Building a global consensus approach to chordoma: a position paper from the medical and patient community

Chordomas are very rare bone malignant tumours that have had a shortage of effective treatments for a long time. New treatments are now available for both the local and the metastatic phase of the disease, but the degree of uncertainty in selecting the most appropriate treatment remains high and their adoption remains inconsistent across the world, resulting in suboptimum outcomes for many patients. In December, 2013, the European Society for Medical Oncology (ESMO) convened a consensus meeting to update its clinical practice guidelines on sarcomas. ESMO also hosted a parallel consensus meeting on chordoma that included more than 40 chordoma experts from several disciplines and from both sides of the Atlantic, with the contribution and sponsorship of the Chordoma Foundation, a global patient advocacy group. The consensus reached at that meeting is shown in this position paper.

Adult starvation and disease-related malnutrition: A proposal for etiology-based diagnosis in the clinical practice setting from the International Consensus Guideline Committee

Background & aims: Multiple definitions for malnutrition syndromes are found in the literature resulting in confusion. Recent evidence suggests that varying degrees of acute or chronic inflammation are key contributing factors in the pathophysiology of malnutrition that is associated with disease or injury. Methods: An International Guideline Committee was constituted to develop a consensus approach to defining malnutrition syndromes for adults in the clinical setting. Consensus was achieved through a series of meetings held at the ASPEN and ESPEN Congresses. Results: It was agreed that an etiology-based approach that incorporates a current understanding of inflammatory response would be most appropriate. The Committee proposes the following nomenclature for nutrition diagnosis in adults in the clinical practice setting. ""Starvation-related malnutrition"", when there is chronic starvation without inflammation, ""chronic disease-related malnutrition"", when inflammation is chronic and of mild to moderate degree, and ""acute disease or injury-related malnutrition"", when inflammation is acute and of severe degree. Conclusions: This commentary is intended to present a simple etiology-based construct for the diagnosis of adult malnutrition in the clinical setting. Development of associated laboratory, functional, food intake, and body weight criteria and their application to routine clinical practice will require validation. (C) 2009 European Society for Clinical Nutrition and Metabolism and ASPEN American Society for Parenteral and Enteral Nutrition. Published by Elsevier Ltd. All rights reserved.

Adult Starvation and Disease-Related Malnutrition: A Proposal for Etiology-Based Diagnosis in the Clinical Practice Setting From the International Consensus Guideline Committee

Background & Aims: Multiple definitions for malnutrition syndromes are found in the literature resulting in confusion. Recent evidence suggests that varying degrees of acute or chronic inflammation are key contributing factors in the pathophysiology of malnutrition that is associated with disease or injury. Methods: An International Guideline Committee was constituted to develop a consensus approach to defining malnutrition syndromes for adults in the clinical setting. Consensus was achieved through a series of meetings held at the ASPEN. and ESPEN Congresses. Results: It was agreed that an etiology-based approach that incorporates a current understanding of inflammatory response would be most appropriate. The Committee proposes the following nomenclature for nutrition diagnosis in adults in the clinical practice setting. ""Starvation-related malnutrition,"" when there is chronic starvation without inflammation, ""chronic disease-related malnutrition"", when inflammation is chronic and of mild to moderate degree, and ""acute disease or injury-related malnutrition"", when inflammation is acute and of severe degree. Conclusions: This commentary is intended to present a simple etiology-based construct for the diagnosis of adult malnutrition in the clinical setting. Development of associated laboratory, functional, food intake, and body weight criteria and their application to routine clinical practice will require validation. (JPEN J Parenter Enteral Mar. 2010;34:156-159)

Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution

Arising from either retrotransposition or genomic duplication of functional genes, pseudogenes are “genomic fossils” valuable for exploring the dynamics and evolution of genes and genomes. Pseudogene identification is an important problem in computational genomics, and is also critical for obtaining an accurate picture of a genome’s structure and function. However, no consensus computational scheme for defining and detecting pseudogenes has been developed thus far. As part of the ENCyclopedia Of DNA Elements (ENCODE) project, we have compared several distinct pseudogene annotation strategies and found that different approaches and parameters often resulted in rather distinct sets of pseudogenes. We subsequently developed a consensus approach for annotating pseudogenes (derived from protein coding genes) in the ENCODE regions, resulting in 201 pseudogenes, two-thirds of which originated from retrotransposition. A survey of orthologs for these pseudogenes in 28 vertebrate genomes showed that a significant fraction (∼80%) of the processed pseudogenes are primate-specific sequences, highlighting the increasing retrotransposition activity in primates. Analysis of sequence conservation and variation also demonstrated that most pseudogenes evolve neutrally, and processed pseudogenes appear to have lost their coding potential immediately or soon after their emergence. In order to explore the functional implication of pseudogene prevalence, we have extensively examined the transcriptional activity of the ENCODE pseudogenes. We performed systematic series of pseudogene-specific RACE analyses. These, together with complementary evidence derived from tiling microarrays and high throughput sequencing, demonstrated that at least a fifth of the 201 pseudogenes are transcribed in one or more cell lines or tissues.

Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution.

Arising from either retrotransposition or genomic duplication of functional genes, pseudogenes are "genomic fossils" valuable for exploring the dynamics and evolution of genes and genomes. Pseudogene identification is an important problem in computational genomics, and is also critical for obtaining an accurate picture of a genome's structure and function. However, no consensus computational scheme for defining and detecting pseudogenes has been developed thus far. As part of the ENCyclopedia Of DNA Elements (ENCODE) project, we have compared several distinct pseudogene annotation strategies and found that different approaches and parameters often resulted in rather distinct sets of pseudogenes. We subsequently developed a consensus approach for annotating pseudogenes (derived from protein coding genes) in the ENCODE regions, resulting in 201 pseudogenes, two-thirds of which originated from retrotransposition. A survey of orthologs for these pseudogenes in 28 vertebrate genomes showed that a significant fraction ( approximately 80%) of the processed pseudogenes are primate-specific sequences, highlighting the increasing retrotransposition activity in primates. Analysis of sequence conservation and variation also demonstrated that most pseudogenes evolve neutrally, and processed pseudogenes appear to have lost their coding potential immediately or soon after their emergence. In order to explore the functional implication of pseudogene prevalence, we have extensively examined the transcriptional activity of the ENCODE pseudogenes. We performed systematic series of pseudogene-specific RACE analyses. These, together with complementary evidence derived from tiling microarrays and high throughput sequencing, demonstrated that at least a fifth of the 201 pseudogenes are transcribed in one or more cell lines or tissues.

Benchmarking consensus model quality assessment for protein fold recognition

Background: Selecting the highest quality 3D model of a protein structure from a number of alternatives remains an important challenge in the field of structural bioinformatics. Many Model Quality Assessment Programs (MQAPs) have been developed which adopt various strategies in order to tackle this problem, ranging from the so called "true" MQAPs capable of producing a single energy score based on a single model, to methods which rely on structural comparisons of multiple models or additional information from meta-servers. However, it is clear that no current method can separate the highest accuracy models from the lowest consistently. In this paper, a number of the top performing MQAP methods are benchmarked in the context of the potential value that they add to protein fold recognition. Two novel methods are also described: ModSSEA, which based on the alignment of predicted secondary structure elements and ModFOLD which combines several true MQAP methods using an artificial neural network. Results: The ModSSEA method is found to be an effective model quality assessment program for ranking multiple models from many servers, however further accuracy can be gained by using the consensus approach of ModFOLD. The ModFOLD method is shown to significantly outperform the true MQAPs tested and is competitive with methods which make use of clustering or additional information from multiple servers. Several of the true MQAPs are also shown to add value to most individual fold recognition servers by improving model selection, when applied as a post filter in order to re-rank models. Conclusion: MQAPs should be benchmarked appropriately for the practical context in which they are intended to be used. Clustering based methods are the top performing MQAPs where many models are available from many servers; however, they often do not add value to individual fold recognition servers when limited models are available. Conversely, the true MQAP methods tested can often be used as effective post filters for re-ranking few models from individual fold recognition servers and further improvements can be achieved using a consensus of these methods.

Current state of evidence on 'off-label' therapeutic options for systemic lupus erythematosus, including biological immunosuppressive agents, in Germany, Austria and Switzerland--a consensus report

Systemic lupus erythematosus (SLE) can be a severe and potentially life-threatening disease that often represents a therapeutic challenge because of its heterogeneous organ manifestations. Only glucocorticoids, chloroquine and hydroxychloroquine, azathioprine, cyclophosphamide and very recently belimumab have been approved for SLE therapy in Germany, Austria and Switzerland. Dependence on glucocorticoids and resistance to the approved therapeutic agents, as well as substantial toxicity, are frequent. Therefore, treatment considerations will include 'off-label' use of medication approved for other indications. In this consensus approach, an effort has been undertaken to delineate the limits of the current evidence on therapeutic options for SLE organ disease, and to agree on common practice. This has been based on the best available evidence obtained by a rigorous literature review and the authors' own experience with available drugs derived under very similar health care conditions. Preparation of this consensus document included an initial meeting to agree upon the core agenda, a systematic literature review with subsequent formulation of a consensus and determination of the evidence level followed by collecting the level of agreement from the panel members. In addition to overarching principles, the panel have focused on the treatment of major SLE organ manifestations (lupus nephritis, arthritis, lung disease, neuropsychiatric and haematological manifestations, antiphospholipid syndrome and serositis). This consensus report is intended to support clinicians involved in the care of patients with difficult courses of SLE not responding to standard therapies by providing up-to-date information on the best available evidence.

