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

Salivary Cytokines as Potential Diagnostic Biomarkers for Systemic Lupus Erythematosus Disease

Systemic lupus erythematosus (SLE) is a complex autoimmune inflammatory disease characterized by an unknown etiology and a highly variable clinical presentation. This clinical heterogeneity might be explained by dysregulation of tolerance to self and apoptotic mechanisms, overproduction of autoantibodies, and abnormal cytokine levels. Cytokine imbalance levels have been associated with disease activity and severity in SLE patients. In the last years, salivary cytokines related to SLE have gained significant attention and researchers have begun to focus on the identification of cytokines in the saliva of SLE patients using it as a diagnostic fluid for the inflammatory process underlying SLE. This review highlights and summarizes recent studies revealing the cytokines that have been identified in the saliva of individuals with SLE. Data reported and discussed in this report may provide useful additional information to better understand the mechanisms associated with the disease

Antimicrobial Resistance Trends in Staphylococcus aureus Strains Carried by Poultry in North of Morocco: A Preliminary Analysis

The transmission of antibiotic resistance to human population through food consumption is a global public health threat. This study aimed to assess the nasopharyngeal carriage of S. aureus in poultry and to investigate antimicrobial susceptibility and virulence-associated genes. Nasopharyngeal swabs were collected from chickens at the slaughterhouse of Tangier and immediately transported to the microbiological laboratory for phenotypic identification and assessment of antibiotic susceptibility. The presence of 16S rRNA, nuc, mecA, mecC, Panton–Valentine leukocidin (PVL), and the toxic shock syndrome toxin 1 (TSST-1) genes were detected by PCR analysis for all isolates. Overall, 548 nasopharyngeal swabs were collected, of which 17 (3.4%) were S. aureus positive. More than half of the strains (54%) were resistant to penicillin, 29.4% to tetracycline, 23.5% to erythromycin, and 17% showed resistance to ciprofloxacin. The mecA and mecC were not identified in any of the recovered isolates. Of the S. aureus recovered, 29.41% of the isolates were found to be toxinogenic; 17.64% and 11.76% were positive for PVL and TSST-1 encoding genes, respectively. The trends of antibiotic resistance and the toxinogenic S. aureus carried by the poultry intended for consumption in Tangier present a huge concern. Preventive and containment measures should be implemented in order to limit the dissemination of resistance genes through the food chain and to reduce their increased rate

Salivary Biomarkers in Systemic Sclerosis Disease

Scleroderma or systemic sclerosis (SSc) is frequently detected at an advanced stage due to diagnosis difficulties. Salivary biomarkers, if existing, could be used for predictive diagnosis of this disease. Human saliva contains a large number of proteins that can be used for diagnosis and are of great potential in clinical research. The use of proteomic analysis to characterize whole saliva (WS) in SSc has gained an increasing attention in the last years and the identification of salivary proteins specific for SSc could lead to early diagnosis or new therapeutic targets. This review will present an overview about the use of WS in SSc studies. The proteomic technologies currently used for global identification of salivary proteins in SSc, as well as the advantages and limitations for the use of WS as a diagnostic tool, will be presented

Immunological and Clinical Characteristics of Systemic Lupus Erythematosus: A Series from Morocco

Systemic Lupus Erythematosus (SLE) is a complex autoimmune disease with a high female predominance. To date, studies about SLE in Morocco are few. This retrospective study describes the clinical and immunological features in a series of 50 SLE Moroccan patients in University Hospital Center of Rabat, Morocco, between December 2011 and December 2013. All patients were screened for antinuclear antibodies (ANA) and anti-DNA antibodies by indirect immunofluorescence, followed by identification of anti-extractable nuclear antigen antibodies by ELISA. The female to male ratio was 6.1:1. Mean age was 31.72 years. The main clinical manifestations were arthritis (82%), mucocutaneous manifestations (80%), renal manifestations (50%), and hematological features (46%). Of the mucocutaneous features, the highest frequencies were observed in the malar rash (68%) and photosensitivity (60%). Of the hematological features, lymphopenia was most frequently observed in 30% of patients, followed by hemolytic anemia in 16% and leucopenia and thrombocytopenia in 8%. Central nervous system was involved in 10%. ANA were found in 88%, anti-DNA antibodies in 56%, and anti-Sm antibodies in 50%. Anti-SSA, anti-SSB, anti-Sm/RNP, and anti-Scl70 antibodies were detected in 38%, 10%, 48%, and 8%, respectively. Our data show that, in our patients, the main clinical and immunological features of SLE remain comparable to patients from other Arab countries

Changes in food behavior during the first lockdown of COVID-19 pandemic: a multi-country study about changes in eating habits, motivations, and food-related behaviors

AgriFood XXI I&D&I project NORTE01-0145-FEDER-000041.FCT_UIDB/05183/2020. FCT_UIDB/05748/2020. FCT_UIDB/04470/2020. FCT_UIDB/04007/2020.The COVID-19 pandemic resulted in severe, unprecedented changes affecting the world population. Restrictions in mobility, social distancing measures, and the persistent social alarm, during the first period of the pandemic, resulted in dramatic lifestyle changes and affected physical and psychological wellbeing on a global scale. An international research team was constituted to develop a study involving different countries about eating motivations, dietary habits, and behaviors related to food intake, acquisition, and preparation. This study presents results of an online survey, carried out during the first lockdown, in 2020, assessing food-related behavior and how people perceived them to change, comparatively to the period preceding the COVID-19 outbreak. A total of 3332 responses, collected from 16 countries, were considered for analysis [72.8% in Europe, 12.8% in Africa, 2.2% in North America (USA), and 12.2% in South America]. Results suggest that the main motivations perceived to drive food intake were familiarity and liking. Two clusters were identified, based on food intake frequency, which was classified as “healthier” and “unhealthier”. The former was constituted by individuals with higher scholarly levels, to whom intake was more motivated by health, natural concerns, and weight control, and less by liking, pleasure or affect regulation. The second cluster was constituted by individuals with a higher proportion of males and intake more influenced by affect-related motivations. During this period, a generalized lower concern with the convenience attributes of foods was noted (namely, choice of processed products and fast-food meals), alongside an increase in time and efforts dedicated to home cooking. Understanding the main changes and their underlying motivations in a time of unprecedented crisis is of major importance, as it provides the scientific support that allows one to anticipate the implications for the future of the global food and nutrition system and, consequently, to take the appropriate action.info:eu-repo/semantics/publishedVersio