domicile (HAD) permet au patient de bénéficier à son domicile de soins coordonnés de nature hospitalière. La dispensation, définie par le Code de la Santé Publique, comporte trois actes : l’analyse pharmaceutique, la préparation des médicaments et les conseils et informations nécessaires au bon usage des médicaments. La dispensation des produits pharmaceutiques, médicaments et Dispositifs Médicaux au sein des structures d’HAD peut dépendre d’une Pharmacie à Usage Intérieur (PUI) ou d’une officine. L’HAD de l’hôpital de Gap a ouvert en décembre 2016, la dispensation des produits pharmaceutiques dépend de la PUI de l’hôpital. Nous avons dressé un premier état des lieux de la dispensation par l’HAD de Gap. Elle a été appréhendée à travers deux problématiques : la satisfaction des utilisateurs (patients et Infirmiers Diplômés d’État Libéraux -IDEL) et la performance de la délivrance des produits pharmaceutiques. Pour la première, une enquête téléphonique a été réalisée entre le 25 mars et le 21 mai 2019 auprès de 33 IDEL et de 25 patients. Pour la seconde, nous avons évalué l’impact des retours sur l’activité des Préparateurs en Pharmacie Hospitalière (PPH). Nous avons étudié le nombre et la nature des lignes enregistrées de mouvements de stocks sur l'année 2018 à partir du logiciel de gestion des stocks. Des propositions pour la dispensation des produits pharmaceutiques par la PUI et pour la gestion des stocks au domicile des patients par les différents acteurs du circuit ont été formulées pour le service à partir de l’état des lieux réalisé et des outils publiés dans la littérature

L’Expérience "Professionnel de Santé" : regard croisé avec l’Expérience Patient

The patient experience, defined as the sum of all interactions, shaped by an organization’s culture, that influence patient perceptions, across the continuum of care, has been recognised as a major lever for improving healthcare systems. Patient experience measurement and evaluation programmes have been nationally implemented in several countries, as the “e-Satis” program in France. However, these programmes have come up against criticism from the three main actors in the healthcare system: patients and their relatives (difficulty in reporting on their experience), staff (lack of involvement and practical indications on how to improve their practice) and institutions (complexity of transforming quantitative results into operational strategies). The objective of this thesis is to propose an approach to improve the patient experience at the level of an academic hospital federation that uses and completes the existing program to better respond to the needs and expectations of the various stakeholders. Three levels of studies are proposed: analysis of patient comments from e-Satis, a survey of professionals to gather their feelings during their interactions with patients and the comparison of the perceptions of patients and staff on their key interactions. The applied approach allows - through a semi-automated analysis that combines linguistic expertise and automated processing by software – to translate comments into measurable and comparable data at different scales (for example: institutions, departments). This method was applied to 10 061 comments from patients (from e-Satis) and 511 from staff and provides decision support by classifying the themes into four categories. The cross-referencing of patient and professional results allowed the identification of convergences and divergences of perceptions between the two populations and thus to target the most important and relevant improvement actions. This thesis provides an approach to the patient experience which firstly allows to report on patients' experiences, to identify operational actions to improve their experience, and to enhance the use of national systems. Secondly, the inclusion of staff allows to identify their needs and to compare the perceptions of the two populations to inform and support the quality improvement strategies of health care institutions.L’expérience patient, définie comme la somme des interactions entre le patient, ses proches et le système de santé, a été reconnue comme un levier majeur d’amélioration des systèmes de santé. Des dispositifs de mesure ont été mis en place au niveau national dans plusieurs pays, dont le dispositif « e-Satis » en France. Ces dispositifs se heurtent toutefois aux critiques des trois acteurs principaux du système de santé : les patients et leurs proches / accompagnants (difficulté à rendre réellement compte de leur vécu), les professionnels (manque d’implication et d’indications pratiques sur les améliorations à apporter) et les établissements (complexité à transformer les résultats quantitatifs en stratégies opérationnelles). L’objectif de ce travail de thèse est de proposer une approche d’amélioration de l’expérience patient à l’échelle d’un Centre Hospitalier Universitaire (CHU) qui utilise et complète le dispositif existant pour mieux répondre aux besoins et attentes des différents acteurs. Trois niveaux d’études sont avancés : l’analyse des commentaires patients issus d’e-Satis, une enquête auprès des professionnels afin de recueillir leurs ressentis lors de leurs interactions avec les patients et la confrontation des perceptions des patients et des professionnels sur leurs interactions clefs. La méthode permet - au travers d’une analyse semi-automatisée qui concilie une expertise linguistique et un traitement automatisé par un logiciel - de traduire des commentaires en données mesurables et comparables à différentes échelles (par exemple : par établissement, par service). Cette méthode a été appliquée à 10 061 commentaires de patients (issus d’e-Satis) et 511 de professionnels, et aide à la décision en classant les thématiques en quatre catégories. Le croisement des résultats patients et professionnels a permis d’identifier les convergences et divergences de perceptions entre les deux populations et ainsi de cibler les actions d’améliorations les plus importantes et pertinentes. Cette thèse apporte une approche de l’expérience patient qui permet dans un premier temps de rendre compte du vécu des patients, d’identifier des actions opérationnelles pour améliorer leur expérience et de valoriser l’utilisation de dispositifs nationaux. Dans un second temps, l’inclusion des professionnels permet d’identifier leurs besoins et de confronter les perceptions entre les deux populations afin d’éclairer et d’accompagner les stratégies d’amélioration de la qualité des établissements de santé