Optimizing Two-Stage Bigram Language Models for IR

ABSTRACT Although higher order language models (LMs) have shown benefit of capturing word dependencies for Information retrieval (IR), the tuning of the increased number of free parameters remains a formidable engineering challenge. Consequently, in many real-world retrieval systems, applying higher order LMs is an exception rather than the rule. In this study, we address the parameter tuning problem using a framework based on a linear ranking model in which different component models are incorporated as features. Using unigram and bigram LMs with 2-stage smoothing as examples, we show that our method leads to a bigram LM that outperforms significantly its unigram counterpart and the well-tuned BM25 model

A review on Quarantine during COVID-19 Outbreak: Lessons Learned from Previous Epidemics

Background: Since the emergence in December 2019, the novel coronavirus disease 2019 (COVID-19) has caused a global pandemic that has infected so many people all around the world. As there are no vaccination or antiviral treatment available yet, public health measures play a substantial role in the management of this pandemic. Governments of affected countries have imposed different quarantine policies and travel bans. As quarantine can have many controversial aspects, this review intends to clarify its role in disease control and other aspects of human everyday life with due attention to a couple of epidemics in the past (SARS, MERS, and flu) and ongoing COVID-19 outbreak.   Methods: We conducted a thorough search in PubMed, Research Gate, Google Scholar, Excerpta Media Database (EMBASE), and Web of Science databases and collected all relevant articles to Quarantine in the past epidemics (SARS, MERS, and flu) as well as ongoing COVID-19 pandemic.     Results:  A total of 176 articles were extracted in our primary search process. Primarily, 53 articles have been excluded because of duplication. The other 44 articles have been excluded due to different reasons (Lack of useful information and eligibility of data). Finally, 79 articles were selected for more evaluation (published until April 2020).   Conclusion: By having previous epidemics, including SARS, MERS, and flu, in mind, quarantine and isolation seem to be proper choices for this situation. But, as this epidemy is bigger than former ones, stricter public health measurements, such as serious social distancing and community-wide containment, are recommended

Stromal cells regulate mechanics of tumour spheroid

The remarkable contractility and force generation ability exhibited by cancer cells empower them to overcome the resistance and steric hindrance presented by a three-dimensional, interconnected matrix. Cancer cells disseminate by actively remodelling and deforming their extracellular matrix (ECM). The process of tumour growth and its ECM remodelling have been extensively studied, but the effect of the cellular tumour microenvironment (TME) has been ignored in most studies that investigated tumour-cell-mediated ECM deformations and realignment. This study reports the integration of stromal cells in spheroid contractility assays that impacts the ECM remodelling and invasion abilities of cancer spheroids. To investigate this, we developed a novel multilayer in vitro assay that incorporates stromal cells and quantifies the contractile deformations that tumour spheroids exert on the ECM. We observed a negative correlation between the spheroid invasion potential and the levels of collagen deformation. The presence of stromal cells significantly increased cancer cell invasiveness and altered the cancer cells' ability to deform and realign collagen gel, due to upregulation of proinflammatory cytokines. Interestingly, this was observed consistently in both metastatic and non-metastatic cancer cells. Our findings contribute to a better understanding of the vital role played by the cellular TME in regulating the invasive outgrowth of cancer cells and underscore the potential of utilising matrix deformation measurements as a biophysical marker for evaluating invasiveness and informing targeted therapeutic opportunities

The unfinished agenda of communicable diseases among children and adolescents before the COVID-19 pandemic, 1990-2019: a systematic analysis of the Global Burden of Disease Study 2019

