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

Global age-sex-specific mortality, life expectancy, and population estimates in 204 countries and territories and 811 subnational locations, 1950–2021, and the impact of the COVID-19 pandemic: a comprehensive demographic analysis for the Global Burden of Disease Study 2021

Background: Estimates of demographic metrics are crucial to assess levels and trends of population health outcomes. The profound impact of the COVID-19 pandemic on populations worldwide has underscored the need for timely estimates to understand this unprecedented event within the context of long-term population health trends. The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2021 provides new demographic estimates for 204 countries and territories and 811 additional subnational locations from 1950 to 2021, with a particular emphasis on changes in mortality and life expectancy that occurred during the 2020–21 COVID-19 pandemic period. Methods: 22 223 data sources from vital registration, sample registration, surveys, censuses, and other sources were used to estimate mortality, with a subset of these sources used exclusively to estimate excess mortality due to the COVID-19 pandemic. 2026 data sources were used for population estimation. Additional sources were used to estimate migration; the effects of the HIV epidemic; and demographic discontinuities due to conflicts, famines, natural disasters, and pandemics, which are used as inputs for estimating mortality and population. Spatiotemporal Gaussian process regression (ST-GPR) was used to generate under-5 mortality rates, which synthesised 30 763 location-years of vital registration and sample registration data, 1365 surveys and censuses, and 80 other sources. ST-GPR was also used to estimate adult mortality (between ages 15 and 59 years) based on information from 31 642 location-years of vital registration and sample registration data, 355 surveys and censuses, and 24 other sources. Estimates of child and adult mortality rates were then used to generate life tables with a relational model life table system. For countries with large HIV epidemics, life tables were adjusted using independent estimates of HIV-specific mortality generated via an epidemiological analysis of HIV prevalence surveys, antenatal clinic serosurveillance, and other data sources. Excess mortality due to the COVID-19 pandemic in 2020 and 2021 was determined by subtracting observed all-cause mortality (adjusted for late registration and mortality anomalies) from the mortality expected in the absence of the pandemic. Expected mortality was calculated based on historical trends using an ensemble of models. In location-years where all-cause mortality data were unavailable, we estimated excess mortality rates using a regression model with covariates pertaining to the pandemic. Population size was computed using a Bayesian hierarchical cohort component model. Life expectancy was calculated using age-specific mortality rates and standard demographic methods. Uncertainty intervals (UIs) were calculated for every metric using the 25th and 975th ordered values from a 1000-draw posterior distribution. Findings: Global all-cause mortality followed two distinct patterns over the study period: age-standardised mortality rates declined between 1950 and 2019 (a 62·8% [95% UI 60·5–65·1] decline), and increased during the COVID-19 pandemic period (2020–21; 5·1% [0·9–9·6] increase). In contrast with the overall reverse in mortality trends during the pandemic period, child mortality continued to decline, with 4·66 million (3·98–5·50) global deaths in children younger than 5 years in 2021 compared with 5·21 million (4·50–6·01) in 2019. An estimated 131 million (126–137) people died globally from all causes in 2020 and 2021 combined, of which 15·9 million (14·7–17·2) were due to the COVID-19 pandemic (measured by excess mortality, which includes deaths directly due to SARS-CoV-2 infection and those indirectly due to other social, economic, or behavioural changes associated with the pandemic). Excess mortality rates exceeded 150 deaths per 100 000 population during at least one year of the pandemic in 80 countries and territories, whereas 20 nations had a negative excess mortality rate in 2020 or 2021, indicating that all-cause mortality in these countries was lower during the pandemic than expected based on historical trends. Between 1950 and 2021, global life expectancy at birth increased by 22·7 years (20·8–24·8), from 49·0 years (46·7–51·3) to 71·7 years (70·9–72·5). Global life expectancy at birth declined by 1·6 years (1·0–2·2) between 2019 and 2021, reversing historical trends. An increase in life expectancy was only observed in 32 (15·7%) of 204 countries and territories between 2019 and 2021. The global population reached 7·89 billion (7·67–8·13) people in 2021, by which time 56 of 204 countries and territories had peaked and subsequently populations have declined. The largest proportion of population growth between 2020 and 2021 was in sub-Saharan Africa (39·5% [28·4–52·7]) and south Asia (26·3% [9·0–44·7]). From 2000 to 2021, the ratio of the population aged 65 years and older to the population aged younger than 15 years increased in 188 (92·2%) of 204 nations. Interpretation: Global adult mortality rates markedly increased during the COVID-19 pandemic in 2020 and 2021, reversing past decreasing trends, while child mortality rates continued to decline, albeit more slowly than in earlier years. Although COVID-19 had a substantial impact on many demographic indicators during the first 2 years of the pandemic, overall global health progress over the 72 years evaluated has been profound, with considerable improvements in mortality and life expectancy. Additionally, we observed a deceleration of global population growth since 2017, despite steady or increasing growth in lower-income countries, combined with a continued global shift of population age structures towards older ages. These demographic changes will likely present future challenges to health systems, economies, and societies. The comprehensive demographic estimates reported here will enable researchers, policy makers, health practitioners, and other key stakeholders to better understand and address the profound changes that have occurred in the global health landscape following the first 2 years of the COVID-19 pandemic, and longer-term trends beyond the pandemic