Perioperative Treatment of Gastrointestinal Stromal Tumors

This review describes the current multidisciplinary management of gastrointestinal stromal tumor (GIST), which is the most common sarcoma of the gastrointestinal tract. Before 2001, surgery was the only effective therapy for GIST. The discovery of the central role of KIT proto-oncogene mutations in the pathogenesis of this tumor, and the development of specific inhibitors of KIT tyrosine kinase (TK) function, has changed the paradigm of treatment for GISTs. Imatinib and sunitinib are TK inhibitors with activity against GISTs. Their major established role in GIST is in the treatment of advanced disease. A growing body of literature and clinical experience support the potential perioperative use of these drugs. The adjuvant use of imatinib is based on retrospective series and limited prospective studies demonstrating that imatinib reduces the risk of recurrence. Ongoing studies are further defining the length of adjuvant therapy, as well as identifying the patients that could achieve the best results. Neoadjuvant treatment often decreases the tumor size, allowing a less morbid surgery, appears to be safe and beneficial for some patients, and therefore deserves further study.

Gastrointestinal stromal tumor in Brazil: Clinicopathology, immunohistochemistry, and molecular genetics of 513 cases

The aim of the present study was to evaluate the clinicopathological, immunohistochemical, and molecular genetic features of gastrointestinal stromal tumors in Brazil and compare them with cases from other countries. Five hundred and thirteen cases were retrospectively analyzed. HE-stained sections and clinical information were reviewed and the immunohistochemical expression of CD117, CD34, smooth-muscle actin, S-100 protein, desmin, CD44v3 adhesion molecule, p53 protein, epidermal growth factor receptor, and Ki-67 antigen was studied using tissue microarrays. Mutation analysis of KIT and platelet-derived growth factor receptor-alpha genes was also performed. There was a slight female predominance (50.3%) and the median age at diagnosis was 59 years. The tumors were mainly located in the stomach (38.4%). Immunohistochemistry showed that CD117 was expressed in 95.7% of cases. Epidermal growth factor receptor expression was observed in 84.4% of tumors. p53 protein expression was found only in 2.6% of cases but all belonged to the high-risk group for aggressive behavior according to the National Institutes of Health consensus approach. No CD44v3 adhesion molecule expression was detected. KIT exon 11 mutations were the most frequent (62.2%). The present data confirm that gastrointestinal stromal tumors in Brazilian patients do not differ from tumors occurring in other countries.

Effets des changements climatiques sur la santé et la sécurité des travailleurs au Québec

Les impacts des changements climatiques sur la population sont nombreux et ont été relativement bien documentés, ce qui n’est pas le cas de ces impacts sur la santé et la sécurité des travailleurs. L’objectif de cette thèse est de documenter les effets négatifs des changements climatiques sur la santé et la sécurité des travailleurs dans une région d’un pays industrialisé à climat tempéré, comme le Québec. Pour y arriver, deux approches ont été utilisées : a) les dangers et les effets sanitaires ont été identifiés par une revue de la littérature validée par des experts nationaux et internationaux, et des priorités de recherche ont été établies à l’aide d’une méthode de consultation itérative, b) des modèles statistiques, utiles à l’estimation des impacts sanitaires des changements climatiques, ont été développés pour apprécier les associations entre la survenue de lésions professionnelles et l’exposition des travailleurs aux chaleurs estivales et à l’ozone troposphérique, deux problématiques préoccupantes pour le Québec. Le bilan des connaissances a mis en évidence cinq catégories de dangers pouvant affecter directement ou indirectement la santé et la sécurité des travailleurs au Québec (vagues de chaleur, polluants de l’air, rayonnements ultraviolets, événements météorologiques extrêmes, maladies vectorielles transmissibles et zoonoses) et cinq conditions pouvant entraîner des modifications dans l’environnement de travail et pouvant ultimement affecter négativement la santé et la sécurité des travailleurs (changements dans les méthodes agricoles et d’élevage, altérations dans l’industrie de la pêche, perturbations de l’écosystème forestier, dégradation de l’environnement bâti et émergence de nouvelles industries vertes). Quant aux modélisations, elles suggèrent que les indemnisations quotidiennes pour des maladies liées à la chaleur et pour des accidents de travail augmentent avec les températures estivales, et que ces associations varient selon l’âge des travailleurs, le secteur industriel et la catégorie professionnelle (manuelle vs autre). Des associations positives statistiquement non significatives entre les indemnisations pour des atteintes respiratoires aiguës et les concentrations d’ozone troposphérique ont aussi été observées. Dans l’ensemble, cette thèse a permis de dégager douze pistes de recherche prioritaires pour le Québec se rapportant à l’acquisition de connaissances, à la surveillance épidémiologique et au développement de méthodes d’adaptation. Selon les résultats de cette recherche, les intervenants en santé au travail et les décideurs devraient déployer des efforts pour protéger la santé et la sécurité des travailleurs et mettre en place des actions préventives en vue des changements climatiques.

