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

Mortality from gastrointestinal congenital anomalies at 264 hospitals in 74 low-income, middle-income, and high-income countries: a multicentre, international, prospective cohort study

Summary Background Congenital anomalies are the fifth leading cause of mortality in children younger than 5 years globally. Many gastrointestinal congenital anomalies are fatal without timely access to neonatal surgical care, but few studies have been done on these conditions in low-income and middle-income countries (LMICs). We compared outcomes of the seven most common gastrointestinal congenital anomalies in low-income, middle-income, and high-income countries globally, and identified factors associated with mortality. Methods We did a multicentre, international prospective cohort study of patients younger than 16 years, presenting to hospital for the first time with oesophageal atresia, congenital diaphragmatic hernia, intestinal atresia, gastroschisis, exomphalos, anorectal malformation, and Hirschsprung’s disease. Recruitment was of consecutive patients for a minimum of 1 month between October, 2018, and April, 2019. We collected data on patient demographics, clinical status, interventions, and outcomes using the REDCap platform. Patients were followed up for 30 days after primary intervention, or 30 days after admission if they did not receive an intervention. The primary outcome was all-cause, in-hospital mortality for all conditions combined and each condition individually, stratified by country income status. We did a complete case analysis. Findings We included 3849 patients with 3975 study conditions (560 with oesophageal atresia, 448 with congenital diaphragmatic hernia, 681 with intestinal atresia, 453 with gastroschisis, 325 with exomphalos, 991 with anorectal malformation, and 517 with Hirschsprung’s disease) from 264 hospitals (89 in high-income countries, 166 in middleincome countries, and nine in low-income countries) in 74 countries. Of the 3849 patients, 2231 (58·0%) were male. Median gestational age at birth was 38 weeks (IQR 36–39) and median bodyweight at presentation was 2·8 kg (2·3–3·3). Mortality among all patients was 37 (39·8%) of 93 in low-income countries, 583 (20·4%) of 2860 in middle-income countries, and 50 (5·6%) of 896 in high-income countries (p<0·0001 between all country income groups). Gastroschisis had the greatest difference in mortality between country income strata (nine [90·0%] of ten in lowincome countries, 97 [31·9%] of 304 in middle-income countries, and two [1·4%] of 139 in high-income countries; p≤0·0001 between all country income groups). Factors significantly associated with higher mortality for all patients combined included country income status (low-income vs high-income countries, risk ratio 2·78 [95% CI 1·88–4·11], p<0·0001; middle-income vs high-income countries, 2·11 [1·59–2·79], p<0·0001), sepsis at presentation (1·20 [1·04–1·40], p=0·016), higher American Society of Anesthesiologists (ASA) score at primary intervention (ASA 4–5 vs ASA 1–2, 1·82 [1·40–2·35], p<0·0001; ASA 3 vs ASA 1–2, 1·58, [1·30–1·92], p<0·0001]), surgical safety checklist not used (1·39 [1·02–1·90], p=0·035), and ventilation or parenteral nutrition unavailable when needed (ventilation 1·96, [1·41–2·71], p=0·0001; parenteral nutrition 1·35, [1·05–1·74], p=0·018). Administration of parenteral nutrition (0·61, [0·47–0·79], p=0·0002) and use of a peripherally inserted central catheter (0·65 [0·50–0·86], p=0·0024) or percutaneous central line (0·69 [0·48–1·00], p=0·049) were associated with lower mortality. Interpretation Unacceptable differences in mortality exist for gastrointestinal congenital anomalies between lowincome, middle-income, and high-income countries. Improving access to quality neonatal surgical care in LMICs will be vital to achieve Sustainable Development Goal 3.2 of ending preventable deaths in neonates and children younger than 5 years by 2030

Prevalence, associated factors and outcomes of pressure injuries in adult intensive care unit patients: the DecubICUs study

Funder: European Society of Intensive Care Medicine; doi: http://dx.doi.org/10.13039/501100013347Funder: Flemish Society for Critical Care NursesAbstract: Purpose: Intensive care unit (ICU) patients are particularly susceptible to developing pressure injuries. Epidemiologic data is however unavailable. We aimed to provide an international picture of the extent of pressure injuries and factors associated with ICU-acquired pressure injuries in adult ICU patients. Methods: International 1-day point-prevalence study; follow-up for outcome assessment until hospital discharge (maximum 12 weeks). Factors associated with ICU-acquired pressure injury and hospital mortality were assessed by generalised linear mixed-effects regression analysis. Results: Data from 13,254 patients in 1117 ICUs (90 countries) revealed 6747 pressure injuries; 3997 (59.2%) were ICU-acquired. Overall prevalence was 26.6% (95% confidence interval [CI] 25.9–27.3). ICU-acquired prevalence was 16.2% (95% CI 15.6–16.8). Sacrum (37%) and heels (19.5%) were most affected. Factors independently associated with ICU-acquired pressure injuries were older age, male sex, being underweight, emergency surgery, higher Simplified Acute Physiology Score II, Braden score 3 days, comorbidities (chronic obstructive pulmonary disease, immunodeficiency), organ support (renal replacement, mechanical ventilation on ICU admission), and being in a low or lower-middle income-economy. Gradually increasing associations with mortality were identified for increasing severity of pressure injury: stage I (odds ratio [OR] 1.5; 95% CI 1.2–1.8), stage II (OR 1.6; 95% CI 1.4–1.9), and stage III or worse (OR 2.8; 95% CI 2.3–3.3). Conclusion: Pressure injuries are common in adult ICU patients. ICU-acquired pressure injuries are associated with mainly intrinsic factors and mortality. Optimal care standards, increased awareness, appropriate resource allocation, and further research into optimal prevention are pivotal to tackle this important patient safety threat

