Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

The role of B-mode ultrasonography in the musculoskeletal anatomical evaluation of the cervical region of the dog spine

This study characterized the normal musculoskeletal anatomy of the cervical segment of the spine of dogs by means of B-mode ultrasonography. The objective was to establish the role of B-mode ultrasonography for the anatomical evaluation of the cervical spine segment in dogs, by comparing the ultrasonographic findings with images by computed tomography and magnetic resonance imaging. The ultrasound examination, in transverse and median sagittal sections, allowed to identify a part of the epaxial cervical musculature, the bone surface of the cervical vertebrae and parts of the spinal cord through restricted areas with natural acoustic windows, such as between the atlanto-occipital joint, axis and atlas, and axis and the third cervical vertebra. The images, on transverse and sagittal planes, by low-field magnetic resonance imaging, were superior for the anatomical identification of the structures, due to higher contrast between the different tissues in this modality. Computed tomography showed superiority for bone detailing when compared with ultrasonography. As for magnetic resonance imaging, in addition to the muscles and cervical vertebrae, it is possible to identify the cerebrospinal fluid and differentiate between the nucleus pulposus and annulus fibrosus of the intervertebral discs. Although not the scope of this study, with knowledge of the ultrasonographic anatomy of this region, it is believed that some lesions can be identified, yet in a limited manner, when compared with the information obtained mainly with magnetic resonance imaging. The ultrasound examination presented lower morphology diagnostic value compared with the other modalities.Este estudo caracterizou a anatomia musculoesquelética normal do segmento cervical da coluna vertebral de cães por meio da ultrassonografia modo B. O objetivo do trabalho foi estabelecer o papel da ultrassonografia modo B na avaliação anatômica do segmento cervical de cães, comparando os achados ultrassonográficos com imagens por tomografia computadorizada e ressonância magnética. O exame ultrassonográfico, em cortes transversais e sagitais mediano, permitiu a identificação de parte da musculatura epaxial do pescoço, superfície óssea das vértebras cervicais e medula espinhal em áreas restritas com janelas acústicas naturais, como entre a articulação atlantoccipital, áxis e atlas, e áxis e terceira vértebra cervical. As imagens, em planos transversais e sagitais, por ressonância magnética de baixo campo foram superiores na identificação anatômica das estruturas, devido ao maior contraste entre os diferentes tecidos nessa modalidade. A tomografia computadorizada se mostrou superior no detalhamento ósseo da região quando comparada ao exame ultrassonográfico. Já a ressonância magnética, além dos músculos e vértebras cervicais, permitiu a identificação do líquido cefalorraquidiano, e diferenciar núcleo pulposo e anel fibroso dos discos intervertebrais. Embora não seja objetivo direto deste estudo, com o conhecimento da anatomia ultrassonográfica dessa região, acredita-se que algumas lesões possam ser identificadas, contudo de maneira restrita, quando comparadas as informações obtidas, principalmente na imagem por ressonância magnética. O exame ultrassonográfico apresentou valor morfológico inferior.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

International audienceIn 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

MACVIA Clinical Decision Algorithm in Allergic Rhinitis in adolescents and adults

International audienceThe selection of pharmacotherapy for patients with allergic rhinitis depends on several factors, including age, prominent symptoms, symptom severity, control of allergic rhinitis, patient preferences and cost. Allergen exposure and resulting symptoms vary and treatment adjustment is required. Clinical decision support systems (CDSS) may be beneficial for the assessment of disease control. Clinical decision support systems should be based on the best evidence and algorithms to aid patients and health care professionals to jointly determine the treatment and its step-up or step-down strategy depending on AR control. MACVIA-LR (Fighting chronic diseases for active and healthy ageing) one of the reference sites of the European Innovation Partnership on Active and Healthy Ageing, has initiated an allergy sentinel network (MASK: MACVIA-ARIA Sentinel networK). A clinical decision support system is currently being developed to optimize allergic rhinitis control. An algorithm developed by consensus is presented in this paper. This algorithm should be confirmed by appropriate trials