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

ПАРАДОКС БАЛАЯНА

This article presents the results of a study of the epidemiology of hepatitis E in the Russian Federation. Obtained data explaining the phenomenon, known as the Balayan paradox - the wide distribution of anamnestic antibodies to the hepatitis E virus in the absence of a registered incidence. It was shown that imported cases of infection are not able to support the epidemiological process of hepatitis E in Russia. The most cases of HEV infection are autochthonous in nature and are associated with zoonotic transmission of genotype 3 virus from pigs.В статье представлены результаты изучения эпидемиологии гепатита Е на территории Российской Федерации. Получены данные, объясняющие феномен, известный как парадокс Балаяна - широкое распространение анамнестических тел к вирусу гепатита Е при отсутствии регистрируемой заболеваемости. Показано, что завозные случаи инфекции не в состоянии поддержать эпидемиологический процесс гепатита Е на территории России. Большинство случаев ВГЕ-инфекции имеют автохтонный характер и связаны с зоонозной передачей вируса 3 генотипа от свиней

Detection of markers of hepatitis B and D virus infection in biological media and dried blood spots

The aim of this study was to assess the rates of detection of the major markers of infection with hepatitis B and Delta (D) viruses in serum, saliva and dry blood dots (DBS) as a possible option for serological studies among the population of the endemic region in conditions of limited laboratory resources. For this purpose, paired samples of blood serum and DBS, blood serum and saliva from patients with chronic hepatitis B with Delta agent living in the Republic of Tyva, which is endemic for this disease. HBsAg was detected in 289 (100%) serum samples, in 88/92 (95.7%) saliva samples, in 60/80 (75%) DBS samples, stored three years at room temperature, and in 111/117 (94.9%) DBS stored one year at the same conditions. Anti-HBcore was detected in 209 (100%) serum samples, while in saliva and DBS samples this marker was detected in only 13.04% (12/92) and 19.7% (23/117), respectively. Anti-HDV antibodies in serum were detected in 209 (100%) samples collected from patients in 2017-2018. In saliva and DBS anti-HDV were not detected in any sample. This difference in the detection rates of anti-HBcore and anti-HDV might be accounted for the fact that the HBV core protein is a very strong immunogen, indusing the production of anti-HBcore in high concentrations. Probably, the concentration of anti-HDV is much lower, which explains its absence in saliva and DBS in patients with hepatitis B+D. Samples of biological media (saliva), as well as DBS can serve as an alternative material for the detection of HBsAg in screening and research prevalence studies. Meanwhile, the definition of anti-HDV in such media is not possible due to the false negative results. Due to the high probability of superinfection with HDV in patients with HBV in endemic areas, the detection of HBsAg in alternative media (saliva or DBS) should be followed by testing for anti-HDV in serum samples

Вирусные гепатиты: прогнозы и проблемы

The problem of viral hepatitis is close to its solution. In 2016 WHO Global Health Sector Strategy for Viral Hepatitis for 2016-2021 has set the task for hepatitis control and elimination, and identified how to address it. The development of such a program has become possible due to the obtained fundamental knowledge about the nature of viral hepatitis, which allows to achieve this ambitious goal. Undoubtedly, the implementation of a program to control viral hepatitis in Russia, based on modern scientific knowledge and the realities of the epidemic process, will make it possible to solve the problem of controlling these diseases. However, new problems arise on this path. This publication addresses some of the current issues, in conjunction with own data. These problems may include: the possibility of the wide spread of hepatitis A virus among certain populations (hepatitis A outbreak in the USA in 2017-2018); the interspecies transmission of HEV from animals to humans; problems encountered in the implementation of the program for mass vaccination against HBV («Vaccine audit»); the history and characteristics of the circulation of the hepatitis D virus in various territories; distribution of circulating forms of the hepatitis C virus with drug resistance to direct-acting drugs (interferon-free therapy). New knowledge on the above mentioned issues are crucial for the successful implementation of the program for the control of viral hepatitis.Проблема вирусных гепатитов близка к решению. Принятая ВОЗ в 2016 г. «Глобальная стратегия сектора здравоохранения по вирусному гепатиту на 2016-2021 гг.» поставила задачу и определила пути её решения. Разработка такой программы стала возможной благодаря полученным новым фундаментальным знаниям о природе вирусных гепатитов. Реализация программы по контролю за вирусными гепатитами в России, основанная на современных научных знаниях и реалиях эпидемического процесса, позволит решить задачу по контролю над этими заболеваниями. В статье рассматриваются некоторые актуальные вопросы, связанные с вирусными гепатитами: возможность широкого распространения вируса гепатита А среди отдельных групп населения (вспышка гепатита А в США в 2017-2018 гг.); межвидовой переход вируса гепатита Е от животных человеку; сложности, возникшие при реализации программ массовой вакцинации против гепатита В («вакцинный аудит»); история и особенности циркуляции вируса гепатита D на различных территориях; распространение циркулирующих форм вируса гепатита С, обладающих лекарственной резистентностью к препаратам прямого действия (безинтерфероновая терапия). Получение новых знаний по этим проблемам необходимо для успешной реализации программы по контролю за вирусными гепатитами

Assessment of Diagnostic Specificity of Anti-SARS-CoV-2 Antibody Tests and Their Application for Monitoring of Seroconversion and Stability of Antiviral Antibody Response in Healthcare Workers in Moscow

Anti-SARS-CoV-2 antibody testing is an efficient tool to assess the proportion of seropositive population due to infection and/or vaccination. Numerous test systems utilizing various antigen composition(s) are routinely used for detection and quantitation of anti-SARS-CoV-2 antibodies. We determined their diagnostic specificity using archived true-negative samples collected before the onset of the COVID-19 pandemic. Using test systems demonstrating 98.5–100% specificity, we assessed the dynamics of SARS-CoV-2 seroconversion and durability of anti-spike (S) antibodies in healthcare professionals (n = 100) working in Moscow during the first two cycles of the pandemic (May 2020 to June 2021) outside of the “red zone”. Analysis revealed a rapid increase in anti-SARS-CoV-2 seropositivity from 19 to 80% (19/100 and 80/100, respectively) due to virus exposition/infection; only 16.3% of seroconversion cases (13/80) were due to vaccination, but not the virus exposure, although massive COVID-19 vaccination of healthcare workers was performed beginning in December 2020. In total, 12.7% (8/63) remained positive for anti-SARS-CoV-2 IgM for >6 months, indicating unsuitability of IgM for identification of newly infected individuals. All except one remained seropositive for anti-S antibodies for >9 months on average. Significant (>15%) declines in anti-SARS-CoV-2 antibody concentrations were observed in only 18% of individuals (9/50). Our data on the high seropositivity rate and stability of anti-SARS-CoV-2 antibody levels in healthcare personnel working outside of the “red zone” indicate their regular exposition to SARS-CoV-2/an increased risk of infection, while a low frequency of vaccine-induced antibody response acquired after the start of vaccination points to vaccine hesitancy. © 2022 by the authors. Licensee MDPI, Basel, Switzerland

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