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

Global, regional, and national burden of disorders affecting the nervous system, 1990–2021: a systematic analysis for the Global Burden of Disease Study 2021

BackgroundDisorders affecting the nervous system are diverse and include neurodevelopmental disorders, late-life neurodegeneration, and newly emergent conditions, such as cognitive impairment following COVID-19. Previous publications from the Global Burden of Disease, Injuries, and Risk Factor Study estimated the burden of 15 neurological conditions in 2015 and 2016, but these analyses did not include neurodevelopmental disorders, as defined by the International Classification of Diseases (ICD)-11, or a subset of cases of congenital, neonatal, and infectious conditions that cause neurological damage. Here, we estimate nervous system health loss caused by 37 unique conditions and their associated risk factors globally, regionally, and nationally from 1990 to 2021.MethodsWe estimated mortality, prevalence, years lived with disability (YLDs), years of life lost (YLLs), and disability-adjusted life-years (DALYs), with corresponding 95% uncertainty intervals (UIs), by age and sex in 204 countries and territories, from 1990 to 2021. We included morbidity and deaths due to neurological conditions, for which health loss is directly due to damage to the CNS or peripheral nervous system. We also isolated neurological health loss from conditions for which nervous system morbidity is a consequence, but not the primary feature, including a subset of congenital conditions (ie, chromosomal anomalies and congenital birth defects), neonatal conditions (ie, jaundice, preterm birth, and sepsis), infectious diseases (ie, COVID-19, cystic echinococcosis, malaria, syphilis, and Zika virus disease), and diabetic neuropathy. By conducting a sequela-level analysis of the health outcomes for these conditions, only cases where nervous system damage occurred were included, and YLDs were recalculated to isolate the non-fatal burden directly attributable to nervous system health loss. A comorbidity correction was used to calculate total prevalence of all conditions that affect the nervous system combined.FindingsGlobally, the 37 conditions affecting the nervous system were collectively ranked as the leading group cause of DALYs in 2021 (443 million, 95% UI 378–521), affecting 3·40 billion (3·20–3·62) individuals (43·1%, 40·5–45·9 of the global population); global DALY counts attributed to these conditions increased by 18·2% (8·7–26·7) between 1990 and 2021. Age-standardised rates of deaths per 100 000 people attributed to these conditions decreased from 1990 to 2021 by 33·6% (27·6–38·8), and age-standardised rates of DALYs attributed to these conditions decreased by 27·0% (21·5–32·4). Age-standardised prevalence was almost stable, with a change of 1·5% (0·7–2·4). The ten conditions with the highest age-standardised DALYs in 2021 were stroke, neonatal encephalopathy, migraine, Alzheimer's disease and other dementias, diabetic neuropathy, meningitis, epilepsy, neurological complications due to preterm birth, autism spectrum disorder, and nervous system cancer.InterpretationAs the leading cause of overall disease burden in the world, with increasing global DALY counts, effective prevention, treatment, and rehabilitation strategies for disorders affecting the nervous system are needed

Study of serum Granzyme B in heavy cigarette smokers with and without chronic obstructive pulmonary disease

Background: Inflammation of the airways is present in COPD with increased number of inflammatory cells including killer cells that lyse their target cells by two mechanisms; membranolysis in which secreted molecules such as granzymes form pores in the membrane of target cells; and apoptosis. Granzyme B has the strongest apoptotic activity of all granzymes. Aim of this work: Aim of this work was to study the relation between Granzyme B, tobacco smoking and chronic obstructive pulmonary disease. Methods: The study included 40 clinically stable COPD patients classified according to GOLD (2013) criteria into two groups; moderate (GOLD II) and severe (GOLD III) plus 40 apparently healthy control subjects (20 smokers and 20 nonsmokers). Pulmonary function results and serum levels of Granzyme B (measured by ELISA) were recorded. Results: Granzyme B levels are elevated in COPD. Cigarette smoking appears to be a direct stimulus to Granzyme B production. Granzyme B could play a role in the pathogenesis of COPD. Aging seems to be a risk factor for Granzyme B production and pathogenesis of COPD. Conclusion: Granzyme B levels are elevated in COPD. Cigarette smoking appears to be a direct stimulus to Granzyme B production. Granzyme B could play a role in the pathogenesis of COPD. Aging seems to be a risk factor for Granzyme B production and pathogenesis of COPD