Correction to: Prevalence, associated factors and outcomes of pressure injuries in adult intensive care unit patients: the DecubICUs study

The original version of this article unfortunately contained a mistake

Prevalence, associated factors and outcomes of pressure injuries in adult intensive care unit patients: the DecubICUs study

Funder: European Society of Intensive Care Medicine; doi: http://dx.doi.org/10.13039/501100013347Funder: Flemish Society for Critical Care NursesAbstract: Purpose: Intensive care unit (ICU) patients are particularly susceptible to developing pressure injuries. Epidemiologic data is however unavailable. We aimed to provide an international picture of the extent of pressure injuries and factors associated with ICU-acquired pressure injuries in adult ICU patients. Methods: International 1-day point-prevalence study; follow-up for outcome assessment until hospital discharge (maximum 12 weeks). Factors associated with ICU-acquired pressure injury and hospital mortality were assessed by generalised linear mixed-effects regression analysis. Results: Data from 13,254 patients in 1117 ICUs (90 countries) revealed 6747 pressure injuries; 3997 (59.2%) were ICU-acquired. Overall prevalence was 26.6% (95% confidence interval [CI] 25.9–27.3). ICU-acquired prevalence was 16.2% (95% CI 15.6–16.8). Sacrum (37%) and heels (19.5%) were most affected. Factors independently associated with ICU-acquired pressure injuries were older age, male sex, being underweight, emergency surgery, higher Simplified Acute Physiology Score II, Braden score 3 days, comorbidities (chronic obstructive pulmonary disease, immunodeficiency), organ support (renal replacement, mechanical ventilation on ICU admission), and being in a low or lower-middle income-economy. Gradually increasing associations with mortality were identified for increasing severity of pressure injury: stage I (odds ratio [OR] 1.5; 95% CI 1.2–1.8), stage II (OR 1.6; 95% CI 1.4–1.9), and stage III or worse (OR 2.8; 95% CI 2.3–3.3). Conclusion: Pressure injuries are common in adult ICU patients. ICU-acquired pressure injuries are associated with mainly intrinsic factors and mortality. Optimal care standards, increased awareness, appropriate resource allocation, and further research into optimal prevention are pivotal to tackle this important patient safety threat

Les versions françaises de la Chirurgia Parva de Lanfranc de Milan. Étude de la tradition manuscrite

The Chirurgia Parva dedicated to king Philip the Fair, has been written by Lanfranc of Milano at Lyons in 1296. Four known French versions exist in fifteenth century manuscripts and we have discovered another one, with no beginning, several lacunae and no end, preserved in some thirty dismembered folios, which are part of the heterogeneous ms. Bern, Burgerbibl. A 95 and could be ascribed to the beginning of the 14th century. We have studied the relationship between those five copies, and the circulation of the Chirurgia Parva in vernacular languages. In spite of their numerous discordances they all are likely descending from the same and unique translation, made in North Eastern France, very soon after the completion of the latin text. Furthermore, this unique translation could have been the basis for one, or may be several, german versions of the Chirurgia Parva. This paper gives the description of the manuscripts containing the French versions of Lanfranc's treatise and a detailed analysis of all the medical texts. Then follows a comparative study of the French versions and the Latin original. We have tried to isolate the linguistic criteria which caracterize such practical translation : changing of words, dialectal peculiarities, a.s.o. Some examples borrowed to other medical texts translated from French, especially in the Flanders and Germany, inisst upon the importance of vernacular languages for the circulation of didactical littérature.La Chirurgia Parva de Lanfranc de Milan a été écrite à Lyon en 1296 et dédiée à Philippe le Bel. On en connaissait jusqu'ici quatre rédactions françaises, copiées dans des manuscrits du XVe siècle. Or il en existe une cinquième, acéphale et mutilée, conservée sur des feuillets détachés, dans le recueil factice Berne, Bürgerbibl. A. 95 ; on peut la dater du début du XIVe siècle. La présente étude porte sur les rapports existant entre ces cinq copies, et sur la diffusion de la Chirurgia Parva en langue vernaculaire. Bien qu'elles soient fortement divergentes, en particulier deux d'entre elles, toutes les copies dérivent, bien vraisemblablement, d'une seule et même traduction élaborée dans le Nord-Est de la France peu de temps après la rédaction du texte latin. En outre, il est possible que cette traduction ait servi de base à une ou plusieurs rédactions de la Chirurgia Parva en langue allemande. On trouvera dans cet article une description des manuscrits qui contiennent les rédactions françaises du traité de Lanfranc, et l'analyse de leur contenu. Les notices sont suivies d'une étude comparée des textes vernaculaires en fonction du texte latin ; on s'est particulièrement attaché à dégager les critères linguistiques susceptibles d'éclairer l'histoire d'une traduction d'utilité pratique : modifications dans le vocabulaire, coloration dialectale. Enfin quelques exemples empruntés à d'autres textes médicaux traduits du français, en Flandre et dans les terres d'Empire, confirment l'importance de la langue vernaculaire dans la diffusion d'une littérature didactique de vulgarisation.De Tovar Claude. Les versions françaises de la Chirurgia Parva de Lanfranc de Milan. Étude de la tradition manuscrite. In: Revue d'histoire des textes, bulletin n°12-13 (1982-1983), 1985. pp. 195-262

