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

Indagine conoscitiva sulla violenza verso il maschile

Riassunto La violenza di genere costituisce una tipologia di reato in costante espansione e di continuo interesse da parte della comunità scientifica. Il fenomeno nella sua globalità è complesso da analizzare in quanto gli autori di reato commettono gli episodi perlopiù entro le mura domestiche e ciò comporta, dato il legame spesso di natura intrafamiliare tra autore e vittima, il silenzio di quest’ultima che concorre ad accrescere il cosiddetto “numero oscuro”. Da ciò derivano i limiti dell’analisi di un fenomeno per sua natura sommerso, del quale non è facile tracciare i contorni. Una conoscenza approfondita del fenomeno nel suo insieme, tuttavia, è essenziale per lo sviluppo delle politiche e dei servizi, a partire dalle campagne di sensibilizzazione per arrivare alle contromisure legislative finalizzate a prevenire e/o contenere la violenza. Va rilevato come inchieste, sondaggi e ricerche che analizzano tale comportamento deviante e che vengono proposte con continuità a livello istituzionale e mediatico da diversi decenni, sono solite prendere in considerazione solo l’eventualità che la vittima della violenza di genere sia donna e che l’autore di reato sia uomo. Tale informazione, distorta alla sua origine, passa tramite canali ufficiali (dai media alle campagne di prevenzione) determinando una conseguente sensibilizzazione unidirezionale che relega ad eccezioni - spesso non prese neppure in considerazione - le ipotesi che la violenza possa essere subita e/o agita da appartenenti ad entrambi i sessi. L’indagine presentata in questo articolo è finalizzata a raccogliere elementi di valutazione ancora inesistenti nel nostro Paese, utili a verificare se esista, ed eventualmente in che misura, una realtà diversa da quella fondata esclusivamente su condizionamenti, luoghi comuni e pregiudizi. La violence de genre constitue l’un des crimes qui connaît une forte croissance et qui fait l’objet d’un intérêt certain pour la communauté scientifique. Le phénomène est complexe à analyser dans sa globalité car la plupart des auteurs commettent leurs crimes dans le foyer domestique. Étant donné le lien intrafamilial existant entre l’auteur et la victime, cette dernière reste dans le silence qui contribue à faire augmenter le « chiffre noir ». Par conséquent, l’analyse de ce phénomène, caché à cause de sa propre nature, montre ses limites. Des campagnes de sensibilisation à l’adoption de mesures législatives pour la prévention et répression de la violence, une connaissance approfondie de ce phénomène dans sa globalité est toutefois primordial pour le développement des politiques et des services d’aide aux victimes. Il faut souligner que les enquêtes et les recherches analysant ce comportement déviant et, depuis plusieurs décennies, proposées en permanence à des niveaux institutionnel et médiatique, ont tendance à considérer que la victime de la violence de genre ne peut être qu’une femme et que son auteur, un homme. Cette information, altérée dès le début, passe à travers des chaînes officielles (des médias aux campagnes de prévention) provoquant une sensibilisation unidirectionnelle qui relègue à l’état d’exceptions – qui souvent ne sont même pas prises en considération – les hypothèses que la violence puisse être subie et/ou perpêtrée aussi bien par les hommes que par les femmes. L’enquête présentée dans cet article a pour objectif de collecter des éléments d’évaluation encore inexistants en Italie. Ces données peuvent être utilisées pour vérifier s’il existe une réalité différente de celle qui n’est basée que sur les lieux communs et sur les préjudices et quelle serait sa dimension. Gender-based violence is a constantly increasing crime and continuously attracting a lot of interest in the scientific community. This is a complex phenomenon to analyse as a whole because perpetrators usually commit the acts of violence at home. For this reason, and also due to the intimate relationship between the author and the victim, this latter remains silent, so the dark number increases. Consequently, the analysis of this phenomenon, hidden just because of its nature, has its limits. A deep knowledge of this phenomenon as a whole, however, is important for the development of policies and services, for example sensibilisation campaigns and countermeasures to prevent and combat violence. It is important to point out that surveys and researches studying this deviant behaviour, and continuously proposed at an institutional level and disseminated by mass media, usually consider that the victim of gender-based violence is a woman and the perpetrator a man. This distorted information is transmitted through official channels (for example, mass media and sensibilisation campaigns) producing a consequent unidirectional sensibilisation which relegates as exceptions – often not taken into consideration – hypothesis that violence may be endured and/or committed by both sexes. The purpose of the survey presented in this article is to collect some evaluation data that do not exist yet in our country, data that will be useful in order to verify if it exists in reality, and if yes what extension it has, different from the one based exclusively on common sense and prejudices