BACKGROUND: Communicable disease control has long been a focus of global health policy. There have been substantial reductions in the burden and mortality of communicable diseases among children younger than 5 years, but we know less about this burden in older children and adolescents, and it is unclear whether current programmes and policies remain aligned with targets for intervention. This knowledge is especially important for policy and programmes in the context of the COVID-19 pandemic. We aimed to use the Global Burden of Disease (GBD) Study 2019 to systematically characterise the burden of communicable diseases across childhood and adolescence. METHODS: In this systematic analysis of the GBD study from 1990 to 2019, all communicable diseases and their manifestations as modelled within GBD 2019 were included, categorised as 16 subgroups of common diseases or presentations. Data were reported for absolute count, prevalence, and incidence across measures of cause-specific mortality (deaths and years of life lost), disability (years lived with disability [YLDs]), and disease burden (disability-adjusted life-years [DALYs]) for children and adolescents aged 0-24 years. Data were reported across the Socio-demographic Index (SDI) and across time (1990-2019), and for 204 countries and territories. For HIV, we reported the mortality-to-incidence ratio (MIR) as a measure of health system performance. FINDINGS: In 2019, there were 3·0 million deaths and 30·0 million years of healthy life lost to disability (as measured by YLDs), corresponding to 288·4 million DALYs from communicable diseases among children and adolescents globally (57·3% of total communicable disease burden across all ages). Over time, there has been a shift in communicable disease burden from young children to older children and adolescents (largely driven by the considerable reductions in children younger than 5 years and slower progress elsewhere), although children younger than 5 years still accounted for most of the communicable disease burden in 2019. Disease burden and mortality were predominantly in low-SDI settings, with high and high-middle SDI settings also having an appreciable burden of communicable disease morbidity (4·0 million YLDs in 2019 alone). Three cause groups (enteric infections, lower-respiratory-tract infections, and malaria) accounted for 59·8% of the global communicable disease burden in children and adolescents, with tuberculosis and HIV both emerging as important causes during adolescence. HIV was the only cause for which disease burden increased over time, particularly in children and adolescents older than 5 years, and especially in females. Excess MIRs for HIV were observed for males aged 15-19 years in low-SDI settings. INTERPRETATION: Our analysis supports continued policy focus on enteric infections and lower-respiratory-tract infections, with orientation to children younger than 5 years in settings of low socioeconomic development. However, efforts should also be targeted to other conditions, particularly HIV, given its increased burden in older children and adolescents. Older children and adolescents also experience a large burden of communicable disease, further highlighting the need for efforts to extend beyond the first 5 years of life. Our analysis also identified substantial morbidity caused by communicable diseases affecting child and adolescent health across the world. FUNDING: The Australian National Health and Medical Research Council Centre for Research Excellence for Driving Investment in Global Adolescent Health and the Bill & Melinda Gates Foundation

Global, regional, and national progress towards Sustainable Development Goal 3.2 for neonatal and child health: all-cause and cause-specific mortality findings from the Global Burden of Disease Study 2019