À propos de la Chirurgie de l'abbé Poutrel

De Tovar Claude. À propos de la Chirurgie de l'abbé Poutrel. In: Romania, tome 103 n°410-411, 1982. pp. 345-362

Contamination, interférences et tentatives de systématisation dans la tradition manuscrite des réceptaires médicaux français. Le réceptaire de Jean Sauvage (Deuxième partie)

Contamination, interferences and systematical tentatives in the manuscript tradition of the French medical « Receptaire » : The « Receptaire » of Jean Sauvage. End of the work published under the same title in the former volume of this revue.Suite, et fin, de l'article paru sous le même titre dans le volume précédent.De Tovar Claude. Contamination, interférences et tentatives de systématisation dans la tradition manuscrite des réceptaires médicaux français. Le réceptaire de Jean Sauvage (Deuxième partie). In: Revue d'histoire des textes, bulletin n°4 (1974), 1975. pp. 239-288

Contamination, interférences et tentatives de systématisation dans la tradition manuscrite des réceptaires médicaux français : le réceptaire de Jean Sauvage

Contamination, interferences and systematical tentatives in the manuscript tradition of the French medical « Receptaire » : The « Receptaire » of Jean Sauvage. The Receptaire written by Jean Sauvage, from Picquigny, is found in three collections of medical texts : Paris, Bibl. Arsenal 3174 ; Paris, Bibl. nat., fr. 1319, and Berlin, Hamilton 407 ; the Paris manuscripts are closely related, the Berlin one contains a different series of texts ; a detailed and accurate description is given of each manuscript. The Receptaire written at Blois, by an author coming from Picardy, in the middle of the 14th century, could therefore be replaced in a precise historical background. The translation in octosyllabic verses Jean Sauvage made of the Thesaurus pauperum of Pierre d'Espagne forms the main bulk of his work, into which he has interpolated other vernacular texts, among them, in its whole, the short and anonymous prose Receptaire otherwise known as Lettre d'Hippocrate à César ; These texts belong to several linguistic areas ; other minor borrowings are found besides the main sources. The whole corpus is built with a peculiar didactic care.Le réceptaire de Jean Sauvage de Picquigny qui a servi de base à cette recherche se trouve dans trois collections médicales : les mss. : Paris, Bibl. de l'Arsenal 3174, Paris, Bibl. nat., fr. 1319, très voisins, et Berlin, Bibl. Hamilton 407, celui-ci donnant un ensemble différent de textes ; leur contenu est analysé dans des notices détaillées. Le réceptaire originairement écrit à Blois, par un Picard, vers le milieu du XIVe siècle, peut être situé dans un contexte historique relativement précis. Jean Sauvage traduit en octosyllabes le Thesaurus pauperum de Pierre d'Espagne, qui forme la base de son ouvrage. Il y interpole d'autres textes en langue vulgaire, principalement le petit réceptaire anonyme, en prose, appelé Lettre d'Hippocrate à César, qu'il transcrit tel quel. Ces textes appartiennent à des zones linguistiques différentes. On retrouve en dehors de ces trois sources d'autres emprunts de moindre importance. La présentation de l'ensemble témoigne d'un souci didactique original.De Tovar Claude. Contamination, interférences et tentatives de systématisation dans la tradition manuscrite des réceptaires médicaux français : le réceptaire de Jean Sauvage. In: Revue d'histoire des textes, bulletin n°3 (1973), 1974. pp. 115-191