Predictive role of erythrocyte macrocytosis during treatment with pemetrexed in advanced non-small cell lung cancer patients

Pemetrexed has been approved for the treatment of advanced non-small cell lung cancer (NSCLC) non-squamous histology, both as first- and second-line therapy. Pemetrexed is an antimetabolite drug, that inhibits enzymes involved in nucleotides bio-synthesis arresting cancer cells cycle. The aim of this study was the evaluation of the impact of pemetrexed on erythrocyte mean corpuscular volume (MCV) change and its possible correlation with disease control rate (DCR), progression free (PFS) and overall survival (OS) in NSCLC patients

Multicentric, observational, longitudinal study for the evaluation of nutritional management implications in newly diagnosed Italian cancer patients: the Italian Registry of Malnutrition in Oncology (IRMO)

Background Malnutrition is a frequent problem in oncology and is associated with reduced response to cancer treatments, increased drug-related toxicity, higher rates of clinical complications, reduced quality of life (QoL) and worse prognosis. Guidelines on clinical nutrition in oncology emphasise the usefulness of early assessment of nutritional status for a prompt identification of malnutrition and the implementation of effective interventions, but no real-world clinical data are available on the adequate management of nutritional support in patients with cancer in Italy.Methods and analysis This is an observational, longitudinal, multicentre registry of patients with a new diagnosis of cancer or metastatic disease, candidates for active treatment. They will be identified in at least 15 Italian oncological centres, members of the Alliance Against Cancer Working Group ‘Survivorship Care and Nutritional Support’. At least 1500 patients with cancer are expected to be enrolled each year. Detailed clinical and nutritional data will be collected by oncologists and clinical nutritionists during the visits foreseen in the clinical practice, through an ad hoc developed digital platform (e-Nutracare). The effects of malnutrition and nutritional support—at diagnosis and during follow-up—on overall survival and progression-free survival, as well as on patients’ symptoms and QoL, will be investigated.Ethics and dissemination The study protocol was approved by the Ethics Committee of the Fondazione IRCCS Policlinico San Matteo, Pavia, Italy and from the Ethics Committees of all other participating centres. An informed consent will be obtained from each patient enrolled in the study. Study findings will be disseminated through peer-reviewed journals, conferences and patients with cancer or professional associations. The registry will allow a better monitoring of the nutritional status of patients with cancer, promoting adequate and sustainable nutritional support, with the ultimate goal of improving the care and prognosis of these patients

Symptomatic COVID-19 in advanced-cancer patients treated with immune-checkpoint inhibitors: prospective analysis from a multicentre observational trial by FICOG

Background:This prospective, multicentre, observational INVIDIa-2 study is investigating the clinical efficacy of influenza vaccination in advanced-cancer patients receiving immune-checkpoint inhibitors (ICIs), enrolled in 82 Italian centres, from October 2019 to January 2020. The primary endpoint was the incidence of influenza-like illness (ILI) until 30 April 2020. All the ILI episodes, laboratory tests, complications, hospitalizations and pneumonitis were recorded. Therefore, the study prospectively recorded all the COVID-19 ILI events.Patients and methods:Patients were included in this non-prespecified COVID-19 analysis, if alive on 31 January 2020, when the Italian government declared the national emergency. The prevalence of confirmed COVID-19 cases was detected as ILI episode with laboratory confirmation of SARS-CoV-2. Cases with clinical-radiological diagnosis of COVID-19 (COVID-like ILIs), were also reported.Results:Out of 1257 enrolled patients, 955 matched the inclusion criteria for this unplanned analysis. From 31 January to 30 April 2020, 66 patients had ILI: 9 of 955 cases were confirmed COVID-19 ILIs, with prevalence of 0.9% [95% confidence interval (CI): 0.3-2.4], a hospitalization rate of 100% and a mortality rate of 77.8%. Including 5 COVID-like ILIs, the overall COVID-19 prevalence was 1.5% (95% CI: 0.5-3.1), with 100% hospitalization and 64% mortality. The presence of elderly, males and comorbidities was significantly higher among patients vaccinated against influenza versus unvaccinated (p = 0.009, p < 0.0001, p < 0.0001). Overall COVID-19 prevalence was 1.2% for vaccinated (six of 482 cases, all confirmed) and 1.7% for unvaccinated (8 of 473, 3 confirmed COVID-19 and 5 COVID-like), p = 0.52. The difference remained non-significant, considering confirmed COVID-19 only (p = 0.33).Conclusion:COVID-19 has a meaningful clinical impact on the cancer-patient population receiving ICIs, with high prevalence, hospitalization and an alarming mortality rate among symptomatic cases. Influenza vaccination does not protect from SARS-CoV-2 infection

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 science. © The Author(s) 2019. Published by Oxford University Press