Study of effect of inhaled versus oral corticosteroids on sputum granzyme B in patients with moderate persistent bronchial asthma

Background: Asthma is a major public health problem with a high economic burden. It involves several inflammatory cells and multiple mediators. Granzyme B is an inflammatory mediator expressed and secreted by both immune and non immune cells. Recently it was found to play a role in the pathogenesis of asthma. The aim of this work: was to evaluate the effect of both inhaled and oral corticosteroids on sputum granzyme B in asthmatic patients with moderate severity. Methods: The study included 25 patients with moderate persistent asthma plus 15 healthy subjects as a control group. Granzyme B was measured before treatment with corticosteroids then after inhalation therapy and oral therapy. Results: It was found that expected pulmonary function parameters were significantly lower in asthmatic patients than in controls. Sputum granzyme B levels were significantly higher in asthmatic patients than in controls. Sputum granzyme B levels were significantly lower after treatment with inhaled corticosteroids than basal levels. Oral corticosteroids further significantly lowered granzyme B, but the lowering effect of inhaled steroids was significantly higher than that of oral drugs. There was no statistically significant correlation between granzyme B and PFTs in asthmatic patients. Conclusion: Granzyme B levels are elevated in bronchial asthma. Granzyme B could play a role in the pathogenesis of bronchial asthma. Both inhaled and oral corticosteroids lowered granzyme B levels significantly. The lowering effect of inhaled corticosteroids on sputum granzyme B is more than that of the oral corticosteroids

New Synthesis Routes toward Improvement of Natural Filler/Synthetic Polymer Interfacial Crosslinking

Among the critical issues dictating bio-composite performance is the interfacial bonding between the natural fibers and polymer matrix. In this regard, this article presents new synthesis routes comprising the treatment and functionalization of both date palm powder (DPP) filler and a polypropylene (PP) matrix to enhance filler&ndash;polymer adhesion in the newly developed bio-composites. Specifically, four bio-composite forms are considered: untreated DPP filled PP (DPP-UT/PP), treated DPP filled PP (DPP-T/PP), treated DPP filled functionalized PP using 2-isocyanatoethyl methacrylate (DPP-T/PP-g-IEM), and treated and functionalized DPP using 4-toluenesulfonyl chloride filled functionalized PP using 2-acrylamide ((DPP-T)-g-TsCl/PP-g-AcAm). The functional groups created on the surface of synthesized PP-g-IEM react with activated hydroxyl groups attached to the filler, resulting in chemical crosslinking between both components. Similarly, the reaction of TsCl with NH2 chemical groups residing on the mating surfaces of the filler and polymer generates an amide bond in the interface region. Fourier transform infrared spectroscopy (FTIR) is used to confirm the successful coupling between the filler and polypropylene matrix after applying the treatment and functionalization schemes. Owing to the introduced crosslinking, the DPP-T/PP-g-IEM bio-composite exhibits the best mechanical properties as compared to the neat polymer, unfunctionalized polymer-based bio-composite, and (DPP-T)-g-TsCl/PP-g-AcAm counterpart. The applied compatibilizers assist in reducing the water uptake of the manufactured bio-composites, increasing their durability

The desensitization of the transient receptor potential vanilloid 1 by nonpungent agonists and its resensitization by bradykinin