Background Sustainable Development Goal 3.2 has targeted elimination of preventable child mortality, reduction of neonatal death to less than 12 per 1000 livebirths, and reduction of death of children younger than 5 years to less than 25 per 1000 livebirths, for each country by 2030. To understand current rates, recent trends, and potential trajectories of child mortality for the next decade, we present the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2019 findings for all-cause mortality and cause-specific mortality in children younger than 5 years of age, with multiple scenarios for child mortality in 2030 that include the consideration of potential effects of COVID-19, and a novel framework for quantifying optimal child survival. Methods We completed all-cause mortality and cause-specific mortality analyses from 204 countries and territories for detailed age groups separately, with aggregated mortality probabilities per 1000 livebirths computed for neonatal mortality rate (NMR) and under-5 mortality rate (USMR). Scenarios for 2030 represent different potential trajectories, notably including potential effects of the COVID-19 pandemic and the potential impact of improvements preferentially targeting neonatal survival. Optimal child survival metrics were developed by age, sex, and cause of death across all GBD location-years. The first metric is a global optimum and is based on the lowest observed mortality, and the second is a survival potential frontier that is based on stochastic frontier analysis of observed mortality and Healthcare Access and Quality Index. Findings Global U5MR decreased from 71.2 deaths per 1000 livebirths (95% uncertainty interval WI] 68.3-74-0) in 2000 to 37.1 (33.2-41.7) in 2019 while global NMR correspondingly declined more slowly from 28.0 deaths per 1000 live births (26.8-29-5) in 2000 to 17.9 (16.3-19-8) in 2019. In 2019,136 (67%) of 204 countries had a USMR at or below the SDG 3.2 threshold and 133 (65%) had an NMR at or below the SDG 3.2 threshold, and the reference scenario suggests that by 2030,154 (75%) of all countries could meet the U5MR targets, and 139 (68%) could meet the NMR targets. Deaths of children younger than 5 years totalled 9.65 million (95% UI 9.05-10.30) in 2000 and 5.05 million (4.27-6.02) in 2019, with the neonatal fraction of these deaths increasing from 39% (3.76 million 95% UI 3.53-4.021) in 2000 to 48% (2.42 million; 2.06-2.86) in 2019. NMR and U5MR were generally higher in males than in females, although there was no statistically significant difference at the global level. Neonatal disorders remained the leading cause of death in children younger than 5 years in 2019, followed by lower respiratory infections, diarrhoeal diseases, congenital birth defects, and malaria. The global optimum analysis suggests NMR could be reduced to as low as 0.80 (95% UI 0.71-0.86) deaths per 1000 livebirths and U5MR to 1.44 (95% UI 1-27-1.58) deaths per 1000 livebirths, and in 2019, there were as many as 1.87 million (95% UI 1-35-2.58; 37% 95% UI 32-43]) of 5.05 million more deaths of children younger than 5 years than the survival potential frontier. Interpretation Global child mortality declined by almost half between 2000 and 2019, but progress remains slower in neonates and 65 (32%) of 204 countries, mostly in sub-Saharan Africa and south Asia, are not on track to meet either SDG 3.2 target by 2030. Focused improvements in perinatal and newborn care, continued and expanded delivery of essential interventions such as vaccination and infection prevention, an enhanced focus on equity, continued focus on poverty reduction and education, and investment in strengthening health systems across the development spectrum have the potential to substantially improve USMR. Given the widespread effects of COVID-19, considerable effort will be required to maintain and accelerate progress. Copyright (C) 2021 The Author(s). Published by Elsevier Ltd

Comparative Study on Functional Effects of Allotransplantation of Bone Marrow Stromal Cells and Adipose Derived Stromal Vascular Fraction on Tendon Repair: A Biomechanical Study in Rabbits

Objective: Tendon never returns to its complete biological and mechanical properties after repair. Bone marrow and, recently, adipose tissue have been used as sources of mesenchymal stem cells which have been proven to enhance tendon healing. In the present study, we compared the effects of allotransplantation of bone marrow derived mesenchymal stromal cells (BMSCs) and adipose derived stromal vascular fraction (SVF) on tendon mechanical properties after experimentally induced flexor tendon transection. Materials and Methods: In this experimental study, we used 48 adult male New Zealand white rabbits. Twelve of rabbits were used as donors of bone marrow and adipose tissue, the rest were divided into control and treatment groups. The injury model was a unilateral complete transection of the deep digital flexor tendon. Immediately after suture repair, 4×106 cells of either fresh SVF from enzymatic digestion of adipose tissue or cultured BMSCs were intratendinously injected into tendon stumps in the treatment groups. Controls received phosphate-buffered saline (PBS). Immobilization with a cast was continued for two weeks after surgery. Animals were sacrificed three and eight weeks after surgery and tendons underwent mechanical evaluations. The differences among the groups were analyzed using the analysis of variance (ANOVA) test followed by Tukey’s multiple comparisons test. Results: Stromal cell transplantation resulted in a significant increase in ultimate and yield loads, energy absorption, and stress of repairs compared to the controls. However, there were no statistically significant changes detected in terms of stiffness. In comparison, we observed no significant differences at the third week between SVF and BMSCs treated tendons in terms of all load related properties. However, at the eighth week SVF transplantation resulted in significantly increased energy absorption, stress and stiffness compared to BMSCs. Conclusion: The enhanced biomechanical properties of repairs in this study advocates the application of adipose derived SVF as an excellent source of multipotent cells instead of traditional BMSCs and may seem more encouraging in cell-based therapy for tendon injuries