Rekonstruktion der eiszeitlichen Verbreitung und Artbildung vier alpiner Primeln durch Artenverbreitungsmodelle und Phylogeographie

Aim: Previous studies revealed that diversification events in the western clade of the alpine Primula sect. Auricula were concentrated in the Quaternary cold periods. This implies that allopatric speciation in isolated glacial refugia was the most common mode of speciation. In the first part of the present dissertation, this hypothesis is further investigated by locating refugial areas of two sister species, Primula marginata & P. latifolia during the last glacial maximum, 21,000 years ago. In the second part, the glacial and postglacial history of P. hirsuta and P. daonensis is investigated. Location: European Alps. Methods: Glacial refugia were located using species distribution models, which are projected to last glacial maximum climate. These refugia are validated with geographic distribution patterns of intra-specific genetic diversity, rarity and variation. Results 1) Speciation: Glacial refugia of the sister taxa Primula marginata and P. latifolia were largely separated, only a small overlapping zone at the southern margin of the former glacier in the Maritime Alps exists. This overlapping zone is too small to indicate sympatric speciation. The largely separated glacial distribution of both species rather confirms our hypothesis of allopatric speciation in isolated glacial refugia. Results 2) Glacial and postglacial history: Surprizingly, the modelled potential refugia of three out of four Primula species are situated within the former ice-shield, except for P. marginata. This indicates that peripheral and central nunataks played an important role for the glacial survival in P. latifolia, P. hirsuta and P. daonensis, while peripheral refugia outside the maximum extend of the glacier were crucial in P. marginata. In P. hirsuta and P. latifolia SDMs allowed to exclude several hypothetical refugial areas that overlap with today’s distribution as potential refugia for the species. In P. marginata, hypothetical refugial areas at the periphery of the former ice-shield that overlap with today’s distribution were confirmed by the models. The results from the SDMs are confirmed by population genetic patterns in three out of four species. P. daonensis represents an exception, where population genetic data contradict the SDMs. Main conclusions: Species distribution models provide species specific scenarios of glacial distribution and postglacial re-colonization, which can be validated using population genetic analyses. This combined approach is useful and helps to understand the complex processes that have lead to the genetic and floristic patterns of biodiversity that is found today in the Alps.

Le cancer du sein sans envahissement ganglionnaire. Au-delà des consensus internationaux: une approche pragmatique [Node negative breast cancer. Beyond international consensus: a pragmatic approach].

Apart from therapeutic advances related to new treatments, our practices in the management of early breast cancer have been modified by to key organizational settings (1) mass screening, substantially altering the presentation and epidemiology of breast cancer and (2) the development of guidelines to ensure that any patient management is in agreement with the demonstrated impact in the adjuvant treatment. In daily practice, the impact of screening and guidelines recommendations has put us now in a paradoxical situation: while the majority of non-metastatic breast cancers treated in the hexagon are node negative, most of the results of clinical studies on chemotherapy and targeted therapies today arise from populations predominantly node positive. Therefore, it seemed legitimate to convene a working group around a reflection on the directions of adjuvant chemotherapy in a growing node negative population in order to better respond to the questions of the field oncologists, trying to address the discrepancies between different existing guidelines.

Multidisciplinary consensus on the approach to hospital malnutrition in Spain

Rationale: Disease-related malnutrition constitutes a highly prevalent healthcare problem with high costs associated. In Spain, the prevalence of malnutrition in hospitalized patients has been reported from 30% to 50%. Objectives: Main purposes of this consensus document were to establish recommendations that facilitate decision- making and action to prevent and early-diagnose disease-related hospital malnutrition, on the management of nutritional support methods and actions to evaluate nutritional treatment compliance and efficacy. Methods: A systematic bibliographical search of authors was performed, complemented by updated bibliography by author references up to 2010. From this review, some recommendations were defined, modified and critically evaluated by the representatives of scientific societies in a consensus conference (Dec 2010) following a structured brainstorming technique: the Metaplan® technique. A double validation process was undertaken until final recommendations were obtained. Results: 30 consensus recommendations for the prevention and management of hospital malnutrition are presented in this document. Recommendations cover all clinical care settings as well as prevention, screening, diagnosis, treatment and follow-up of disease-related malnutrition. Conclusions: Nutritional screening is strongly recommended at all clinical settings when nutritional risk factors are identified or there is clinical suspicion of malnutrition. Nutritional assessment should be designed and performed according to centers’ resources, but clearly identified protocols should be available.