Transient receptor potential vanilloid type-1 (TRPV1) channels have crucial roles in inflammatory hyperalgesia. Different inflammatory mediators can modulate TRPV1 sensitization. Bradykinin is an algogenic substance released at the site of inflammation. The aim of the present study is to investigate the desensitization of TRPV1 receptor by nonpungent agonists and to determine how bradykinin and prostaglandin E2 receptors (EP3 and EP4) modulate the resensitization of TRPV1 receptor after being desensitized by nonpungent agonists. Tail flick test was used to investigate capsaicin-induced thermal hyperalgesia and the desensitization of TRPV1 by the nonpungent agonists (olvanil and arvanil) in male BALB/c mice weighed (22-25 g). Resensitization of TRPV1 by bradykinin and the role of prostaglandin receptors in mediating sensitization of TRPV1 were also investigated. Intraplantar injection of capsaicin (0.3 µg) produced a robust thermal hyperalgesia in mice, while olvanil (0.3 µg) or arvanil (0.3 µg) produced no hyperalgesia, emphasizing their lack of pungency. Olvanil and arvanil significantly attenuated capsaicin-induced thermal hyperalgesia in mice. Bradykinin significantly reversed the desensitizing effects of arvanil, but not olvanil. EP4 but not EP3 receptors mediate the sensitization of TRPV1 By bradykinin in vivo. The present study provides evidence for a novel signaling pathway through which bradykinin can regulate the TRPV1 ion channel function via EP4 receptor.Scopu

Integrative Seed and Leaf Treatment with Ascorbic Acid Extends the Planting Period by Improving Tolerance to Late Sowing Influences in Parsley

Abnormal production of reactive oxygen species (ROS) is an undesirable event which occurs in plants due to stress. To meet this event, plants synthesize ROS-neutralizing compounds, including the non-enzymatic oxidant scavenger known as vitamin C: ascorbic acid (AsA). In addition to scavenging ROS, AsA modulates many vital functions in stressed or non-stressed plants. Thus, two-season (2018/2019 and 2019/2020) trials were conducted to study the effect of integrative treatment (seed soaking + foliar spray) using 1.0 or 2.0 mM AsA vs. distilled water (control) on the growth, seed yield, and oil yield of parsley plants under three sowing dates (SDs; November, December, and January, which represent adverse conditions of late sowing) vs. October as the optimal SD (control). The ion balance, osmotic-modifying compounds, and different antioxidants were also studied. The experimental layout was a split plot in a completely randomized block design. Late sowing (December and January) noticeably reduced growth traits, seed and oil yield components, and chlorophyll and nutrient contents. However, soluble sugar, proline, and AsA contents were significantly increased along with the activities of catalase (CAT) and superoxide dismutase (SOD). Under late sowing conditions, the use of AsA significantly increased growth, different yields, essential oil fractions, CAT and SOD activities, and contents of chlorophylls, nutrients, soluble sugars, free proline, and AsA. The interaction treatments of SDs and AsA concentrations indicated that AsA at a concentration of 2 mM was more efficient in conferring greater tolerance to adverse conditions of late sowing in parsley plants. Therefore, this study recommends 2.0 mM AsA for integrative (seed soaking + foliar spraying) treatment to prolong the sowing period of parsley seeds (from October up to December) and avoid damage caused by adverse conditions of late sowing

Integrative Seed and Leaf Treatment with Ascorbic Acid Extends the Planting Period by Improving Tolerance to Late Sowing Influences in Parsley

Abnormal production of reactive oxygen species (ROS) is an undesirable event which occurs in plants due to stress. To meet this event, plants synthesize ROS-neutralizing compounds, including the non-enzymatic oxidant scavenger known as vitamin C: ascorbic acid (AsA). In addition to scavenging ROS, AsA modulates many vital functions in stressed or non-stressed plants. Thus, two-season (2018/2019 and 2019/2020) trials were conducted to study the effect of integrative treatment (seed soaking + foliar spray) using 1.0 or 2.0 mM AsA vs. distilled water (control) on the growth, seed yield, and oil yield of parsley plants under three sowing dates (SDs; November, December, and January, which represent adverse conditions of late sowing) vs. October as the optimal SD (control). The ion balance, osmotic-modifying compounds, and different antioxidants were also studied. The experimental layout was a split plot in a completely randomized block design. Late sowing (December and January) noticeably reduced growth traits, seed and oil yield components, and chlorophyll and nutrient contents. However, soluble sugar, proline, and AsA contents were significantly increased along with the activities of catalase (CAT) and superoxide dismutase (SOD). Under late sowing conditions, the use of AsA significantly increased growth, different yields, essential oil fractions, CAT and SOD activities, and contents of chlorophylls, nutrients, soluble sugars, free proline, and AsA. The interaction treatments of SDs and AsA concentrations indicated that AsA at a concentration of 2 mM was more efficient in conferring greater tolerance to adverse conditions of late sowing in parsley plants. Therefore, this study recommends 2.0 mM AsA for integrative (seed soaking + foliar spraying) treatment to prolong the sowing period of parsley seeds (from October up to December) and avoid damage caused by adverse conditions of late sowing